Module Expr Str Import alias identifier Import alias Import alias Import alias Import alias identifier Import alias identifier ImportFrom alias alias ImportFrom alias ImportFrom alias ImportFrom alias identifier ImportFrom alias alias ImportFrom alias identifier alias identifier ImportFrom alias ImportFrom alias ImportFrom alias alias ImportFrom alias alias alias identifier alias ImportFrom alias alias alias alias alias ImportFrom alias alias alias alias ImportFrom alias ImportFrom alias ImportFrom alias ImportFrom alias alias ImportFrom alias ImportFrom alias ImportFrom alias alias ImportFrom alias ImportFrom alias alias alias alias alias alias alias alias Assign TupleStore NameStore NameStore TupleLoad Str Str Assign NameStore TupleLoad Str Str Assign NameStore TupleLoad Str Str Str Str Str Expr Call AttributeLoad NameLoad attr keyword Str ClassDef bases NameLoad body FunctionDef arguments args NameParam NameParam NameParam defaults body Assign AttributeStore NameLoad attr Call AttributeLoad NameLoad attr NameLoad Assign AttributeStore NameLoad attr NameLoad Assign AttributeStore NameLoad attr NameLoad decorator_list FunctionDef arguments args NameParam defaults body Return Call NameLoad ListComp AttributeLoad NameLoad attr comprehension NameStore AttributeLoad NameLoad attr decorator_list NameLoad FunctionDef arguments args NameParam NameParam NameParam defaults body Assign NameStore Call AttributeLoad AttributeLoad NameLoad attr attr Assign NameStore Call NameLoad NameLoad For TupleStore TupleStore NameStore NameStore TupleStore NameStore NameStore Call NameLoad NameLoad Num body Assign TupleStore NameStore NameStore TupleLoad SubscriptLoad Call AttributeLoad NameLoad attr Str Index Num SubscriptLoad Call AttributeLoad NameLoad attr Str Index Num If CompareNotEq Call NameLoad TupleLoad NameLoad NameLoad NameLoad body Continue Assign NameStore Call NameLoad NameLoad NameLoad AugAssignAdd SubscriptStore NameLoad Index TupleLoad NameLoad NameLoad NameLoad AugAssignAdd SubscriptStore NameLoad Index TupleLoad NameLoad NameLoad NameLoad decorator_list decorator_list ClassDef bases NameLoad body FunctionDef arguments args NameParam NameParam NameParam NameParam NameParam NameParam defaults Lambda arguments args NameParam defaults AttributeLoad NameLoad attr NameLoad body Assign AttributeStore NameLoad attr NameLoad Assign AttributeStore NameLoad attr NameLoad Assign AttributeStore NameLoad attr NameLoad Assign AttributeStore NameLoad attr NameStore NameLoad Assign AttributeStore NameLoad attr NameLoad Assign AttributeStore NameLoad attr SubscriptLoad Call AttributeLoad NameLoad attr Str Index Num Assign AttributeStore NameLoad attr Dict Assign AttributeStore NameLoad attr Dict Assign AttributeStore NameLoad attr Dict Assign AttributeStore NameLoad attr Dict Assign AttributeStore NameLoad attr Dict For TupleStore NameStore NameStore Call AttributeLoad NameLoad attr body Assign SubscriptStore AttributeLoad NameLoad attr Index NameLoad NameStore ListComp Call NameLoad NameLoad comprehension NameStore NameLoad Assign SubscriptStore AttributeLoad NameLoad attr Index NameLoad Call NameLoad NameLoad Assign NameStore ListComp TupleLoad AttributeLoad NameLoad attr Call NameLoad NameLoad comprehension NameStore NameLoad Assign SubscriptStore AttributeLoad NameLoad attr Index NameLoad Call NameLoad NameLoad Assign SubscriptStore AttributeLoad NameLoad attr Index NameLoad Call AttributeLoad NameLoad attr NameLoad Assign SubscriptStore AttributeLoad NameLoad attr Index NameLoad Call AttributeLoad NameLoad attr ListComp AttributeLoad NameLoad attr comprehension NameStore NameLoad Assign NameStore Call NameLoad GeneratorExp TupleLoad NameLoad SubscriptLoad AttributeLoad NameLoad attr Index NameLoad NameLoad comprehension TupleStore NameStore NameStore Call AttributeLoad AttributeLoad NameLoad attr attr Assign TupleStore NameStore NameStore NameStore Call NameLoad NameLoad Assign AttributeStore NameLoad attr NameLoad Assign AttributeStore NameLoad attr Num decorator_list FunctionDef arguments args NameParam defaults body Assign NameStore Dict Assign NameStore AttributeLoad NameLoad attr Assign NameStore AttributeLoad NameLoad attr For TupleStore NameStore NameStore Call NameLoad AttributeLoad NameLoad attr Num body Assign NameStore Call NameLoad SubscriptLoad NameLoad Index NameLoad SubscriptLoad NameLoad Index NameLoad keyword NameLoad Assign SubscriptStore NameLoad Index TupleLoad NameLoad NameLoad SubscriptStore NameLoad Index TupleLoad NameLoad NameLoad NameLoad For NameStore AttributeLoad NameLoad attr body Assign NameStore Call NameLoad ListLoad Num SubscriptLoad NameLoad Index NameLoad keyword NameLoad Assign NameStore Call NameLoad SubscriptLoad NameLoad Index NameLoad ListLoad AttributeLoad NameLoad attr keyword NameLoad If CompareLt AttributeLoad NameLoad attr Num body Assign TupleStore NameStore NameStore TupleLoad NameLoad NameLoad Assign SubscriptStore NameLoad Index TupleLoad NameLoad NameLoad SubscriptStore NameLoad Index TupleLoad NameLoad NameLoad NameLoad Assign SubscriptStore NameLoad Index TupleLoad NameLoad NameLoad SubscriptStore NameLoad Index TupleLoad NameLoad NameLoad NameLoad Assign AttributeStore NameLoad attr NameLoad Return NameLoad decorator_list decorator_list ClassDef bases NameLoad body Expr Str FunctionDef arguments args NameParam NameParam NameParam NameParam NameParam NameParam NameParam NameParam NameParam NameParam NameParam NameParam NameParam NameParam NameParam defaults Lambda arguments args NameParam defaults AttributeLoad NameLoad attr NameLoad NameLoad NameLoad Num Num Num Num body Assign AttributeStore NameLoad attr NameLoad Assign AttributeStore NameLoad attr AttributeLoad NameLoad attr Assign AttributeStore NameLoad attr AttributeLoad NameLoad attr Assign AttributeStore NameLoad attr NameLoad Assign AttributeStore NameLoad attr NameLoad Assign AttributeStore NameLoad attr NameLoad Assign AttributeStore NameLoad attr NameLoad Assign AttributeStore NameLoad attr NameLoad Assign AttributeStore NameLoad attr NameLoad Assign AttributeStore NameLoad attr NameLoad Expr Call AttributeLoad NameLoad attr For NameStore AttributeLoad NameLoad attr body Assign TupleStore NameStore NameStore Call AttributeLoad NameLoad attr Str Num If CompareEq NameLoad NameLoad body Assign AttributeStore NameLoad attr Call AttributeLoad Str attr NameLoad Break Assign NameStore Call AttributeLoad Str attr NameLoad Assign NameStore Call NameLoad NameLoad BinOpMult Call NameLoad NameLoad ListLoad Num Expr Call NameLoad NameLoad AttributeLoad NameLoad attr NameLoad Str NameLoad keyword NameLoad Assign NameStore Call AttributeLoad NameLoad attr Assert CompareEq Call NameLoad NameLoad Call NameLoad NameLoad Assign NameStore Call NameLoad NameLoad NameLoad Assign NameStore Call NameLoad NameLoad Expr Call NameLoad NameLoad AttributeLoad NameLoad attr NameLoad Str NameLoad keyword NameLoad Assign NameStore Call AttributeLoad NameLoad attr Assign NameStore ListComp TupleLoad NameLoad SubscriptLoad NameLoad Index NameLoad comprehension NameStore NameLoad Expr Call NameLoad NameLoad AttributeLoad NameLoad attr NameLoad Str NameLoad keyword NameLoad FunctionDef arguments args NameParam NameParam NameParam defaults Num body Assign NameStore IfExp Call NameLoad NameLoad Str AttributeLoad NameLoad attr NameLoad Assign NameStore ListComp SubscriptLoad NameLoad Index NameLoad comprehension NameStore NameLoad Assign NameStore ListComp TupleLoad NameLoad SubscriptLoad NameLoad Index NameLoad comprehension NameStore NameLoad Assign NameStore Call AttributeLoad Str attr NameLoad NameLoad If NameLoad body Assign NameStore Call AttributeLoad SubscriptLoad Call AttributeLoad Call AttributeLoad Str attr NameLoad attr Str Index Num attr Str Str AugAssignAdd NameStore BinOpAdd Str NameLoad Expr Call NameLoad NameLoad AttributeLoad NameLoad attr NameLoad NameLoad NameLoad keyword NameLoad Return NameLoad decorator_list Assign NameStore Num Assign TupleStore NameStore NameStore TupleLoad NameLoad NameLoad While NameLoad body Expr Call AttributeLoad NameLoad attr Call AttributeLoad Str attr NameLoad Assign NameStore Call NameLoad NameLoad Assign TupleStore NameStore NameStore NameStore Call AttributeLoad NameLoad attr NameLoad NameLoad NameLoad Assign NameStore Call NameLoad NameLoad keyword NameLoad Assign NameStore Call NameLoad NameLoad Expr Call AttributeLoad NameLoad attr Str NameLoad keyword NameLoad keyword NameLoad Assign TupleStore NameStore NameStore Call NameLoad NameLoad keyword NameLoad keyword NameLoad keyword NameLoad keyword NameLoad keyword NameLoad Assign NameStore Call NameLoad NameLoad Str If BoolOpAnd NameLoad CompareLtE NameLoad NameLoad body Expr Call AttributeLoad NameLoad attr Call AttributeLoad Str attr NameLoad Break Assign NameStore Call AttributeLoad NameLoad attr NameLoad Assign TupleStore NameStore NameStore TupleLoad NameLoad NameLoad Expr Call NameLoad NameLoad AttributeLoad NameLoad attr NameLoad Call AttributeLoad Str attr NameLoad NameLoad keyword NameLoad Expr Call AttributeLoad NameLoad attr Call AttributeLoad Str attr NameLoad AugAssignAdd NameStore Num Assign NameStore Call AttributeLoad NameLoad attr NameLoad Assign AttributeStore NameLoad attr Call NameLoad NameLoad For NameStore TupleLoad AttributeLoad NameLoad attr NameLoad body Expr Call NameLoad NameLoad AttributeLoad NameLoad attr NameLoad Str AttributeLoad NameLoad attr decorator_list FunctionDef arguments args NameParam NameParam NameParam NameParam defaults body Expr Str Assign NameStore Call NameLoad GeneratorExp TupleLoad NameLoad NameLoad comprehension TupleStore NameStore NameStore Call NameLoad NameLoad Assign NameStore ListLoad Assign NameStore ListLoad For NameStore AttributeLoad NameLoad attr body Assign NameStore Call NameLoad SubscriptLoad NameLoad Index AttributeLoad NameLoad attr Assign NameStore Dict For TupleStore NameStore NameStore NameLoad body Assign NameStore SubscriptLoad NameLoad Index NameLoad Assign SubscriptStore NameLoad Index NameLoad Call AttributeLoad NameLoad attr AttributeLoad NameLoad attr NameLoad keyword NameLoad Expr Call AttributeLoad NameLoad attr NameLoad Expr Call AttributeLoad NameLoad attr NameLoad Assign NameStore ListComp SubscriptLoad NameLoad Index NameLoad comprehension TupleStore NameStore NameStore NameLoad Return TupleLoad NameLoad NameLoad NameLoad decorator_list FunctionDef arguments args NameParam NameParam defaults body Assign TupleStore NameStore NameStore Call NameLoad NameLoad Assign NameStore ListComp SubscriptLoad AttributeLoad NameLoad attr Index NameLoad comprehension NameStore NameLoad Return Call AttributeLoad NameLoad attr NameLoad keyword NameLoad decorator_list FunctionDef arguments args NameParam NameParam NameParam NameParam defaults Num body Assign NameStore Call AttributeLoad AttributeLoad NameLoad attr attr TupleLoad NameLoad NameLoad ListLoad If CompareLt NameLoad Num body Assign NameStore SubscriptLoad NameLoad Slice Num Return NameLoad decorator_list FunctionDef arguments args NameParam NameParam NameParam NameParam defaults Num body Assign NameStore Call AttributeLoad NameLoad attr NameLoad NameLoad keyword NameLoad Return ListComp Call AttributeLoad NameLoad attr NameLoad comprehension NameStore NameLoad decorator_list FunctionDef arguments args NameParam defaults body Assign AttributeStore NameLoad attr ListLoad For NameStore AttributeLoad NameLoad attr body Assign NameStore SubscriptLoad AttributeLoad NameLoad attr Index NameLoad Assign NameStore Dict For NameStore AttributeLoad NameLoad attr body Assign NameStore Call AttributeLoad NameLoad attr NameLoad NameLoad If NameLoad body Assign SubscriptStore NameLoad Index NameLoad NameLoad If UnaryOpNot NameLoad body Continue Assign NameStore Call NameLoad NameLoad NameLoad NameLoad keyword AttributeLoad NameLoad attr keyword AttributeLoad NameLoad attr Expr Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad decorator_list FunctionDef arguments args NameParam defaults body Assign NameStore AttributeLoad NameLoad attr Assign NameStore AttributeLoad NameLoad attr Assign NameStore Call AttributeLoad NameLoad attr For TupleStore TupleStore NameStore NameStore NameStore Call AttributeLoad NameLoad attr body Assign NameStore Call AttributeLoad NameLoad attr NameLoad Expr Call AttributeLoad NameLoad attr NameLoad NameLoad keyword NameLoad If BoolOpOr CompareEq NameLoad NameLoad CompareEq NameLoad NameLoad body Continue Expr Call AttributeLoad NameLoad attr NameLoad NameLoad keyword NameLoad Expr Call AttributeLoad NameLoad attr Call AttributeLoad Str attr Call NameLoad NameLoad Call AttributeLoad NameLoad attr Assign NameStore Call AttributeLoad NameLoad attr NameLoad For TupleStore NameStore NameStore Call NameLoad NameLoad Num body If Call AttributeLoad NameLoad attr NameLoad NameLoad body Continue If BoolOpAnd CompareIn NameLoad NameLoad CompareIn NameLoad SubscriptLoad NameLoad Index NameLoad body Assign NameStore SubscriptLoad SubscriptLoad NameLoad Index NameLoad Index NameLoad Expr Call AttributeLoad NameLoad attr NameLoad NameLoad keyword NameLoad Expr Call AttributeLoad NameLoad attr NameLoad NameLoad keyword NameLoad Assign NameStore ListLoad For TupleStore NameStore NameStore NameStore Call AttributeLoad NameLoad attr keyword NameLoad body Expr Call AttributeLoad NameLoad attr TupleLoad NameLoad NameLoad SubscriptLoad NameLoad Index Str If AttributeLoad NameLoad attr body Expr Call AttributeLoad NameLoad attr Str Assign NameStore SubscriptLoad NameLoad Slice Return NameLoad TryExcept body Assign NameStore Call NameLoad NameLoad keyword NameLoad keyword Num Assert BoolOpAnd CompareEq SubscriptLoad NameLoad Index Num NameLoad CompareEq SubscriptLoad NameLoad Index Num NameLoad Assign NameStore SubscriptLoad NameLoad Slice Num Num handlers ExceptHandler body Expr Call AttributeLoad NameLoad attr Str Assign NameStore SubscriptLoad NameLoad Slice Return NameLoad decorator_list FunctionDef arguments args NameParam defaults body Expr Str Assign NameStore AttributeLoad NameLoad attr For NameStore NameLoad body Assign NameStore AttributeLoad NameLoad attr If CompareEq NameLoad AttributeLoad NameLoad attr body Assign NameStore AttributeLoad NameLoad attr For NameStore NameLoad body Assign NameStore AttributeLoad NameLoad attr Assign NameStore ListLoad For TupleStore NameStore NameStore Call AttributeLoad NameLoad attr body If CompareNotIn NameLoad NameLoad body Continue Assign NameStore SubscriptLoad NameLoad Index NameLoad Expr Call AttributeLoad NameLoad attr TupleLoad NameLoad NameLoad Assign AttributeStore NameLoad attr Call NameLoad NameLoad If CompareLt AttributeLoad NameLoad attr Num body Assign AttributeStore NameLoad attr SubscriptLoad AttributeLoad NameLoad attr Slice Num Expr Call AttributeLoad NameLoad attr Assign NameStore Call NameLoad NameLoad For NameStore NameLoad body Assign NameStore AttributeLoad NameLoad attr Assign NameStore AttributeLoad NameLoad attr Assign NameStore AttributeLoad NameLoad attr Assign NameStore AttributeLoad NameLoad attr Assign NameStore AttributeLoad NameLoad attr Assign NameStore AttributeLoad NameLoad attr For TupleStore NameStore NameStore Call NameLoad NameLoad Num body Assign NameStore SubscriptLoad NameLoad Index TupleLoad NameLoad NameLoad Expr Call AttributeLoad SubscriptLoad NameLoad Index TupleLoad NameLoad NameLoad attr TupleLoad NameLoad NameLoad For NameStore NameLoad body Assign TupleStore NameStore NameStore TupleLoad SubscriptLoad NameLoad Index NameLoad BinOpSub NameLoad SubscriptLoad NameLoad Index NameLoad If CompareLt NameLoad Num body Assign TupleStore NameStore NameStore TupleLoad NameLoad NameLoad Expr Call AttributeLoad SubscriptLoad NameLoad Index TupleLoad NameLoad NameLoad attr TupleLoad NameLoad NameLoad Expr Call AttributeLoad SubscriptLoad NameLoad Index TupleLoad NameLoad NameLoad attr TupleLoad NameLoad NameLoad Assign AttributeStore NameLoad attr NameLoad Assign NameStore Call AttributeLoad NameLoad attr Return NameLoad decorator_list FunctionDef arguments args NameParam NameParam NameParam defaults body Expr Str If BoolOpOr UnaryOpNot NameLoad UnaryOpNot NameLoad body Return Num Assign NameStore Call NameLoad BinOpAdd NameLoad NameLoad Assign NameStore Call NameLoad BinOpAdd NameLoad NameLoad Assign NameStore Call NameLoad BinOpAdd NameLoad SubscriptLoad NameLoad Slice Num Assign NameStore Call NameLoad BinOpAdd SubscriptLoad NameLoad Slice Num NameLoad Return BinOpSub SubscriptLoad Call NameLoad NameLoad NameLoad Index Num SubscriptLoad Call NameLoad NameLoad NameLoad Index Num decorator_list FunctionDef arguments args NameParam defaults body Assign NameStore Call NameLoad NameLoad Assign NameStore AttributeLoad NameLoad attr For NameStore AttributeLoad NameLoad attr body Assign NameStore AttributeLoad NameLoad attr Assign NameStore AttributeLoad NameLoad attr If CompareEq NameLoad AttributeLoad NameLoad attr body Assign NameStore AttributeLoad NameLoad attr Assign NameStore AttributeLoad NameLoad attr For TupleStore NameStore NameStore Call NameLoad Call NameLoad Call NameLoad NameLoad Num body Assign TupleStore NameStore NameStore TupleLoad SubscriptLoad NameLoad Index NameLoad SubscriptLoad NameLoad Index NameLoad Assign TupleStore NameStore NameStore TupleLoad Call AttributeLoad NameLoad attr NameLoad ListLoad Call AttributeLoad NameLoad attr NameLoad ListLoad Assign NameStore Call AttributeLoad NameLoad attr NameLoad NameLoad If UnaryOpNot NameLoad body Continue Expr Call AttributeLoad SubscriptLoad NameLoad Index TupleLoad NameLoad NameLoad attr TupleLoad NameLoad NameLoad For TupleStore NameStore NameStore Call AttributeLoad NameLoad attr body Assign SubscriptStore NameLoad Index NameLoad Call AttributeLoad NameLoad attr NameLoad Assign NameStore Call NameLoad GeneratorExp TupleLoad NameLoad NameLoad NameLoad comprehension TupleStore TupleStore NameStore NameStore NameStore Call AttributeLoad NameLoad attr Assign NameStore Call NameLoad NameLoad NameLoad Assign NameStore ListComp Call AttributeLoad NameLoad attr NameLoad Num comprehension NameStore NameLoad Assign NameStore ListComp Call AttributeLoad NameLoad attr NameLoad Num comprehension NameStore NameLoad Assign NameStore BinOpMult BinOpMult NameLoad Call AttributeLoad NameLoad attr Call AttributeLoad NameLoad attr NameLoad NameLoad If CompareLt Call NameLoad NameLoad Num body Assign NameStore UnaryOpUSub NameLoad Return NameLoad decorator_list FunctionDef arguments args NameParam NameParam defaults body Expr Str Assign TupleStore NameStore NameStore Call NameLoad NameLoad Assign NameStore Call NameLoad For NameStore AttributeLoad NameLoad attr body Assign NameStore AttributeLoad NameLoad attr For TupleStore NameStore NameStore NameLoad body Assign NameStore Call AttributeLoad NameLoad attr NameLoad Assign NameStore ListComp Call AttributeLoad NameLoad attr NameLoad NameLoad NameLoad comprehension TupleStore NameStore NameStore SubscriptLoad NameLoad Slice NameLoad Assign NameStore ListComp Call AttributeLoad NameLoad attr NameLoad NameLoad NameLoad comprehension TupleStore NameStore NameStore SubscriptLoad NameLoad Slice BinOpAdd NameLoad Num Assign TupleStore NameStore NameStore TupleLoad Call NameLoad Call NameLoad NameLoad Call NameLoad Call NameLoad NameLoad Assign NameStore Call AttributeLoad NameLoad attr NameLoad NameLoad NameLoad Assign NameStore SubscriptLoad Call NameLoad BinOpAdd BinOpAdd NameLoad NameLoad NameLoad Index Num Assign NameStore SubscriptLoad Call NameLoad BinOpAdd NameLoad NameLoad Index Num Assert CompareGtE NameLoad NameLoad If CompareGt NameLoad NameLoad body Expr Call AttributeLoad NameLoad attr NameLoad Assign NameStore BinOpSub Call NameLoad NameLoad Call NameLoad NameLoad Expr Call AttributeLoad NameLoad attr Call AttributeLoad Str attr NameLoad Return ListComp TupleLoad NameLoad NameLoad comprehension TupleStore NameStore NameStore NameLoad CompareIn NameLoad NameLoad decorator_list FunctionDef arguments args NameParam NameParam defaults body Expr Str Assign NameStore Call NameLoad NameLoad Assign NameStore Call NameLoad NameLoad Assign TupleStore NameStore NameStore Call NameLoad NameLoad For NameStore AttributeLoad NameLoad attr body Assign NameStore AttributeLoad NameLoad attr Assign NameStore AttributeLoad NameLoad attr For TupleStore NameStore NameStore NameLoad body Assign NameStore Call AttributeLoad NameLoad attr NameLoad Assign NameStore ListComp Call AttributeLoad NameLoad attr NameLoad NameLoad NameLoad comprehension TupleStore NameStore NameStore SubscriptLoad NameLoad Slice NameLoad Assign NameStore ListComp Call AttributeLoad NameLoad attr NameLoad NameLoad NameLoad comprehension TupleStore NameStore NameStore SubscriptLoad NameLoad Slice BinOpAdd NameLoad Num Assign TupleStore NameStore NameStore TupleLoad Call NameLoad Call NameLoad NameLoad Call NameLoad Call NameLoad NameLoad Assign NameStore Call AttributeLoad NameLoad attr NameLoad NameLoad Assign NameStore Call NameLoad BinOpAdd BinOpAdd NameLoad NameLoad NameLoad Assign NameStore Call NameLoad BinOpAdd BinOpAdd NameLoad SubscriptLoad NameLoad Slice Num NameLoad Assign NameStore BinOpSub SubscriptLoad NameLoad Index Num SubscriptLoad NameLoad Index Num If UnaryOpNot NameLoad body Continue Expr Call AttributeLoad SubscriptLoad NameLoad Index NameLoad attr TupleLoad NameLoad NameLoad Assign NameStore Num For TupleStore NameStore NameStore Call AttributeLoad NameLoad attr body Assign NameStore Call AttributeLoad NameLoad attr NameLoad Assign NameStore SubscriptLoad NameLoad Index NameLoad Assign NameStore Call AttributeLoad NameLoad attr NameLoad If CompareNotEq NameLoad NameLoad body Assign SubscriptStore NameLoad Index NameLoad NameLoad AugAssignAdd NameStore Num Assign NameStore ListComp TupleLoad NameLoad SubscriptLoad NameLoad Index NameLoad comprehension NameStore NameLoad Expr Call AttributeLoad NameLoad attr Call AttributeLoad Str attr NameLoad Return NameLoad decorator_list decorator_list ClassDef bases NameLoad body FunctionDef arguments args NameParam NameParam NameParam NameParam defaults Str NameLoad body Assign NameStore Call AttributeLoad Call AttributeLoad NameLoad attr attr NameLoad Assign AttributeStore NameLoad attr SubscriptLoad NameLoad Index Num Assign AttributeStore NameLoad attr Call NameLoad SubscriptLoad NameLoad Index Num Assign AttributeStore NameLoad attr SubscriptLoad NameLoad Index Num Assign AttributeStore NameLoad attr Call NameLoad SubscriptLoad NameLoad Index Num Assign AttributeStore NameLoad attr NameLoad decorator_list FunctionDef arguments args NameParam defaults body Assign NameStore Call AttributeLoad Str attr AttributeLoad NameLoad attr AttributeLoad NameLoad attr AttributeLoad NameLoad attr Assign NameStore Call AttributeLoad Str attr AttributeLoad NameLoad attr AttributeLoad NameLoad attr Return Call AttributeLoad Str attr GeneratorExp Call NameLoad NameLoad comprehension NameStore TupleLoad AttributeLoad NameLoad attr BinOpSub AttributeLoad NameLoad attr Num AttributeLoad NameLoad attr NameLoad NameLoad decorator_list NameLoad decorator_list ClassDef bases NameLoad body FunctionDef arguments args NameParam NameParam defaults body Assign AttributeStore NameLoad attr AttributeLoad NameLoad attr Assign AttributeStore NameLoad attr AttributeLoad NameLoad attr Assign TupleStore AttributeStore NameLoad attr NameStore Call AttributeLoad AttributeLoad NameLoad attr attr Str Assign TupleStore AttributeStore NameLoad attr AttributeStore NameLoad attr Call AttributeLoad AttributeLoad NameLoad attr attr Str Assign AttributeStore NameLoad attr Call NameLoad NameLoad Assign AttributeStore NameLoad attr AttributeLoad NameLoad attr Assign AttributeStore NameLoad attr AttributeLoad NameLoad attr Assign AttributeStore NameLoad attr Num decorator_list FunctionDef arguments args NameParam defaults body Assign AttributeStore NameLoad attr SubscriptLoad AttributeLoad NameLoad attr Index Num Assign TupleStore AttributeStore NameLoad attr NameStore Call AttributeLoad AttributeLoad NameLoad attr attr Str Assign AttributeStore NameLoad attr Call NameLoad NameLoad decorator_list FunctionDef arguments args NameParam defaults body Return Call AttributeLoad Str attr GeneratorExp Call NameLoad NameLoad comprehension NameStore TupleLoad AttributeLoad NameLoad attr BinOpSub AttributeLoad NameLoad attr Num AttributeLoad NameLoad attr AttributeLoad NameLoad attr AttributeLoad NameLoad attr decorator_list Assign NameStore NameLoad decorator_list ClassDef bases NameLoad body FunctionDef arguments args NameParam NameParam NameParam NameParam NameParam NameParam defaults NameLoad Num NameLoad Lambda arguments args NameParam defaults AttributeLoad NameLoad attr body Assign NameStore Call NameLoad NameLoad For NameStore NameLoad body Expr Call AttributeLoad NameLoad attr Call NameLoad NameLoad Expr Call AttributeLoad NameLoad attr Assign AttributeStore NameLoad attr Call AttributeLoad NameLoad attr NameLoad Assign AttributeStore NameLoad attr Call AttributeLoad NameLoad attr NameLoad Assign AttributeStore NameLoad attr Call AttributeLoad NameLoad attr NameLoad NameLoad If NameLoad body For NameStore NameLoad body Expr Call AttributeLoad NameLoad attr decorator_list FunctionDef arguments args NameParam defaults body Assign AttributeStore NameLoad attr Call NameLoad NameLoad Assign AttributeStore NameLoad attr Call NameLoad Call NameLoad GeneratorExp AttributeLoad NameLoad attr comprehension NameStore NameLoad Assign AttributeStore NameLoad attr Call NameLoad Call NameLoad GeneratorExp AttributeLoad NameLoad attr comprehension NameStore NameLoad Assign AttributeStore NameLoad attr Call NameLoad Call NameLoad GeneratorExp AttributeLoad NameLoad attr comprehension NameStore NameLoad Expr Call AttributeLoad NameLoad attr Call AttributeLoad Str attr AttributeLoad NameLoad attr Call NameLoad AttributeLoad NameLoad attr decorator_list FunctionDef arguments args NameParam NameParam defaults body Assign NameStore ListComp NameLoad comprehension NameStore NameLoad CompareEq AttributeLoad NameLoad attr NameLoad Return Call NameLoad NameLoad keyword Lambda arguments args NameParam defaults AttributeLoad NameLoad attr decorator_list FunctionDef arguments args NameParam NameParam defaults body Assign NameStore ListComp NameLoad comprehension NameStore NameLoad CompareEq AttributeLoad NameLoad attr NameLoad Return Call NameLoad NameLoad keyword Lambda arguments args NameParam defaults AttributeLoad NameLoad attr decorator_list FunctionDef arguments args NameParam NameParam defaults body Assign NameStore Dict For NameStore AttributeLoad NameLoad attr body Assign NameStore Num Assign NameStore Call AttributeLoad NameLoad attr NameLoad For TupleStore NameStore NameStore Call NameLoad NameLoad body If CompareEq NameLoad Num body Assign AttributeStore NameLoad attr NameLoad Continue If CompareGt BinOpSub AttributeLoad NameLoad attr AttributeLoad SubscriptLoad NameLoad Index BinOpSub NameLoad Num attr NameLoad body AugAssignAdd NameStore Num Assign AttributeStore NameLoad attr NameLoad Assign SubscriptStore NameLoad Index NameLoad NameLoad Return NameLoad decorator_list FunctionDef arguments args NameParam NameParam defaults body Assign NameStore Dict For TupleStore NameStore NameStore Call AttributeLoad AttributeLoad NameLoad attr attr body Assign SubscriptStore NameLoad Index NameLoad Call NameLoad GeneratorExp Call NameLoad NameLoad comprehension NameStore NameLoad Return NameLoad decorator_list FunctionDef arguments args NameParam NameParam NameParam defaults body Assign NameStore Call NameLoad NameLoad For NameStore NameLoad body Expr Call AttributeLoad SubscriptLoad NameLoad Index TupleLoad AttributeLoad NameLoad attr AttributeLoad NameLoad attr attr NameLoad If NameLoad body Assign NameStore NameStore Num For TupleStore NameStore NameStore Call AttributeLoad NameLoad attr body Assign NameStore Call AttributeLoad NameLoad attr NameLoad NameLoad Assign SubscriptStore NameLoad Index NameLoad NameLoad AugAssignAdd NameStore Call NameLoad NameLoad AugAssignAdd NameStore Call NameLoad NameLoad Expr Call AttributeLoad NameLoad attr Call AttributeLoad Str attr Call NameLoad NameLoad NameLoad Return NameLoad decorator_list FunctionDef arguments args NameParam NameParam NameParam defaults body Assign NameStore ListComp Call NameLoad NameLoad comprehension NameStore NameLoad Assign NameStore Call NameLoad NameLoad Assign NameStore ListComp NameLoad comprehension TupleStore NameStore NameStore Call NameLoad NameLoad NameLoad UnaryOpNot NameLoad Return NameLoad decorator_list decorator_list ClassDef bases NameLoad body FunctionDef arguments args NameParam NameParam NameParam NameParam NameParam defaults NameLoad body Assign NameStore Call AttributeLoad NameLoad attr NameLoad Assign AttributeStore NameLoad attr Call NameLoad NameLoad Assign AttributeStore NameLoad attr Call NameLoad Call NameLoad GeneratorExp AttributeLoad NameLoad attr comprehension NameStore NameLoad Assign NameStore BoolOpOr NameLoad Call NameLoad GeneratorExp AttributeLoad NameLoad attr comprehension NameStore NameLoad Assign NameStore ListComp NameLoad comprehension NameStore NameLoad CompareGtE SubscriptLoad AttributeLoad NameLoad attr Index NameLoad NameLoad Assign AttributeStore NameLoad attr Call NameLoad NameLoad Assign AttributeStore NameLoad attr Call NameLoad NameLoad Assign AttributeStore NameLoad attr Call NameLoad GeneratorExp SubscriptLoad AttributeLoad NameLoad attr Index NameLoad comprehension NameStore NameLoad Expr Call AttributeLoad NameLoad attr NameLoad decorator_list FunctionDef arguments args NameParam NameParam defaults body Assign NameStore ListLoad Assign NameStore Call NameLoad For NameStore NameLoad body Assign NameStore TupleLoad AttributeLoad NameLoad attr AttributeLoad NameLoad attr If CompareIn NameLoad NameLoad body Continue Expr Call AttributeLoad NameLoad attr NameLoad Expr Call AttributeLoad NameLoad attr NameLoad Return NameLoad decorator_list FunctionDef arguments args NameParam NameParam defaults body Assign NameStore Call NameLoad ListComp AttributeLoad NameLoad attr comprehension NameStore NameLoad Assign AttributeStore NameLoad attr Call NameLoad ListComp NameLoad comprehension NameStore Call AttributeLoad NameLoad attr CompareEq NameLoad Num Assign AttributeStore NameLoad attr Call NameLoad ListComp NameLoad comprehension NameStore Call AttributeLoad NameLoad attr CompareEq NameLoad Num Assign AttributeStore NameLoad attr Call NameLoad ListComp NameLoad comprehension NameStore Call AttributeLoad NameLoad attr CompareEq NameLoad Num Assign AttributeStore NameLoad attr Call NameLoad ListComp NameLoad comprehension NameStore Call AttributeLoad NameLoad attr CompareGtE NameLoad Num decorator_list FunctionDef arguments args NameParam NameParam NameParam NameParam defaults body Assign SubscriptStore NameLoad Index TupleLoad Str NameLoad AttributeLoad NameLoad attr Assign SubscriptStore NameLoad Index TupleLoad Str NameLoad IfExp AttributeLoad NameLoad attr BinOpDiv BinOpMult AttributeLoad NameLoad attr Num AttributeLoad NameLoad attr Num Assign SubscriptStore NameLoad Index TupleLoad Str NameLoad AttributeLoad NameLoad attr Assign SubscriptStore NameLoad Index TupleLoad Str NameLoad AttributeLoad NameLoad attr Assign SubscriptStore NameLoad Index TupleLoad Str NameLoad Call NameLoad AttributeLoad NameLoad attr NameLoad keyword Num Assign SubscriptStore NameLoad Index TupleLoad Str NameLoad AttributeLoad NameLoad attr Assign SubscriptStore NameLoad Index TupleLoad Str NameLoad AttributeLoad NameLoad attr Assign SubscriptStore NameLoad Index TupleLoad Str NameLoad AttributeLoad NameLoad attr Assign SubscriptStore NameLoad Index TupleLoad Str NameLoad AttributeLoad NameLoad attr decorator_list decorator_list ClassDef bases NameLoad body FunctionDef arguments args NameParam NameParam NameParam NameParam defaults NameLoad body Expr Call AttributeLoad Call NameLoad NameLoad NameLoad attr NameLoad keyword NameLoad Assign AttributeStore NameLoad attr ListComp SubscriptLoad Call AttributeLoad NameLoad attr Index Num comprehension NameStore Call NameLoad NameLoad Expr Call AttributeLoad NameLoad attr NameLoad Assign TupleStore NameStore NameStore NameStore Call AttributeLoad NameLoad attr NameLoad Assign NameStore SubscriptLoad AttributeLoad NameLoad attr Index Num Assign AttributeStore NameLoad attr NameLoad Assign AttributeStore NameLoad attr NameLoad Expr Call AttributeLoad NameLoad attr Call AttributeLoad Str attr Call AttributeLoad NameLoad attr decorator_list FunctionDef arguments args NameParam NameParam NameParam defaults Num body Assign NameStore Call AttributeLoad NameLoad attr For NameStore NameLoad body If CompareNotIn NameLoad NameLoad body Delete SubscriptDel NameLoad Index NameLoad For NameStore NameLoad body If CompareIn NameLoad NameLoad body Continue Assign SubscriptStore NameLoad Index NameLoad NameLoad Expr Call AttributeLoad NameLoad attr Call AttributeLoad Str attr NameLoad NameLoad decorator_list FunctionDef arguments args NameParam NameParam defaults body Return Call NameLoad GeneratorExp TupleLoad NameLoad UnaryOpUSub Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad NameLoad comprehension TupleStore NameStore NameStore Call AttributeLoad NameLoad attr CompareIn NameLoad NameLoad decorator_list decorator_list ClassDef bases NameLoad body FunctionDef arguments args NameParam NameParam defaults body Assign AttributeStore NameLoad attr NameLoad Expr Call AttributeLoad NameLoad attr Expr Call AttributeLoad NameLoad attr decorator_list FunctionDef arguments args NameParam NameParam defaults Num body Assign NameStore BinOpMult ListLoad Num NameLoad Assign NameStore ListLoad For NameStore Call NameLoad NameLoad body Expr Call AttributeLoad NameLoad attr ListLoad For TupleStore NameStore NameStore Call NameLoad Call AttributeLoad AttributeLoad NameLoad attr attr keyword Lambda arguments args NameParam defaults UnaryOpUSub SubscriptLoad NameLoad Index Num body Assign TupleStore NameStore NameStore Call NameLoad GeneratorExp TupleLoad NameLoad NameLoad comprehension TupleStore NameStore NameStore Call NameLoad NameLoad AugAssignAdd SubscriptStore NameLoad Index NameLoad NameLoad Expr Call AttributeLoad SubscriptLoad NameLoad Index NameLoad attr TupleLoad NameLoad NameLoad Assign AttributeStore NameLoad attr NameLoad decorator_list FunctionDef arguments args NameParam NameParam NameParam defaults Num Num body Assign NameStore ListLoad For NameStore AttributeLoad NameLoad attr body Assign NameStore Call NameLoad GeneratorExp NameLoad comprehension TupleStore NameStore NameStore NameLoad Expr Call AttributeLoad NameLoad attr TupleLoad NameLoad BinOpSub Call NameLoad NameLoad Num Assign TupleStore NameStore NameStore Call NameLoad NameLoad Assign NameStore BinOpMult NameLoad NameLoad Assign NameStore BinOpDiv BinOpSub NameLoad NameLoad NameLoad Assign AttributeStore NameLoad attr NameLoad Assign NameStore Dict For TupleStore NameStore NameStore TupleStore NameStore NameStore Call NameLoad TupleLoad Num Num AttributeLoad NameLoad attr NameLoad body Assign NameStore BinOpMult NameLoad NameLoad Assign NameStore BinOpDiv BinOpAdd BinOpAdd Num BinOpMult NameLoad NameLoad NameLoad Num For TupleStore NameStore NameStore NameLoad body Assign NameStore BinOpMult NameLoad NameLoad Assign SubscriptStore NameLoad Index NameLoad TupleLoad NameLoad BinOpSub NameLoad NameLoad NameLoad AugAssignSub NameStore BinOpAdd NameLoad NameLoad Assign AttributeStore NameLoad attr NameLoad decorator_list decorator_list ClassDef bases NameLoad body FunctionDef arguments args NameParam NameParam NameParam NameParam NameParam NameParam defaults Lambda arguments args NameParam defaults AttributeLoad NameLoad attr body Assign NameStore Call AttributeLoad NameLoad attr NameLoad Expr Call AttributeLoad NameLoad attr Call AttributeLoad Str attr Call NameLoad NameLoad NameLoad NameLoad Assign AttributeStore NameLoad attr Call NameLoad GeneratorExp Call NameLoad NameLoad comprehension NameStore NameLoad Assign AttributeStore NameLoad attr ListComp NameLoad comprehension NameStore NameLoad CompareEq AttributeLoad NameLoad attr NameLoad Assign AttributeStore NameLoad attr ListComp AttributeLoad NameLoad attr comprehension NameStore AttributeLoad NameLoad attr UnaryOpNot AttributeLoad NameLoad attr Assign AttributeStore NameLoad attr ListComp AttributeLoad NameLoad attr comprehension NameStore AttributeLoad NameLoad attr AttributeLoad NameLoad attr Assign AttributeStore NameLoad attr Call NameLoad GeneratorExp AttributeLoad NameLoad attr comprehension NameStore AttributeLoad NameLoad attr Assign NameStore Call NameLoad NameLoad NameLoad Assign AttributeStore NameLoad attr ListLoad Assign AttributeStore NameLoad attr Call NameLoad NameLoad For NameStore AttributeLoad NameLoad attr body If CompareNotEq AttributeLoad NameLoad attr NameLoad body Continue Expr Call AttributeLoad SubscriptLoad AttributeLoad NameLoad attr Index AttributeLoad NameLoad attr attr NameLoad Expr Call AttributeLoad AttributeLoad NameLoad attr attr TupleLoad AttributeLoad NameLoad attr Call NameLoad NameLoad Expr Call AttributeLoad AttributeLoad NameLoad attr attr Expr Call AttributeLoad NameLoad attr decorator_list FunctionDef arguments args NameParam NameParam defaults body Assign NameStore Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad Return SubscriptLoad AttributeLoad NameLoad attr Index NameLoad decorator_list FunctionDef arguments args NameParam NameParam NameParam defaults BinOpMult Num Num BinOpMult Num Num body ImportFrom alias Assign TupleStore NameStore NameStore Call NameLoad AttributeLoad NameLoad attr Assign TupleStore NameStore NameStore Call NameLoad Call NameLoad Call NameLoad NameLoad NameLoad Assign NameStore Call NameLoad NameLoad NameLoad Assign NameStore Call AttributeLoad NameLoad attr FunctionDef arguments args NameParam defaults body Assign NameStore Call NameLoad Call NameLoad NameLoad Assign SubscriptStore NameLoad Index CompareLt NameLoad NameLoad NameLoad Assign SubscriptStore NameLoad Index CompareGt NameLoad NameLoad NameLoad Return NameLoad decorator_list Assign AttributeStore NameLoad attr NameLoad Assign AttributeStore NameLoad attr NameLoad decorator_list FunctionDef arguments args NameParam NameParam NameParam NameParam NameParam NameParam NameParam defaults NameLoad body Assign TupleStore NameStore NameStore TupleLoad SubscriptLoad AttributeLoad NameLoad attr Index NameLoad SubscriptLoad AttributeLoad NameLoad attr Index NameLoad Assign NameStore ListLoad For TupleStore NameStore NameStore Call NameLoad NameLoad NameLoad body Assign NameStore Call NameLoad BinOpSub AttributeLoad NameLoad attr AttributeLoad NameLoad attr Assign TupleStore NameStore Call AttributeLoad NameLoad attr ListLoad NameLoad Assign NameStore Call NameLoad Call NameLoad BinOpDiv NameLoad NameLoad Assign NameStore Call NameLoad BinOpSub AttributeLoad NameLoad attr NameLoad Assign NameStore BinOpSub Call NameLoad BinOpSub AttributeLoad NameLoad attr NameLoad NameLoad Assign NameStore BinOpSub BinOpSub NameLoad NameLoad NameLoad If CompareLt NameLoad NameLoad body Assign NameStore NameLoad If CompareGt NameLoad NameLoad body Assign NameStore NameLoad If NameLoad body Print BinOpMult Str Num Print NameLoad Print NameLoad Print AttributeLoad NameLoad attr AttributeLoad NameLoad attr Print Str NameLoad NameLoad NameLoad Print Str NameLoad NameLoad Print Str NameLoad Expr Call AttributeLoad NameLoad attr NameLoad Assign NameStore IfExp NameLoad Call NameLoad NameLoad NameLoad If NameLoad body Print BinOpMult Str Num NameLoad NameLoad NameLoad Return NameLoad decorator_list FunctionDef arguments args NameParam NameParam NameParam NameParam defaults Num Num NameLoad body Assign AttributeStore NameLoad attr ListLoad For TupleStore TupleStore NameStore NameStore NameStore Call NameLoad Call NameLoad AttributeLoad NameLoad attr AttributeLoad NameLoad attr body Assign NameStore Call AttributeLoad NameLoad attr NameLoad NameLoad NameLoad NameLoad NameLoad keyword NameLoad Expr Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad decorator_list decorator_list FunctionDef arguments args NameParam NameParam NameParam defaults body Assign NameStore Num For TupleStore NameStore NameStore Call NameLoad NameLoad NameLoad body Assign NameStore ListComp NameLoad comprehension NameStore NameLoad CompareIn NameLoad NameLoad Assign NameStore ListLoad For NameStore NameLoad body Expr Call AttributeLoad NameLoad attr SubscriptLoad NameLoad Index NameLoad Assign TupleStore NameStore NameStore Call NameLoad NameLoad AugAssignAdd NameStore BinOpMult NameLoad NameLoad Return TupleLoad NameLoad decorator_list FunctionDef arguments args NameParam defaults body If UnaryOpNot NameLoad body Return Num Assign TupleStore NameStore NameStore Call NameLoad NameLoad Assign NameStore Call NameLoad NameLoad NameLoad If Call AttributeLoad NameLoad attr NameLoad body Assign NameStore Num Return NameLoad decorator_list FunctionDef arguments args NameParam NameParam NameParam defaults NameLoad body Return Call NameLoad ListComp Call NameLoad BinOpSub NameLoad NameLoad comprehension TupleStore NameStore NameStore Call NameLoad NameLoad NameLoad decorator_list FunctionDef arguments args NameParam defaults body If CompareEq Call NameLoad NameLoad Num body Return SubscriptLoad NameLoad Index Num Expr Call AttributeLoad NameLoad attr Assign TupleStore NameStore NameStore SubscriptLoad NameLoad Slice Num Return BinOpDiv BinOpAdd NameLoad NameLoad Num decorator_list FunctionDef arguments args defaults body Assign NameStore TupleLoad TupleLoad Str Str TupleLoad Str Str TupleLoad Str Str TupleLoad Str Str TupleLoad Str Str TupleLoad Str Str TupleLoad Str Str TupleLoad Str Str TupleLoad Str Str TupleLoad Str Str Assign NameStore Call NameLoad NameLoad Expr Call AttributeLoad NameLoad attr Call NameLoad decorator_list FunctionDef arguments args NameParam NameParam NameParam defaults body Expr Str Assign NameStore Call NameLoad NameLoad Assign NameStore BinOpMult ListLoad NameLoad NameLoad Assign NameStore BinOpMult ListLoad Num NameLoad For NameStore Call NameLoad Num NameLoad body For NameStore Call NameLoad NameLoad body Assign TupleStore NameStore NameStore TupleLoad SubscriptLoad NameLoad Index NameLoad SubscriptLoad NameLoad Index NameLoad Assign NameStore IfExp CompareEq AttributeLoad NameLoad attr AttributeLoad NameLoad attr NameLoad BinOpAdd NameLoad NameLoad If CompareLt SubscriptLoad NameLoad Index NameLoad BinOpAdd SubscriptLoad NameLoad Index NameLoad NameLoad body Assign SubscriptStore NameLoad Index NameLoad BinOpAdd SubscriptLoad NameLoad Index NameLoad NameLoad Assign SubscriptStore NameLoad Index NameLoad NameLoad Assign NameStore Call NameLoad NameLoad Assign NameStore Call AttributeLoad NameLoad attr NameLoad Assign NameStore Call NameLoad While NameLoad body If CompareLt NameLoad Num body Break Assign NameStore SubscriptLoad NameLoad Index NameLoad Expr Call AttributeLoad NameLoad attr NameLoad Return ListComp NameLoad comprehension TupleStore NameStore NameStore Call NameLoad NameLoad CompareIn NameLoad NameLoad decorator_list FunctionDef arguments args NameParam defaults body Expr Str Assign NameStore Call NameLoad AttributeLoad NameLoad attr Expr Call AttributeLoad NameLoad attr Str keyword Num keyword Str keyword Str Expr Call AttributeLoad NameLoad attr Str keyword NameLoad keyword Str keyword Str Assign TupleStore NameStore NameStore Call AttributeLoad NameLoad attr NameLoad If CompareNotEq Call NameLoad NameLoad Num body Expr Call AttributeLoad NameLoad attr UnaryOpNot Call AttributeLoad NameLoad attr Assign TupleStore NameStore NameLoad Assign NameStore Num Assign NameStore AttributeLoad NameLoad attr Assign NameStore Num Assign NameStore UnaryOpUSub BinOpSub BinOpMult NameLoad NameLoad Num Assign NameStore Call NameLoad NameLoad For TupleStore NameStore NameStore Call AttributeLoad NameLoad attr body Assign NameStore ListComp Call NameLoad NameLoad comprehension NameStore NameLoad Assign NameStore Call NameLoad NameLoad NameLoad NameLoad For TupleStore NameStore NameStore Call NameLoad NameLoad body If CompareEq AttributeLoad NameLoad attr AttributeLoad NameLoad attr body Continue Assert CompareEq AttributeLoad NameLoad attr AttributeLoad NameLoad attr Assign TupleStore NameStore NameStore TupleLoad AttributeLoad NameLoad attr AttributeLoad NameLoad attr If CompareGt NameLoad NameLoad body Assign TupleStore NameStore NameStore TupleLoad NameLoad NameLoad If AttributeLoad NameLoad attr body Assign NameStore NameStore BinOpDiv BinOpAdd NameLoad NameLoad Num Print Call AttributeLoad Str attr GeneratorExp Call NameLoad NameLoad comprehension NameStore TupleLoad AttributeLoad NameLoad attr BinOpSub NameLoad Num NameLoad AugAssignAdd NameStore Num Expr Call AttributeLoad NameLoad attr Call AttributeLoad Str attr NameLoad NameLoad decorator_list FunctionDef arguments args NameParam defaults body Expr Str Assign NameStore Call NameLoad AttributeLoad NameLoad attr Expr Call AttributeLoad NameLoad attr Str keyword Num keyword Str keyword Str Expr Call NameLoad NameLoad Assign TupleStore NameStore NameStore Call AttributeLoad NameLoad attr NameLoad If CompareNotEq Call NameLoad NameLoad Num body Expr Call AttributeLoad NameLoad attr UnaryOpNot Call AttributeLoad NameLoad attr Assign TupleStore NameStore NameStore NameStore NameLoad Assign NameStore AttributeLoad NameLoad attr Assign NameStore SubscriptLoad Call AttributeLoad NameLoad attr Str Num Index Num Assign NameStore BinOpAdd NameLoad Str Assign NameStore BinOpAdd NameLoad Str Assign NameStore Call NameLoad NameLoad Assign NameStore AttributeLoad Call NameLoad NameLoad attr Assign NameStore Str Expr Call NameLoad NameLoad Assign NameStore NameStore NameLoad Assign NameStore Num For TupleStore NameStore NameStore Call NameLoad NameLoad Str body Assign TupleStore NameStore NameStore NameStore Call AttributeLoad SubscriptLoad NameLoad Slice Num attr If CompareNotEq NameLoad NameLoad body Continue Assign NameStore Call AttributeLoad SubscriptLoad NameLoad Index Num attr Assign NameStore ListComp TupleLoad SubscriptLoad NameLoad Slice Num SubscriptLoad NameLoad Index Num comprehension NameStore NameLoad If Call AttributeLoad NameLoad attr Str body Assign NameStore SubscriptLoad Call AttributeLoad NameLoad attr Str Index Num If CompareEq NameLoad NameLoad body AugAssignAdd NameStore Num Continue Assign NameStore NameLoad Assign NameStore Call AttributeLoad Str attr TupleLoad NameLoad Call AttributeLoad Str attr NameLoad NameLoad Str If Call NameLoad NameLoad NameLoad body Assign NameStore Call NameLoad NameLoad Str Expr Call NameLoad NameLoad NameLoad NameLoad NameLoad keyword NameLoad keyword Str Expr Call AttributeLoad NameLoad attr Expr Call AttributeLoad NameLoad attr Call AttributeLoad Str attr NameLoad NameLoad Expr Call NameLoad ListLoad NameLoad NameLoad Str Assign NameStore Call NameLoad ListLoad NameLoad NameLoad Call AttributeLoad Str attr NameLoad Expr Call NameLoad Call AttributeLoad Str attr NameLoad NameLoad If CompareIn NameLoad TupleLoad Str Str Str Str body For NameStore Call NameLoad Num body Assign NameStore BinOpAdd SubscriptLoad Call AttributeLoad NameLoad attr Str Num Index Num Call AttributeLoad Str attr NameLoad Expr Call NameLoad Call AttributeLoad Str attr NameLoad NameLoad NameLoad orelse Expr Call NameLoad Call AttributeLoad Str attr NameLoad NameLoad AugAssignAdd NameStore Num Expr Call AttributeLoad NameLoad attr NameLoad Assign NameStore Str Expr Call NameLoad NameLoad Assign NameStore Call AttributeLoad Str attr NameLoad Expr Call NameLoad NameLoad decorator_list FunctionDef arguments args NameParam defaults body Expr Str Assign NameStore Call NameLoad AttributeLoad NameLoad attr Expr Call AttributeLoad NameLoad attr Str keyword Num keyword Str keyword Str Expr Call AttributeLoad NameLoad attr Str keyword Num keyword Str keyword Str Expr Call AttributeLoad NameLoad attr Str keyword Num keyword Str keyword Str Expr Call AttributeLoad NameLoad attr keyword Str Assign TupleStore NameStore NameStore Call AttributeLoad NameLoad attr NameLoad If CompareNotEq Call NameLoad NameLoad Num body Expr Call AttributeLoad NameLoad attr UnaryOpNot Call AttributeLoad NameLoad attr Assign TupleStore NameStore NameLoad Assign NameStore SubscriptLoad Call AttributeLoad NameLoad attr Str Num Index Num Assign NameStore BinOpAdd NameLoad Str Assign NameStore BinOpAdd NameLoad Str Assign NameStore Call NameLoad NameLoad keyword NameLoad Assign NameStore Call NameLoad NameLoad Assign TupleStore NameStore NameStore TupleLoad AttributeLoad NameLoad attr AttributeLoad NameLoad attr Assign NameStore AttributeLoad NameLoad attr Assign NameStore AttributeLoad NameLoad attr Assign NameStore BinOpAdd NameLoad Str Assign NameStore Call NameLoad NameLoad Str For TupleStore NameStore NameStore Call AttributeLoad NameLoad attr body Assign NameStore Call NameLoad NameLoad Assign NameStore Call NameLoad NameLoad NameLoad Assign NameStore AttributeLoad NameLoad attr Assign NameStore ListComp NameLoad comprehension NameStore NameLoad AttributeLoad NameLoad attr Assign NameStore BinOpMult ListLoad NameLoad Call NameLoad NameLoad For TupleStore NameStore NameStore Call AttributeLoad NameLoad attr body If CompareLt NameLoad NameLoad body Continue Assign NameStore Call NameLoad NameLoad NameLoad NameLoad NameLoad Expr Call AttributeLoad NameLoad attr keyword NameLoad keyword NameLoad keyword NameLoad Assert CompareEq Call NameLoad AttributeLoad NameLoad attr Call NameLoad NameLoad For TupleStore NameStore NameStore Call NameLoad NameLoad body Assign NameStore SubscriptLoad AttributeLoad NameLoad attr Index NameLoad If CompareIs NameLoad NameLoad body Assign SubscriptStore NameLoad Index NameLoad NameLoad orelse If NameLoad body Assign SubscriptStore NameLoad Index NameLoad Call NameLoad NameLoad NameLoad Print NameLoad Assign NameStore Num For NameStore NameLoad body If AttributeLoad NameLoad attr body Assign AttributeStore NameLoad attr BoolOpOr SubscriptLoad NameLoad Index NameLoad NameLoad Assign AttributeStore NameLoad attr IfExp CompareEq AttributeLoad NameLoad attr Num Str Str AugAssignAdd NameStore Num Print NameLoad NameLoad Expr Call AttributeLoad NameLoad attr Expr Call NameLoad ListLoad NameLoad Str decorator_list FunctionDef arguments args NameParam defaults body Assign NameStore SubscriptLoad Call AttributeLoad Call AttributeLoad NameLoad attr NameLoad attr Str Index Num Return Call AttributeLoad Call AttributeLoad NameLoad attr Str Str attr Str Str decorator_list FunctionDef arguments args NameParam defaults body Expr Str Assign NameStore Call NameLoad AttributeLoad NameLoad attr Expr Call AttributeLoad NameLoad attr Str Str keyword Str keyword Str Expr Call AttributeLoad NameLoad attr Str Assign TupleStore NameStore NameStore Call AttributeLoad NameLoad attr NameLoad If CompareLt Call NameLoad NameLoad Num body Expr Call AttributeLoad NameLoad attr UnaryOpNot Call AttributeLoad NameLoad attr Assign NameStore NameLoad Assign NameStore AttributeLoad NameLoad attr Assign NameStore Call NameLoad NameLoad Assign NameStore Call NameLoad Assign NameStore Call NameLoad For NameStore NameLoad body Assign NameStore Call NameLoad Call AttributeLoad NameLoad attr Expr Call AttributeLoad NameLoad attr NameLoad TryExcept body Assign NameStore Call NameLoad NameLoad keyword NameLoad If CompareLt AttributeLoad NameLoad attr Num body Expr Call AttributeLoad NameLoad attr Str Print AttributeLoad NameLoad attr Call AttributeLoad NameLoad attr orelse Expr Call AttributeLoad NameLoad attr Call NameLoad AttributeLoad NameLoad attr handlers ExceptHandler type TupleLoad NameLoad NameLoad body Continue Expr Call AttributeLoad NameLoad attr keyword NameLoad keyword NameLoad Expr Call AttributeLoad NameLoad attr Call AttributeLoad Str attr Call NameLoad NameLoad NameLoad Assert CompareEq Call NameLoad NameLoad Call NameLoad NameLoad Str Expr Call NameLoad NameLoad keyword AttributeLoad NameLoad attr decorator_list FunctionDef arguments args NameParam defaults body Expr Str Assign NameStore Call NameLoad AttributeLoad NameLoad attr Expr Call AttributeLoad NameLoad attr Str Str keyword Str keyword Str Expr Call AttributeLoad NameLoad attr Str Assign TupleStore NameStore NameStore Call AttributeLoad NameLoad attr NameLoad If CompareLt Call NameLoad NameLoad Num body Expr Call AttributeLoad NameLoad attr UnaryOpNot Call AttributeLoad NameLoad attr Assign NameStore NameLoad Assign NameStore AttributeLoad NameLoad attr Assign NameStore Call NameLoad NameLoad Assign NameStore Call NameLoad Assign NameStore Call NameLoad For NameStore NameLoad body Assign NameStore Call NameLoad Call AttributeLoad NameLoad attr Expr Call AttributeLoad NameLoad attr NameLoad TryExcept body Assign NameStore Call NameLoad NameLoad Assign AttributeStore NameLoad attr Call AttributeLoad Str attr NameLoad AttributeLoad NameLoad attr Assign AttributeStore NameLoad attr ListLoad Call AttributeLoad Str attr AttributeLoad NameLoad attr AttributeLoad NameLoad attr Expr Call AttributeLoad NameLoad attr NameLoad handlers ExceptHandler type TupleLoad NameLoad NameLoad body Continue Expr Call AttributeLoad NameLoad attr keyword NameLoad keyword NameLoad Expr Call AttributeLoad NameLoad attr Call AttributeLoad Str attr Call NameLoad NameLoad NameLoad Assert CompareEq Call NameLoad NameLoad Call NameLoad NameLoad Str Expr Call NameLoad NameLoad keyword AttributeLoad NameLoad attr decorator_list FunctionDef arguments args NameParam NameParam defaults Str body If Call AttributeLoad NameLoad attr NameLoad body Expr Call AttributeLoad NameLoad attr Call AttributeLoad Str attr NameLoad Return Assign NameStore Call NameLoad NameLoad Str For NameStore Call NameLoad NameLoad body Assign NameStore Num Print NameLoad NameLoad NameLoad Expr Call AttributeLoad NameLoad attr Call AttributeLoad Str attr NameLoad decorator_list FunctionDef arguments args NameParam NameParam defaults body Assign TupleStore NameStore NameStore Call NameLoad Call AttributeLoad NameLoad attr keyword Lambda arguments args NameParam defaults SubscriptLoad NameLoad Index Num If CompareGt Call AttributeLoad Call AttributeLoad NameLoad attr attr NameLoad Num body Print AttributeLoad NameLoad attr Str NameLoad NameLoad Return TupleLoad NameLoad NameLoad Return TupleLoad NameLoad NameLoad decorator_list FunctionDef arguments args NameParam defaults body Assert CompareIn NameLoad NameLoad Return IfExp CompareEq NameLoad Str Lambda arguments args NameParam defaults AttributeLoad NameLoad attr Lambda arguments args NameParam defaults AttributeLoad NameLoad attr decorator_list FunctionDef arguments args NameParam NameParam NameParam NameParam NameParam NameParam defaults NameLoad body If NameLoad body Assign NameStore Call NameLoad NameLoad If NameLoad body Print NameLoad Call AttributeLoad Str attr NameLoad NameLoad NameLoad Print NameLoad Call AttributeLoad Str attr GeneratorExp Call AttributeLoad Str attr NameLoad comprehension NameStore NameLoad decorator_list FunctionDef arguments args NameParam defaults body Assign NameStore Dict Num Num Num Str Str Str Return ListComp TupleLoad NameLoad SubscriptLoad NameLoad Index NameLoad comprehension TupleStore NameStore NameStore NameLoad decorator_list FunctionDef arguments args NameParam defaults body Expr Str Assign NameStore NameLoad Assign NameStore Call NameLoad AttributeLoad NameLoad attr Expr Call AttributeLoad NameLoad attr Str Str keyword NameLoad Expr Call AttributeLoad NameLoad attr Str Str keyword NameLoad Expr Call AttributeLoad NameLoad attr Str Str keyword Str keyword Str Expr Call AttributeLoad NameLoad attr Str keyword Num keyword Str keyword Str Expr Call AttributeLoad NameLoad attr Str keyword NameLoad keyword Str keyword Str Expr Call AttributeLoad NameLoad attr Str keyword Str keyword NameLoad keyword Str Expr Call AttributeLoad NameLoad attr Str keyword Str keyword NameLoad keyword Str Expr Call AttributeLoad NameLoad attr Str keyword Num keyword Str keyword Str Expr Call AttributeLoad NameLoad attr Str keyword Str Expr Call AttributeLoad NameLoad attr Str keyword Str Expr Call AttributeLoad NameLoad attr Str keyword Num keyword Str keyword Str Expr Call AttributeLoad NameLoad attr Str keyword Num keyword Str keyword Str Expr Call AttributeLoad NameLoad attr Str keyword NameLoad keyword Str keyword Str Expr Call AttributeLoad NameLoad attr Str keyword NameLoad keyword Str keyword Str Expr Call AttributeLoad NameLoad attr Str keyword NameLoad keyword Str keyword Str Expr Call AttributeLoad NameLoad attr keyword Num Assign NameStore Call NameLoad NameLoad Str Expr Call AttributeLoad NameLoad attr NameLoad Expr Call AttributeLoad NameLoad attr Str keyword Num keyword Str keyword Str Expr Call AttributeLoad NameLoad attr Str keyword Num keyword Str keyword Str Expr Call AttributeLoad NameLoad attr Str keyword Num keyword Str keyword Str Assign TupleStore NameStore NameStore NameStore Call AttributeLoad NameLoad attr NameLoad keyword Str If CompareNotEq Call NameLoad NameLoad Num body Expr Call AttributeLoad NameLoad attr UnaryOpNot Call AttributeLoad NameLoad attr Assign TupleStore NameStore NameStore NameLoad Assign NameStore BoolOpOr AttributeLoad NameLoad attr NameLoad Assign NameStore BoolOpOr AttributeLoad NameLoad attr NameLoad Assign NameStore SubscriptLoad Call AttributeLoad NameLoad attr Str Num Index Num Assign NameStore BinOpAdd NameLoad Str Assign NameStore AttributeLoad NameLoad attr Assign NameStore AttributeLoad NameLoad attr Assign NameStore AttributeLoad NameLoad attr Assign NameStore AttributeLoad NameLoad attr Assign NameStore AttributeLoad NameLoad attr Assign NameStore AttributeLoad NameLoad attr Assign NameStore AttributeLoad NameLoad attr Assign NameStore AttributeLoad NameLoad attr Assign NameStore AttributeLoad NameLoad attr If CompareLt SubscriptLoad AttributeLoad NameLoad attr Slice Num TupleLoad Num Num body Expr Call AttributeLoad NameLoad attr Call AttributeLoad Str attr Call AttributeLoad SubscriptLoad Call AttributeLoad AttributeLoad NameLoad attr attr Index Num attr Assign NameStore Num Assign NameStore Call NameLoad AttributeLoad NameLoad attr Assign NameStore Call NameLoad NameLoad keyword NameLoad keyword AttributeLoad NameLoad attr keyword UnaryOpNot AttributeLoad NameLoad attr Assign NameStore AttributeLoad NameLoad attr Assign NameStore AttributeLoad NameLoad attr Assign NameStore Call NameLoad NameLoad NameLoad Assign NameStore AttributeLoad NameLoad attr Assign NameStore AttributeLoad NameLoad attr Assign NameStore AttributeLoad NameLoad attr Assign NameStore AttributeLoad NameLoad attr Expr Call AttributeLoad NameLoad attr Call AttributeLoad Str attr NameLoad Assign NameStore SubscriptLoad Dict Str Str Str Str Str NameLoad NameLoad NameLoad AttributeLoad NameLoad attr AttributeLoad NameLoad attr Index NameLoad Assign NameStore Call NameLoad For NameStore AttributeLoad NameLoad attr body Expr Call AttributeLoad NameLoad attr NameLoad If NameLoad body Expr Call AttributeLoad NameLoad attr Call AttributeLoad Str attr NameLoad Assign NameStore Call NameLoad NameLoad For NameStore NameLoad body Expr Call AttributeLoad NameLoad attr Call AttributeLoad Call AttributeLoad NameLoad attr attr Str orelse Expr Call AttributeLoad NameLoad attr Call AttributeLoad Str attr NameLoad For NameStore NameLoad body If CompareEq NameLoad NameLoad body Continue Assign NameStore Call NameLoad NameLoad For NameStore NameLoad body Assign NameStore Call NameLoad NameLoad NameLoad Expr Call AttributeLoad NameLoad attr NameLoad TupleLoad NameLoad NameLoad Assign NameStore Call NameLoad NameLoad For TupleStore TupleStore NameStore NameStore NameStore Call AttributeLoad NameLoad attr body Expr Call AttributeLoad SubscriptLoad NameLoad Index NameLoad attr TupleLoad NameLoad NameLoad For TupleStore NameStore NameStore Call AttributeLoad NameLoad attr body If CompareEq SubscriptLoad Call AttributeLoad NameLoad attr Str Index Num NameLoad body Continue Assign NameStore Call NameLoad NameLoad Assign TupleStore NameStore NameStore Call NameLoad NameLoad NameLoad If CompareIs NameLoad NameLoad body Continue Expr Call AttributeLoad NameLoad attr NameLoad NameLoad Assign NameStore Call NameLoad NameLoad For NameStore NameLoad body Assign NameStore Call NameLoad NameLoad NameLoad Assign NameStore AttributeLoad NameLoad attr Assign NameStore Dict For TupleStore NameStore NameStore Call AttributeLoad AttributeLoad NameLoad attr attr body Assign NameStore SubscriptLoad NameLoad Index NameLoad Assign NameStore SubscriptLoad Call AttributeLoad NameLoad attr Str Index Num Assign NameStore SubscriptLoad NameLoad Index NameLoad If CompareNotIn NameLoad NameLoad body Assign SubscriptStore NameLoad Index NameLoad Num If CompareLt NameLoad NameLoad body Continue AugAssignAdd SubscriptStore NameLoad Index NameLoad BinOpMult NameLoad NameLoad Assign TupleStore NameStore NameStore Call NameLoad NameLoad NameLoad If CompareIs NameLoad NameLoad body Continue Expr Call AttributeLoad SubscriptLoad NameLoad Index NameLoad attr NameLoad Assign NameStore BinOpAdd NameLoad Str Assign NameStore BinOpAdd NameLoad Str Assign NameStore AttributeLoad Call NameLoad NameLoad attr Assign NameStore Call NameLoad NameLoad Str Assign NameStore Call NameLoad NameLoad Str Assign NameStore ListLoad For TupleStore NameStore NameStore Call NameLoad Call AttributeLoad NameLoad attr body If BoolOpAnd NameLoad CompareNotIn NameLoad NameLoad body Continue Assign NameStore Call AttributeLoad Str attr NameLoad Assign NameStore Call NameLoad GeneratorExp SubscriptLoad Call AttributeLoad NameLoad attr Str Index Num comprehension NameStore NameLoad If CompareNotIn NameLoad NameLoad body Expr Call AttributeLoad NameLoad attr Call AttributeLoad Str attr NameLoad Continue Expr Call AttributeLoad NameLoad attr Call AttributeLoad Str attr NameLoad Assign NameStore Call NameLoad NameLoad NameLoad NameLoad NameLoad NameLoad NameLoad keyword NameLoad keyword NameLoad keyword NameLoad keyword NameLoad keyword NameLoad keyword NameLoad keyword NameLoad keyword NameLoad Expr Call AttributeLoad NameLoad attr NameLoad Expr Call AttributeLoad NameLoad attr If AttributeLoad NameLoad attr body Assign NameStore Dict Assign NameStore Dict For NameStore NameLoad body Assign SubscriptStore NameLoad Index AttributeLoad NameLoad attr BinOpAdd Call NameLoad GeneratorExp SubscriptLoad NameLoad Index NameLoad comprehension TupleStore NameStore NameStore AttributeLoad NameLoad attr BinOpMult BinOpSub Call NameLoad AttributeLoad NameLoad attr Num NameLoad For TupleStore NameStore TupleStore NameStore NameStore Call NameLoad Call NameLoad Call AttributeLoad NameLoad attr keyword Lambda arguments args NameParam defaults UnaryOpUSub SubscriptLoad NameLoad Index Num body Assign NameStore Call AttributeLoad Str attr BinOpAdd NameLoad Num Expr Call AttributeLoad NameLoad attr Call AttributeLoad Str attr NameLoad NameLoad NameLoad Assign SubscriptStore NameLoad Index NameLoad NameLoad For NameStore NameLoad body Assign AttributeStore NameLoad attr SubscriptLoad NameLoad Index AttributeLoad NameLoad attr Assign NameStore Call AttributeLoad Str attr Call AttributeLoad Str attr NameLoad Assign NameStore Call AttributeLoad Str attr NameLoad Call NameLoad NameLoad Expr Call AttributeLoad NameLoad attr NameLoad keyword NameLoad For NameStore Call NameLoad NameLoad keyword Lambda arguments args NameParam defaults AttributeLoad NameLoad attr body Expr Call NameLoad AttributeLoad NameLoad attr AttributeLoad NameLoad attr NameLoad NameLoad keyword NameLoad keyword Str Expr Call AttributeLoad NameLoad attr Expr Call AttributeLoad NameLoad attr Call AttributeLoad Str attr NameLoad Expr Call AttributeLoad NameLoad attr Call AttributeLoad Str attr NameLoad Expr Call NameLoad ListLoad NameLoad NameLoad Assign NameStore BinOpAdd NameLoad Str Expr Call NameLoad ListLoad NameLoad NameLoad Call AttributeLoad Str attr NameLoad If UnaryOpNot AttributeLoad NameLoad attr body Expr Call NameLoad ListLoad NameLoad Call AttributeLoad Str attr AttributeLoad NameLoad attr Call AttributeLoad Str attr AttributeLoad NameLoad attr decorator_list FunctionDef arguments args NameParam NameParam NameParam defaults body Assign NameStore Call NameLoad NameLoad Assign NameStore Call NameLoad GeneratorExp AttributeLoad NameLoad attr comprehension NameStore NameLoad Assign NameStore AttributeLoad Call NameLoad NameLoad attr Assign NameStore Call NameLoad NameLoad Str For NameStore Call NameLoad Call AttributeLoad NameLoad attr body If CompareIn NameLoad NameLoad body Continue Expr Call NameLoad NameLoad ListLoad TupleLoad NameLoad Str NameLoad NameLoad Expr Call AttributeLoad NameLoad attr Call AttributeLoad Str attr NameLoad decorator_list FunctionDef arguments args NameParam defaults body Expr Str Assign NameStore Call NameLoad AttributeLoad NameLoad attr Expr Call AttributeLoad NameLoad attr keyword Str keyword NameLoad Expr Call AttributeLoad NameLoad attr Assign TupleStore NameStore NameStore Call AttributeLoad NameLoad attr NameLoad If CompareNotEq Call NameLoad NameLoad Num body Expr Call AttributeLoad NameLoad attr UnaryOpNot Call AttributeLoad NameLoad attr Assign TupleStore NameStore NameStore NameLoad Assign NameStore SubscriptLoad Call AttributeLoad NameLoad attr Str Num Index Num Assign NameStore BinOpAdd NameLoad Str Assign NameStore BinOpAdd NameLoad Str Assign NameStore AttributeLoad NameLoad attr Assign NameStore AttributeLoad NameLoad attr Assign NameStore Call NameLoad NameLoad Assign NameStore AttributeLoad NameLoad attr Assign NameStore Call NameLoad NameLoad Assign TupleStore NameStore NameStore NameStore AttributeLoad NameLoad attr Assign NameStore Dict Assign NameStore ListLoad Assign NameStore Call NameLoad AttributeLoad NameLoad attr Str Print NameLoad Str For NameStore NameLoad body Assign NameStore ListComp NameLoad comprehension NameStore NameLoad CompareEq AttributeLoad NameLoad attr NameLoad Assign NameStore Call NameLoad NameLoad NameLoad NameLoad Assign SubscriptStore NameLoad Index TupleLoad Str NameLoad AttributeLoad NameLoad attr Expr Call AttributeLoad NameLoad attr NameLoad NameLoad NameLoad Expr Call AttributeLoad NameLoad attr NameLoad Print NameLoad Call NameLoad NameLoad keyword NameLoad keyword NameLoad Assign NameStore Dict Assign NameStore Call NameLoad NameLoad Print NameLoad Str Assign NameStore Call NameLoad GeneratorExp AttributeLoad NameLoad attr comprehension NameStore NameLoad UnaryOpNot AttributeLoad NameLoad attr Assign NameStore Call NameLoad GeneratorExp AttributeLoad NameLoad attr comprehension NameStore NameLoad BoolOpAnd UnaryOpNot AttributeLoad NameLoad attr CompareNotEq AttributeLoad NameLoad attr Str Assign NameStore BinOpSub Call NameLoad Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad For TupleStore NameStore NameStore TupleLoad TupleLoad Str NameLoad TupleLoad Str NameLoad TupleLoad Str NameLoad body Assign NameStore ListComp NameLoad comprehension NameStore NameLoad CompareIn AttributeLoad NameLoad attr NameLoad Assign NameStore Call NameLoad NameLoad NameLoad NameLoad keyword NameLoad Expr Call AttributeLoad NameLoad attr NameLoad NameLoad NameLoad Print NameLoad Call NameLoad NameLoad keyword NameLoad keyword NameLoad decorator_list FunctionDef arguments args NameParam defaults body Expr Str Assign NameStore Call NameLoad AttributeLoad NameLoad attr Expr Call AttributeLoad NameLoad attr Str keyword NameLoad keyword Str keyword Str Assign TupleStore NameStore NameStore Call AttributeLoad NameLoad attr NameLoad If CompareNotEq Call NameLoad NameLoad Num body Expr Call AttributeLoad NameLoad attr UnaryOpNot Call AttributeLoad NameLoad attr Assign TupleStore NameStore NameStore NameLoad Assign NameStore SubscriptLoad Call AttributeLoad NameLoad attr Str Num Index Num Assign NameStore BinOpAdd NameLoad Str Assign NameStore BinOpAdd NameLoad Str Assign NameStore BinOpAdd NameLoad Str If Call NameLoad TupleLoad NameLoad NameLoad NameLoad body Expr Call NameLoad ListLoad NameLoad NameLoad NameLoad Assign NameStore BinOpAdd NameLoad Str If Call NameLoad TupleLoad NameLoad NameLoad NameLoad body Expr Call NameLoad NameLoad NameLoad NameLoad Assign NameStore BinOpAdd NameLoad Str If Call NameLoad TupleLoad NameLoad NameLoad NameLoad body Expr Call NameLoad ListLoad NameLoad NameLoad NameLoad Assign NameStore BinOpAdd NameLoad Str If Call NameLoad TupleLoad NameLoad NameLoad NameLoad body Expr Call AttributeLoad Call NameLoad TupleLoad NameLoad NameLoad NameLoad attr Assign NameStore BinOpAdd NameLoad Str If Call NameLoad TupleLoad NameLoad NameLoad NameLoad body Expr Call AttributeLoad Call NameLoad TupleLoad NameLoad NameLoad NameLoad attr Assign NameStore BinOpAdd NameLoad Str If Call NameLoad TupleLoad NameLoad NameLoad NameLoad NameLoad body Expr Call NameLoad ListLoad NameLoad NameLoad NameLoad Assign NameStore BinOpAdd SubscriptLoad Call AttributeLoad NameLoad attr Str Num Index Num Str If Call NameLoad TupleLoad NameLoad NameLoad NameLoad body Assign NameStore Call AttributeLoad Str attr NameLoad NameLoad NameLoad Expr Call NameLoad NameLoad If AttributeLoad NameLoad attr body Expr Call NameLoad ListLoad NameLoad NameLoad NameLoad NameLoad NameLoad BinOpAdd NameLoad Str Str Expr Call NameLoad ListLoad NameLoad Str decorator_list FunctionDef arguments args NameParam defaults body Expr Call AttributeLoad NameLoad attr Str Str keyword Str keyword Str Expr Call AttributeLoad NameLoad attr Str keyword Str keyword NameLoad keyword Str Expr Call AttributeLoad NameLoad attr Str keyword Num keyword Str keyword Str Expr Call AttributeLoad NameLoad attr Str keyword NameLoad keyword Str keyword Str decorator_list FunctionDef arguments args NameParam defaults body Expr Str ImportFrom alias alias alias alias alias alias ImportFrom alias alias alias Assign NameStore Call NameLoad AttributeLoad NameLoad attr Expr Call AttributeLoad NameLoad attr Str keyword Str Expr Call NameLoad NameLoad Assign TupleStore NameStore NameStore NameStore Call AttributeLoad NameLoad attr NameLoad keyword Str If CompareNotEq Call NameLoad NameLoad Num body Expr Call AttributeLoad NameLoad attr UnaryOpNot Call AttributeLoad NameLoad attr Assign TupleStore NameStore NameStore NameLoad Assign NameStore SubscriptLoad Call AttributeLoad NameLoad attr Str Num Index Num Assign NameStore BinOpAdd NameLoad Str Assign NameStore BinOpAdd NameLoad Str Assign NameStore AttributeLoad NameLoad attr Assign NameStore AttributeLoad NameLoad attr Assign NameStore Call NameLoad AttributeLoad NameLoad attr Assign NameStore Call NameLoad NameLoad keyword NameLoad Assign NameStore AttributeLoad NameLoad attr Assign NameStore AttributeLoad NameLoad attr Assign NameStore Call NameLoad NameLoad NameLoad Assert CompareIn NameLoad NameLoad Call AttributeLoad Str attr NameLoad NameLoad Assign NameStore Call NameLoad NameLoad NameLoad Assign NameStore ListComp NameLoad comprehension TupleStore NameStore NameStore Call AttributeLoad AttributeLoad NameLoad attr attr CompareGtE NameLoad NameLoad While UnaryOpNot NameLoad body AugAssignDiv NameStore Num Expr Call AttributeLoad NameLoad attr Call AttributeLoad Str attr NameLoad Assign NameStore ListComp NameLoad comprehension TupleStore NameStore NameStore Call AttributeLoad AttributeLoad NameLoad attr attr CompareGtE NameLoad NameLoad Assign NameStore Dict For NameStore NameLoad body Assign NameStore Call AttributeLoad NameLoad attr NameLoad Assign NameStore Call NameLoad GeneratorExp Call NameLoad NameLoad comprehension NameStore NameLoad Assign SubscriptStore NameLoad Index NameLoad NameLoad Assign NameStore Call AttributeLoad NameLoad attr Num TupleLoad AttributeLoad NameLoad attr AttributeLoad NameLoad attr Assign NameStore Call AttributeLoad NameLoad attr ListLoad Num Num Num Num Assign NameStore Call NameLoad keyword Str keyword Str keyword Str If AttributeLoad NameLoad attr body Expr Call AttributeLoad NameLoad attr Num Num AttributeLoad NameLoad attr keyword Str keyword NameLoad keyword Num Assign NameStore Call AttributeLoad NameLoad attr ListLoad Num Num Num Num Assign NameStore Call AttributeLoad NameLoad attr ListLoad Num Num Num Num Assign TupleStore NameStore NameStore TupleLoad Num Num Assign NameStore Call NameLoad NameLoad Assign NameStore AttributeLoad NameLoad attr Assign NameStore Num Assign NameStore Dict Assign NameStore Call NameLoad GeneratorExp TupleLoad NameLoad SubscriptLoad NameLoad Index NameLoad comprehension TupleStore NameStore NameStore Call NameLoad NameLoad Assign NameStore Call NameLoad GeneratorExp TupleLoad NameLoad SubscriptLoad NameLoad Index SubscriptLoad Call AttributeLoad NameLoad attr Str Index Num comprehension NameStore NameLoad Assign NameStore Dict For TupleStore NameStore TupleStore NameStore NameStore NameStore Call AttributeLoad NameLoad attr body Assign NameStore Call AttributeLoad NameLoad attr NameLoad Assign NameStore ListComp TupleLoad AttributeLoad NameLoad attr Call NameLoad NameLoad comprehension NameStore NameLoad Assign NameStore ListComp TupleLoad AttributeLoad NameLoad attr Call NameLoad NameLoad comprehension NameStore NameLoad CompareEq AttributeLoad NameLoad attr NameLoad Assign TupleStore NameStore NameStore Call NameLoad NameLoad Assign NameStore Call NameLoad NameLoad NameLoad Assign SubscriptStore NameLoad Index NameLoad NameLoad Assign NameStore CompareLt NameLoad Num Assign NameStore Call NameLoad NameLoad NameLoad NameLoad NameLoad NameLoad keyword NameLoad keyword NameLoad Assign NameStore IfExp CompareLt NameLoad Num BinOpMult Num NameLoad BinOpMult Num NameLoad Assign NameStore IfExp CompareLt NameLoad Num Str Str Assign NameStore SubscriptLoad Call AttributeLoad NameLoad attr Str Index Num Assign NameStore Call NameLoad Call AttributeLoad NameLoad attr Str Str Assign NameStore Call AttributeLoad Str attr NameLoad SubscriptLoad NameLoad Index NameLoad Expr Call AttributeLoad NameLoad attr BinOpAdd NameLoad NameLoad BinOpDiv BinOpAdd NameLoad NameLoad Num NameLoad keyword SubscriptLoad NameLoad Index NameLoad keyword NameLoad keyword Str keyword Num Expr Call AttributeLoad NameLoad attr AttributeLoad NameLoad attr Assign NameStore Call NameLoad NameLoad Assign NameStore ListComp NameLoad comprehension NameStore NameLoad CompareEq AttributeLoad NameLoad attr NameLoad Assign NameStore Call NameLoad GeneratorExp AttributeLoad NameLoad attr comprehension NameStore NameLoad Assign NameStore BinOpSub NameLoad NameLoad Assign NameStore BinOpDiv NameLoad NameLoad Assign NameStore Lambda arguments args NameParam defaults BinOpSub NameLoad BinOpMult NameLoad NameLoad Assign NameStore ListComp Call NameLoad AttributeLoad NameLoad attr comprehension NameStore NameLoad UnaryOpNot AttributeLoad NameLoad attr Expr Call NameLoad NameLoad Num NameLoad NameLoad keyword BinOpMult Num NameLoad keyword NameLoad keyword Num Assign NameStore Call AttributeLoad Str attr NameLoad Call NameLoad NameLoad keyword Num Expr Call AttributeLoad NameLoad attr Num BinOpAdd NameLoad NameLoad NameLoad keyword Str Assign NameStore Call NameLoad NameLoad For NameStore AttributeLoad NameLoad attr body Assign NameStore AttributeLoad NameLoad attr If CompareNotIn NameLoad NameLoad body Continue Assign NameStore Num Assign NameStore Call NameLoad AttributeLoad NameLoad attr Assign NameStore SubscriptLoad SubscriptLoad NameLoad Index AttributeLoad NameLoad attr Index Num Assign NameStore SubscriptLoad NameLoad Index NameLoad Assign NameStore IfExp CompareLt NameLoad NameLoad UnaryOpUSub NameLoad NameLoad AugAssignMult NameStore Num AugAssignAdd NameStore NameLoad AugAssignSub NameStore NameLoad Expr Call AttributeLoad NameLoad attr TupleLoad NameLoad NameLoad TupleLoad NameLoad NameLoad Str keyword SubscriptLoad NameLoad Index AttributeLoad NameLoad attr Expr Call AttributeLoad SubscriptLoad NameLoad Index AttributeLoad NameLoad attr attr TupleLoad AttributeLoad NameLoad attr Call NameLoad NameLoad Assign TupleStore NameStore NameStore Call NameLoad TupleLoad NameLoad NameLoad Assign NameStore Lambda arguments args NameParam defaults BinOpAdd NameLoad BinOpMult NameLoad NameLoad Assign NameStore ListComp AttributeLoad NameLoad attr comprehension NameStore NameLoad UnaryOpNot AttributeLoad NameLoad attr Assign NameStore ListComp Call NameLoad NameLoad comprehension NameStore NameLoad Expr Call NameLoad NameLoad NameLoad NameLoad NameLoad keyword BinOpMult Num NameLoad keyword NameLoad keyword Num Expr Call NameLoad NameLoad NameLoad NameLoad Assign NameStore Num Assign NameStore BinOpDiv BinOpSub BinOpSub NameLoad BinOpMult NameLoad Call NameLoad NameLoad NameLoad Call NameLoad Call AttributeLoad NameLoad attr Assign NameStore ListLoad For TupleStore NameStore NameStore Call NameLoad Call AttributeLoad NameLoad attr body Assign NameStore BinOpMult NameLoad NameLoad AugAssignSub NameStore NameLoad Assign NameStore BinOpAdd Num BinOpDiv NameLoad Num Assign NameStore BinOpDiv NameLoad Num Assign NameStore SubscriptLoad NameLoad Index NameLoad Assign NameStore Call AttributeLoad NameLoad attr ListLoad NameLoad NameLoad NameLoad NameLoad Assign NameStore BinOpAdd NameLoad BinOpDiv NameLoad Num AugAssignSub NameStore NameLoad Assign NameStore SubscriptLoad NameLoad Index NameLoad Assign TupleStore NameStore NameStore Call NameLoad NameLoad Expr Call AttributeLoad NameLoad attr NameLoad Num BinOpMult Num NameLoad keyword Str Expr Call AttributeLoad NameLoad attr NameLoad NameLoad Str keyword NameLoad Assign NameStore SubscriptLoad NameLoad Index NameLoad Expr Call AttributeLoad NameLoad attr Num BinOpSub Num BinOpDiv BinOpMult Num NameLoad NameLoad Call AttributeLoad Str attr NameLoad keyword Str keyword Str keyword AttributeLoad NameLoad attr keyword Str Assign NameStore Call NameLoad Call AttributeLoad NameLoad attr Str Str Expr Call AttributeLoad NameLoad attr TupleLoad NameLoad NameLoad NameLoad Expr Call AttributeLoad NameLoad attr Num NameLoad Expr Call AttributeLoad NameLoad attr Num NameLoad Expr Call AttributeLoad NameLoad attr ListLoad While BoolOpAnd CompareLt BinOpDiv NameLoad Call NameLoad Call AttributeLoad NameLoad attr Num CompareGtE Call NameLoad Call AttributeLoad NameLoad attr Num body Expr Call AttributeLoad NameLoad attr SubscriptLoad Call AttributeLoad NameLoad attr Slice Num Assign NameStore ListComp Call NameLoad NameLoad comprehension NameStore Call AttributeLoad NameLoad attr Expr Call AttributeLoad NameLoad attr NameLoad keyword Str If CompareLt NameLoad Num body Expr Call AttributeLoad NameLoad attr For TupleStore NameStore TupleStore NameStore NameStore NameStore Call NameLoad NameLoad body Assign NameStore Str If CompareGt Call NameLoad NameLoad Num body Assign NameStore IfExp BinOpMod NameLoad Num Str Str Expr Call AttributeLoad NameLoad attr Num NameLoad NameLoad keyword NameLoad keyword Num keyword NameLoad keyword Str If AttributeLoad NameLoad attr body Assign NameStore TupleLoad TupleLoad Num Num Str TupleLoad Num Num Str Expr Call NameLoad NameLoad NameLoad Expr Call NameLoad TupleLoad NameLoad NameLoad NameLoad Assign NameStore BinOpAdd BinOpAdd NameLoad Str AttributeLoad NameLoad attr Expr Call NameLoad NameLoad keyword AttributeLoad NameLoad attr keyword NameLoad Expr Call AttributeLoad NameLoad attr NameLoad Return NameLoad decorator_list FunctionDef arguments args NameParam defaults body Expr Str Assign NameStore Call NameLoad AttributeLoad NameLoad attr Expr Call NameLoad NameLoad Assign TupleStore NameStore NameStore NameStore Call AttributeLoad NameLoad attr NameLoad keyword Str If CompareNotEq Call NameLoad NameLoad Num body Expr Call AttributeLoad NameLoad attr UnaryOpNot Call AttributeLoad NameLoad attr Assign TupleStore NameStore NameLoad Assign NameStore SubscriptLoad Call AttributeLoad NameLoad attr Str Num Index Num Assign NameStore BinOpAdd NameLoad Str Assign NameStore Call NameLoad NameLoad Assign NameStore ListComp NameLoad comprehension TupleStore NameStore NameStore Call AttributeLoad NameLoad attr CompareGt Call NameLoad NameLoad Num For NameStore Call NameLoad NameLoad body Expr Call NameLoad BinOpAdd NameLoad ListLoad NameLoad decorator_list If CompareEq NameLoad Str body Expr Call NameLoad
N/A N/A 
Scaffold Ordering with Weighted Maps.
 N/A os.path op N/A os N/A sys N/A logging N/A numpy np N/A networkx nx itertools combinations product collections defaultdict functools partial jcvi __version__ version jcvi.algorithms.formula reject_outliers spearmanr jcvi.algorithms.lis longest_monotonic_subseq_length_loose lms longest_monotonic_subsequence_loose lmseq jcvi.algorithms.tsp hamiltonian jcvi.algorithms.matrix determine_signs jcvi.algorithms.ec GA_setup GA_run jcvi.formats.agp AGP order_to_agp build agp_build reindex jcvi.formats.base DictFile FileMerger FileShredder must_open read_block jcvi.formats.bed Bed BedLine natsorted sort jcvi.formats.chain fromagp jcvi.formats.sizes Sizes jcvi.graphics.landscape draw_gauge jcvi.utils.cbook human_size percentage jcvi.utils.counter Counter jcvi.utils.grouper Grouper jcvi.utils.iter flatten pairwise jcvi.utils.table tabulate jcvi.apps.base OptionParser OptionGroup ActionDispatcher sh need_update get_today SUPPRESS_HELP mkdir N/A N/A START END N/A START END N/A distance_choices N/A cM rank N/A linkage_choices N/A single double complete average median N/A N/A N/A np seterr invalid ignore Scaffold N/A object N/A __init__ N/A N/A self seqid mapc N/A N/A N/A N/A self markers N/A N/A mapc extract seqid N/A N/A self seqid seqid N/A N/A self mapc mapc N/A mlg_counts N/A N/A self N/A N/A N/A N/A Counter N/A N/A x mlg N/A x N/A self markers N/A property add_LG_pairs N/A N/A self G mappair N/A N/A N/A cc N/A N/A N/A self mlg_counts items N/A mappair N/A sorted mappair N/A N/A N/A ak av N/A bk bv N/A combinations cc 2 N/A N/A N/A aks bks N/A N/A N/A N/A ak split - N/A 0 N/A N/A N/A bk split - N/A 0 N/A N/A N/A sorted N/A aks bks mappair N/A N/A N/A weight N/A min av bv N/A N/A G N/A N/A ak bk weight N/A N/A G N/A N/A bk ak weight N/A N/A LinkageGroup N/A object N/A __init__ N/A N/A self lg length markers function linkage N/A N/A N/A N/A x N/A N/A x rank min N/A N/A N/A self lg lg N/A N/A self length length N/A N/A self markers markers N/A N/A self function f function N/A N/A self linkage linkage N/A N/A self mapname N/A N/A N/A lg split - N/A 0 N/A N/A self series N/A N/A N/A self nmarkers N/A N/A N/A self oo N/A N/A N/A self position N/A N/A N/A self guide N/A N/A N/A k v N/A N/A markers items N/A N/A N/A N/A self series N/A k xs N/A N/A f x N/A x v N/A N/A N/A self nmarkers N/A k N/A len v N/A physical_to_cm N/A N/A N/A x pos N/A f x N/A x v N/A N/A N/A self oo N/A k N/A get_rho physical_to_cm N/A N/A N/A self position N/A k N/A N/A np median xs N/A N/A N/A self guide N/A k N/A N/A np median N/A N/A x cm N/A x v N/A path N/A sorted N/A N/A v N/A N/A self guide N/A k k N/A N/A k v N/A N/A N/A self position items N/A N/A vv gg path N/A zip path N/A N/A self path path N/A N/A self rho 0 N/A populate_pairwise_distance N/A N/A self N/A N/A N/A distances N/A N/A series N/A self series N/A linkage N/A self linkage N/A N/A a b N/A combinations N/A self path 2 N/A N/A d N/A linkage_distance N/A series N/A a N/A series N/A b linkage linkage N/A N/A distances N/A N/A a b N/A distances N/A N/A b a d N/A p N/A self path N/A N/A adist N/A linkage_distance N/A 0 N/A series N/A p linkage linkage N/A bdist N/A linkage_distance N/A series N/A p N/A N/A self length linkage linkage N/A N/A N/A self rho 0 N/A N/A N/A adist bdist N/A bdist adist N/A N/A distances N/A N/A START p N/A distances N/A N/A p START adist N/A N/A distances N/A N/A END p N/A distances N/A N/A p END bdist N/A N/A self distances distances N/A distances N/A N/A ScaffoldOO N/A object N/A N/A 
    This contains the routine to construct order and orientation for the
    scaffolds per partition.
     __init__ N/A N/A self lgs scaffolds mapc pivot weights sizes function linkage fwtour skipconcorde ngen npop cpus seed N/A N/A N/A N/A x N/A N/A x rank min None False 500 100 8 666 N/A N/A N/A self lgs lgs N/A N/A self lengths N/A mapc lengths N/A N/A self bins N/A mapc bins N/A N/A self sizes sizes N/A N/A self scaffolds scaffolds N/A N/A self pivot pivot N/A N/A self weights weights N/A N/A self function function N/A N/A self linkage linkage N/A N/A self skipconcorde skipconcorde N/A N/A N/A self prepare_linkage_groups N/A mlg N/A self lgs N/A N/A N/A mapname lg N/A N/A mlg rsplit - 1 N/A N/A mapname pivot N/A N/A N/A self object N/A N/A chr{0} format lg N/A N/A tag N/A N/A | join lgs N/A tour N/A zip scaffolds N/A N/A len scaffolds N/A 1 N/A N/A print_tour fwtour N/A self object tag INIT tour recode True N/A signs N/A N/A self assign_orientation N/A N/A N/A len signs N/A len scaffolds N/A tour N/A zip scaffolds signs N/A scaffolds_oo N/A dict tour N/A N/A print_tour fwtour N/A self object tag FLIP tour recode True N/A tour N/A N/A self assign_order N/A tour N/A N/A x N/A scaffolds_oo N/A x N/A x tour N/A N/A print_tour fwtour N/A self object tag TSP tour recode True callback N/A N/A tour gen i N/A 0 N/A N/A fitness N/A N/A hasattr tour fitness N/A tour fitness None N/A tour N/A N/A scaffolds N/A x N/A x tour N/A tour N/A N/A x N/A scaffolds_oo N/A x N/A x tour N/A label N/A N/A GA{0}-{1} format i gen N/A fitness N/A N/A fitness N/A N/A N/A N/A N/A N/A N/A {0} format fitness split . N/A 0 replace ( N/A label N/A - fitness N/A N/A print_tour fwtour N/A self object tag label tour recode True N/A tour N/A N/A i 0 N/A N/A best_tour best_fitness N/A None None N/A True N/A N/A N/A N/A logging debug N/A N/A Start EC round {0} format i N/A scaffolds_oo N/A dict tour N/A N/A scfs tour ww N/A N/A self prepare_ec scaffolds tour weights N/A callbacki N/A partial callback i i N/A toolbox N/A GA_setup tour N/A N/A N/A toolbox register evaluate colinear_evaluate_multi scfs scfs weights ww N/A N/A tour fitness N/A GA_run toolbox ngen ngen npop npop cpus cpus seed seed callback callbacki N/A tour N/A callbacki tour FIN N/A N/A best_fitness N/A fitness best_fitness N/A N/A N/A N/A logging debug N/A N/A No fitness improvement: {0}. Exit EC. format best_fitness N/A N/A tour N/A N/A self fix_orientation tour N/A N/A best_tour best_fitness N/A tour fitness N/A N/A print_tour fwtour N/A self object tag N/A N/A GA{0}-FIXORI format i tour recode True N/A N/A N/A logging debug N/A N/A Current best fitness: {0} format best_fitness N/A i 1 N/A tour N/A N/A self fix_tour tour N/A N/A self tour N/A recode_tour tour N/A fw N/A N/A sys stderr fwtour N/A N/A N/A print_tour fw N/A self object tag FINAL N/A self tour N/A prepare_ec N/A N/A self scaffolds tour weights N/A N/A N/A 
        Prepare Evolutionary Computation. This converts scaffold names into
        indices (integer) in the scaffolds array.
         N/A scaffolds_ii N/A dict N/A N/A s i N/A N/A i s N/A enumerate scaffolds N/A scfs N/A N/A ww N/A N/A mlg N/A self linkage_groups N/A N/A w N/A float N/A weights N/A N/A mlg mapname N/A scf N/A N/A N/A s o tour N/A N/A si N/A scaffolds_ii N/A s N/A N/A scf N/A si N/A N/A self get_series N/A mlg lg s orientation o N/A N/A N/A scfs append scf N/A N/A N/A ww append w N/A tour N/A N/A scaffolds_ii N/A x N/A N/A x o tour N/A N/A scfs tour ww N/A weighted_mean N/A N/A self a N/A N/A N/A N/A a w N/A zip a N/A w N/A N/A N/A self weights N/A x N/A x w N/A N/A N/A np average a weights w N/A get_markers N/A N/A self lg scaffold orientation N/A 0 N/A N/A xs N/A N/A N/A self bins get N/A lg scaffold N/A N/A N/A orientation 0 N/A N/A xs N/A xs N/A -1 N/A xs N/A get_series N/A N/A self lg scaffold orientation N/A 0 N/A N/A xs N/A N/A self get_markers lg scaffold orientation orientation N/A N/A N/A N/A self function x N/A x xs N/A prepare_linkage_groups N/A N/A self N/A N/A N/A N/A self linkage_groups N/A N/A lg N/A self lgs N/A N/A length N/A N/A self lengths N/A lg N/A markers N/A N/A s N/A self scaffolds N/A N/A xs N/A N/A self get_markers lg s N/A xs N/A N/A N/A markers N/A s xs N/A N/A markers N/A N/A N/A LG N/A LinkageGroup lg length markers function N/A self function linkage N/A self linkage N/A N/A N/A N/A self linkage_groups append LG N/A distances_to_tour N/A N/A self N/A N/A N/A scaffolds N/A self scaffolds N/A distances N/A self distances N/A G N/A N/A nx DiGraph N/A N/A N/A a b v N/A N/A distances items N/A N/A d N/A N/A self weighted_mean v N/A N/A N/A G add_edge a b weight d N/A N/A N/A a START N/A b END N/A N/A N/A N/A N/A G add_edge b a weight d N/A N/A N/A logging debug N/A N/A Graph size: |V|={0}, |E|={1}. format N/A len G N/A N/A G size N/A L N/A N/A nx all_pairs_dijkstra_path_length G N/A N/A a b N/A combinations scaffolds 2 N/A N/A N/A N/A G has_edge a b N/A N/A N/A N/A N/A a L N/A b N/A L N/A a N/A N/A l N/A N/A L N/A a N/A b N/A N/A N/A G add_edge a b weight l N/A N/A N/A G add_edge b a weight l N/A edges N/A N/A N/A a b d N/A N/A G edges data True N/A N/A N/A N/A edges append N/A a b N/A d N/A weight N/A N/A self skipconcorde N/A N/A N/A N/A logging debug concorde-TSP skipped. Use default scaffold ordering. N/A tour N/A scaffolds N/A N/A tour N/A N/A N/A tour N/A hamiltonian edges directed True precision 2 N/A N/A N/A N/A tour N/A 0 START N/A N/A tour N/A -1 END N/A tour N/A tour N/A 1 -1 N/A N/A N/A N/A N/A N/A logging debug concorde-TSP failed. Use default scaffold ordering. N/A tour N/A scaffolds N/A N/A tour N/A assign_order N/A N/A self N/A N/A N/A 
        The goal is to assign scaffold orders. To help order the scaffolds, two
        dummy node, START and END, mark the ends of the chromosome. We connect
        START to each scaffold (directed), and each scaffold to END.
         N/A linkage_groups N/A self linkage_groups N/A mlg linkage_groups N/A N/A mapname N/A mlg mapname N/A N/A mapname N/A self pivot N/A N/A pivot_position N/A mlg position N/A mlg linkage_groups N/A N/A position N/A mlg position N/A common N/A N/A N/A a ap N/A N/A position items N/A N/A N/A a pivot_position N/A N/A N/A pp N/A pivot_position N/A a N/A N/A N/A common append N/A ap pp N/A N/A mlg rho N/A get_rho common N/A N/A N/A mlg rho 0 N/A N/A N/A mlg path N/A N/A mlg path N/A -1 N/A N/A N/A mlg populate_pairwise_distance N/A distances N/A defaultdict list N/A mlg linkage_groups N/A N/A mapname N/A mlg mapname N/A position N/A mlg position N/A length N/A mlg length N/A path N/A mlg path N/A rho N/A mlg rho N/A dd N/A mlg distances N/A N/A a b N/A combinations path 2 N/A N/A d N/A dd N/A N/A a b N/A N/A N/A N/A distances N/A N/A a b append N/A d mapname N/A p path N/A N/A N/A adist bdist N/A N/A position N/A p N/A length N/A position N/A p N/A N/A rho 0 N/A N/A N/A adist bdist N/A bdist adist N/A N/A N/A N/A distances N/A N/A START p append N/A adist mapname N/A N/A N/A N/A distances N/A N/A p END append N/A bdist mapname N/A N/A self distances distances N/A tour N/A N/A self distances_to_tour N/A tour N/A get_orientation N/A N/A self si sj N/A N/A N/A 
        si, sj are two number series. To compute whether these two series have
        same orientation or not. We combine them in the two orientation
        configurations and compute length of the longest monotonic series.
         N/A N/A N/A si N/A sj N/A N/A 0 N/A a N/A lms N/A si sj N/A b N/A lms N/A sj si N/A c N/A lms N/A si N/A sj N/A -1 N/A d N/A lms N/A N/A sj N/A -1 si N/A N/A N/A N/A max a b N/A 0 N/A N/A max c d N/A 0 N/A assign_orientation N/A N/A self N/A N/A N/A signs N/A defaultdict list N/A scaffolds N/A self scaffolds N/A mlg N/A self linkage_groups N/A N/A mapname N/A mlg mapname N/A series N/A mlg series N/A N/A mapname N/A self pivot N/A N/A pivot_oo N/A mlg oo N/A pivot_nmarkers N/A mlg nmarkers N/A N/A i j N/A combinations N/A range N/A len scaffolds 2 N/A N/A N/A si sj N/A N/A scaffolds N/A i N/A scaffolds N/A j N/A N/A si sj N/A N/A N/A series get si N/A N/A N/A series get sj N/A N/A d N/A N/A self get_orientation si sj N/A N/A d N/A N/A N/A N/A N/A N/A signs N/A N/A i j append N/A d mapname N/A N/A e v N/A N/A signs items N/A N/A N/A signs N/A e N/A N/A self weighted_mean v N/A signs_edges N/A sorted N/A N/A a b w N/A N/A N/A a b w N/A N/A signs items N/A signs N/A determine_signs scaffolds signs_edges N/A pivot_oo N/A N/A N/A pivot_oo get x 0 N/A x scaffolds N/A nmarkers N/A N/A N/A pivot_nmarkers get x 0 N/A x scaffolds N/A flipr N/A N/A signs N/A N/A np sign N/A N/A np array pivot_oo nmarkers N/A N/A N/A sum flipr 0 N/A N/A signs N/A signs N/A signs N/A fix_tour N/A N/A self tour N/A N/A N/A 
        Test each scaffold if dropping does not decrease LMS.
         N/A N/A scaffolds oos N/A zip tour N/A keep N/A set N/A mlg N/A self linkage_groups N/A N/A lg N/A mlg lg N/A N/A s o tour N/A N/A i N/A N/A scaffolds index s N/A L N/A N/A N/A self get_series lg x xo N/A N/A x xo N/A tour N/A i N/A U N/A N/A N/A self get_series lg x xo N/A N/A x xo N/A tour N/A N/A i 1 N/A N/A L U N/A N/A list N/A flatten L N/A list N/A flatten U N/A M N/A N/A self get_series lg s o N/A score_with N/A N/A lms N/A N/A L M U N/A 0 N/A score_without N/A N/A lms N/A L U N/A 0 N/A N/A score_with score_without N/A N/A score_with score_without N/A N/A N/A N/A keep add s N/A dropped N/A N/A len tour N/A len keep N/A N/A N/A logging debug N/A N/A Dropped {0} minor scaffolds format dropped N/A N/A N/A s o N/A N/A s o tour N/A s keep N/A fix_orientation N/A N/A self tour N/A N/A N/A 
        Test each scaffold if flipping will increass longest monotonic chain
        length.
         N/A orientations N/A dict tour N/A scaffold_oo N/A defaultdict list N/A N/A scaffolds oos N/A zip tour N/A mlg N/A self linkage_groups N/A N/A lg N/A mlg lg N/A mapname N/A mlg mapname N/A N/A s o tour N/A N/A i N/A N/A scaffolds index s N/A L N/A N/A N/A self get_series lg x xo N/A N/A x xo N/A tour N/A i N/A U N/A N/A N/A self get_series lg x xo N/A N/A x xo N/A tour N/A N/A i 1 N/A N/A L U N/A N/A list N/A flatten L N/A list N/A flatten U N/A M N/A N/A self get_series lg s N/A plus N/A lms N/A N/A L M U N/A minus N/A lms N/A N/A L N/A M N/A -1 U N/A d N/A N/A plus N/A 0 N/A minus N/A 0 N/A N/A d N/A N/A N/A N/A N/A N/A scaffold_oo N/A s append N/A d mapname N/A fixed 0 N/A N/A s v N/A N/A scaffold_oo items N/A N/A d N/A N/A self weighted_mean v N/A old_d N/A orientations N/A s N/A new_d N/A N/A np sign d N/A N/A new_d old_d N/A N/A N/A orientations N/A s new_d N/A fixed 1 N/A tour N/A N/A x N/A orientations N/A x N/A x scaffolds N/A N/A N/A logging debug N/A N/A Fixed orientations for {0} scaffolds. format fixed N/A tour N/A N/A CSVMapLine N/A object N/A __init__ N/A N/A self row sep mapname N/A , None N/A N/A args N/A N/A N/A N/A row strip split sep N/A N/A self seqid N/A args N/A 0 N/A N/A self pos N/A int N/A args N/A 1 N/A N/A self lg N/A args N/A 2 N/A N/A self cm N/A float N/A args N/A 3 N/A N/A self mapname mapname N/A bedline N/A N/A self N/A N/A N/A marker N/A N/A {0}-{1}:{2:.6f} format N/A self mapname N/A self lg N/A self cm N/A track N/A N/A {0}:{1} format N/A self seqid N/A self pos N/A N/A N/A join N/A N/A str x N/A x N/A N/A self seqid N/A N/A self pos 1 N/A self pos marker track N/A property N/A Marker N/A object N/A __init__ N/A N/A self b N/A N/A N/A N/A self seqid N/A b seqid N/A N/A self pos N/A b start N/A N/A N/A self mlg cm N/A N/A N/A b accn split : N/A N/A N/A self mapname N/A self lg N/A N/A N/A b accn split - N/A N/A self cm N/A float cm N/A N/A self accn N/A b accn N/A N/A self args N/A b args N/A N/A self rank -1 N/A parse_scaffold_info N/A N/A self N/A N/A N/A N/A self scaffoldaccn N/A N/A self args N/A -1 N/A N/A N/A self scaffoldid scaffoldpos N/A N/A N/A self scaffoldaccn split : N/A N/A self scaffoldpos N/A int scaffoldpos N/A __str__ N/A N/A self N/A N/A N/A N/A N/A join N/A N/A str x N/A x N/A N/A self seqid N/A N/A self pos 1 N/A self pos N/A self accn N/A self rank N/A N/A __repr__ __str__ N/A Map N/A list N/A __init__ N/A N/A self filename scaffold_info compress remove_outliers function N/A False 1e-06 False N/A N/A N/A x N/A N/A x rank N/A N/A bed N/A Bed filename N/A b bed N/A N/A N/A N/A self append N/A Marker b N/A N/A N/A self report N/A N/A self ranks N/A N/A self compute_ranks compress N/A N/A self lengths N/A N/A self compute_lengths function N/A N/A self bins N/A N/A self get_bins function remove_outliers N/A scaffold_info N/A N/A b self N/A N/A N/A N/A b parse_scaffold_info N/A report N/A N/A self N/A N/A N/A N/A self nmarkers N/A len self N/A N/A self seqids N/A sorted N/A set N/A N/A x seqid N/A x self N/A N/A self mapnames N/A sorted N/A set N/A N/A x mapname N/A x self N/A N/A self mlgs N/A sorted N/A set N/A N/A x mlg N/A x self N/A N/A N/A logging debug N/A N/A Map contains {0} markers in {1} linkage groups. format N/A self nmarkers N/A len N/A self mlgs N/A extract N/A N/A self seqid N/A N/A N/A r N/A x N/A x self N/A N/A x seqid seqid N/A N/A sorted r key N/A N/A N/A x N/A N/A x pos N/A extract_mlg N/A N/A self mlg N/A N/A N/A r N/A x N/A x self N/A N/A x mlg mlg N/A N/A sorted r key N/A N/A N/A x N/A N/A x cm N/A compute_ranks N/A N/A self compress N/A N/A N/A ranks N/A N/A mlg N/A self mlgs N/A N/A rank 0 N/A mlg_set N/A N/A self extract_mlg mlg N/A N/A i marker N/A enumerate mlg_set N/A N/A N/A i 0 N/A N/A N/A marker rank rank N/A N/A N/A N/A N/A marker cm N/A N/A mlg_set N/A N/A i 1 cm compress N/A N/A rank 1 N/A N/A marker rank rank N/A N/A ranks N/A mlg mlg_set N/A ranks N/A compute_lengths N/A N/A self function N/A N/A N/A lengths N/A N/A N/A mlg v N/A N/A N/A self ranks items N/A N/A N/A lengths N/A mlg N/A max N/A N/A function x N/A x v N/A lengths N/A get_bins N/A N/A self function remove_outliers N/A N/A N/A s N/A defaultdict list N/A m self N/A N/A N/A N/A N/A s N/A N/A N/A m mlg N/A m seqid append m N/A remove_outliers N/A N/A original clean 0 N/A N/A pair markers N/A N/A s items N/A N/A cm N/A N/A self remove_outliers markers function N/A N/A s N/A pair cm N/A original N/A len markers N/A clean N/A len cm N/A N/A N/A logging debug N/A N/A Retained {0} clean markers. format N/A percentage clean original N/A s N/A remove_outliers N/A N/A self markers function N/A N/A N/A data N/A N/A function x N/A x markers N/A reject N/A reject_outliers data N/A clean_markers N/A m N/A N/A m r N/A zip markers reject N/A r N/A clean_markers N/A N/A MapSummary N/A object N/A __init__ N/A N/A self markers l50 s scaffolds N/A None N/A N/A markers N/A N/A self unique_markers markers N/A N/A self num_markers N/A len markers N/A N/A self num_lgs N/A len N/A set N/A N/A x mlg N/A x markers N/A scaffolds N/A scaffolds N/A set N/A N/A x seqid N/A x markers N/A n50_scaffolds N/A x N/A x scaffolds N/A N/A N/A s mapping N/A x l50 N/A N/A self num_scaffolds N/A len scaffolds N/A N/A self num_n50_scaffolds N/A len n50_scaffolds N/A N/A self total_bases N/A sum N/A N/A N/A s mapping N/A x N/A x scaffolds N/A N/A N/A self tally_markers markers N/A unique_markers N/A N/A self markers N/A N/A N/A umarkers N/A N/A seen N/A set N/A m markers N/A N/A mt N/A N/A m seqid N/A m pos N/A N/A mt seen N/A N/A N/A N/A N/A umarkers append m N/A N/A N/A seen add mt N/A umarkers N/A tally_markers N/A N/A self markers N/A N/A N/A counter N/A Counter N/A N/A x seqid N/A x markers N/A N/A self scaffold_1m N/A len N/A x N/A x N/A N/A counter values N/A x 1 N/A N/A self scaffold_2m N/A len N/A x N/A x N/A N/A counter values N/A x 2 N/A N/A self scaffold_3m N/A len N/A x N/A x N/A N/A counter values N/A x 3 N/A N/A self scaffold_4m N/A len N/A x N/A x N/A N/A counter values N/A x 4 N/A export_table N/A N/A self r mapname total N/A N/A N/A N/A r N/A N/A Markers (unique) mapname N/A self num_markers N/A N/A r N/A N/A Markers per Mb mapname N/A N/A self total_bases N/A N/A N/A self num_markers 1000000.0 N/A self total_bases 0 N/A N/A r N/A N/A Scaffolds mapname N/A self num_scaffolds N/A N/A r N/A N/A N50 Scaffolds mapname N/A self num_n50_scaffolds N/A N/A r N/A N/A Total bases mapname N/A percentage N/A self total_bases total mode 1 N/A N/A r N/A N/A Scaffolds with 1 marker mapname N/A self scaffold_1m N/A N/A r N/A N/A Scaffolds with 2 markers mapname N/A self scaffold_2m N/A N/A r N/A N/A Scaffolds with 3 markers mapname N/A self scaffold_3m N/A N/A r N/A N/A Scaffolds with >=4 markers mapname N/A self scaffold_4m N/A N/A Weights N/A DictFile N/A __init__ N/A N/A self filename mapnames cast N/A int N/A N/A N/A N/A N/A super Weights self __init__ filename cast cast N/A N/A self maps N/A N/A N/A N/A x split N/A 0 N/A x N/A must_open filename N/A N/A N/A self update_maps mapnames N/A N/A pivot_weight o pivot N/A N/A self get_pivot mapnames N/A ref N/A N/A self maps N/A 0 N/A N/A self pivot pivot N/A N/A self ref ref N/A N/A N/A logging debug N/A N/A Map weights: {0} format N/A N/A self items N/A update_maps N/A N/A self mapnames default N/A 1 N/A N/A keys N/A N/A self keys N/A m keys N/A N/A N/A m mapnames N/A N/A N/A self N/A m N/A m mapnames N/A N/A N/A m self N/A N/A N/A N/A self N/A m default N/A N/A N/A logging debug N/A N/A Weight for `{0}` set to {1}. format m default N/A get_pivot N/A N/A self mapnames N/A N/A N/A N/A max N/A N/A w N/A N/A N/A N/A self maps index m m N/A N/A m w N/A N/A self items N/A m mapnames N/A N/A Layout N/A object N/A __init__ N/A N/A self mlgsizes N/A N/A N/A N/A self mlgsizes mlgsizes N/A N/A N/A self partition N/A N/A N/A self calculate_coords N/A partition N/A N/A self N N/A 2 N/A N/A endtime N/A N/A 0 N N/A parts N/A N/A i N/A xrange N N/A N/A N/A N/A parts append N/A N/A N/A mlg mlgsize N/A sorted N/A N/A N/A self mlgsizes items key N/A N/A N/A x N/A N/A N/A x N/A -1 N/A N/A N/A mt mi N/A min N/A N/A x i N/A N/A i x N/A enumerate endtime N/A N/A endtime N/A mi mlgsize N/A N/A N/A N/A parts N/A mi append N/A mlg mlgsize N/A N/A self parts parts N/A calculate_coords N/A N/A self r gapsize N/A 0.8 0.1 N/A N/A part_sizes N/A N/A p N/A self parts N/A N/A ps N/A sum N/A ms N/A N/A m ms p N/A N/A N/A part_sizes append N/A ps N/A N/A len p 1 N/A N/A max_part_size ngaps N/A max part_sizes N/A gaps N/A gapsize ngaps N/A ratio N/A N/A r gaps max_part_size N/A N/A self ratio ratio N/A coords N/A N/A N/A x p N/A ps ngaps N/A zip N/A 0.25 0.75 N/A self parts part_sizes N/A N/A gaps N/A gapsize ngaps N/A ystart N/A N/A N/A 1 N/A ratio ps gaps 2 N/A N/A m ms p N/A N/A mlen N/A ratio ms N/A N/A coords N/A m N/A x N/A ystart mlen ystart N/A ystart N/A mlen gapsize N/A N/A self coords coords N/A N/A GapEstimator N/A object N/A __init__ N/A N/A self mapc agp seqid mlg function N/A N/A N/A N/A x N/A N/A x cm N/A N/A mm N/A N/A mapc extract_mlg mlg N/A N/A N/A logging debug N/A N/A Extracted {0} markers for {1}-{2} format N/A len mm seqid mlg N/A N/A self mlgsize N/A max N/A N/A function x N/A x mm N/A N/A self agp N/A x N/A x agp N/A N/A x object seqid N/A N/A self scaffolds N/A N/A x component_id N/A x N/A self agp N/A N/A x is_gap N/A N/A self pp N/A N/A x object_beg N/A x N/A self agp N/A x is_gap N/A N/A self chrsize N/A max N/A N/A x object_end N/A x N/A self agp N/A s N/A Scaffold seqid mapc N/A N/A self scatter_data N/A N/A N/A self scaffold_markers N/A defaultdict list N/A x N/A s markers N/A N/A N/A N/A x mlg mlg N/A N/A N/A N/A N/A N/A N/A self scaffold_markers N/A N/A x scaffoldid append x N/A N/A N/A N/A self scatter_data append N/A N/A x pos N/A function x N/A N/A N/A N/A self scatter_data sort N/A N/A N/A self get_splines N/A get_gapsize N/A N/A self scaffold N/A N/A N/A i N/A N/A N/A self scaffolds index scaffold N/A N/A N/A self gapsizes N/A i N/A get_splines N/A N/A self floor ceil N/A N/A 25 1e-09 N/A 25 1e-06 N/A scipy.interpolate UnivariateSpline N/A N/A mx my N/A zip N/A self scatter_data N/A N/A yy xx N/A zip N/A lmseq N/A zip my mx N/A spl N/A UnivariateSpline xx yy N/A spld N/A N/A spl derivative spl_derivative N/A N/A x N/A N/A N/A s N/A abs N/A spld x N/A N/A s N/A N/A s floor floor N/A N/A s N/A N/A s ceil ceil N/A s N/A N/A N/A self spl spl N/A N/A self spld spl_derivative N/A compute_one_gap N/A N/A self a b gappos minsize maxsize verbose N/A False N/A N/A N/A ma mb N/A N/A N/A self scaffold_markers N/A a N/A N/A self scaffold_markers N/A b N/A all_marker_pairs N/A N/A N/A x y N/A product ma mb N/A N/A cm_dist N/A abs N/A N/A x cm N/A y cm N/A N/A ratio N/A N/A self spld N/A gappos N/A converted_dist N/A int N/A round N/A cm_dist ratio N/A overhang_x N/A abs N/A N/A x pos gappos N/A overhang_y N/A N/A abs N/A N/A y pos gappos minsize N/A estimated N/A N/A converted_dist overhang_x overhang_y N/A N/A estimated minsize N/A N/A estimated minsize N/A N/A estimated maxsize N/A N/A estimated maxsize N/A verbose N/A N/A N/A = 10 N/A x N/A y N/A N/A x scaffoldaccn N/A y scaffoldaccn N/A Converted dist: cm_dist ratio converted_dist N/A Overhangs: overhang_x overhang_y N/A Estimated estimated N/A N/A N/A all_marker_pairs append estimated N/A gapsize N/A all_marker_pairs N/A min all_marker_pairs None N/A verbose N/A N/A N/A * 5 a b gapsize N/A gapsize N/A compute_all_gaps N/A N/A self minsize maxsize verbose N/A 100 500000 False N/A N/A N/A self gapsizes N/A N/A N/A N/A a b gappos N/A zip N/A pairwise N/A self scaffolds N/A self pp N/A N/A gapsize N/A N/A self compute_one_gap a b gappos minsize maxsize verbose verbose N/A N/A N/A N/A self gapsizes append gapsize N/A N/A colinear_evaluate_multi N/A N/A tour scfs weights N/A N/A N/A weighted_score 0 N/A N/A scf w N/A zip scfs weights N/A N/A subtour N/A x N/A x tour N/A x scf N/A series N/A N/A t subtour N/A N/A N/A N/A series extend N/A scf N/A t N/A N/A score diff N/A lms series N/A weighted_score N/A score w N/A N/A weighted_score N/A get_rho N/A N/A xy N/A N/A N/A N/A xy N/A N/A 0 N/A N/A x y N/A zip xy N/A rho N/A spearmanr x y N/A N/A N/A np isnan rho N/A N/A rho 0 N/A rho N/A linkage_distance N/A N/A a b linkage N/A min N/A N/A N/A linkage N/A N/A abs N/A i j N/A N/A i j N/A product a b N/A double_linkage N/A N/A L N/A N/A N/A N/A N/A len L 1 N/A N/A N/A L N/A 0 N/A N/A N/A L sort N/A N/A a b N/A L N/A 2 N/A N/A N/A a b 2.0 N/A main N/A N/A N/A N/A N/A actions N/A N/A animation visualize history of scaffold OO N/A merge merge csv maps and convert to bed format N/A mergebed merge maps in bed format N/A path construct golden path given a set of genetic maps N/A estimategaps estimate sizes of inter-scaffold gaps N/A build build associated FASTA and CHAIN file N/A split split suspicious scaffolds N/A summary report summary stats for maps and final consensus N/A plot plot matches between goldenpath and maps for single object N/A plotall plot matches between goldenpath and maps for all objects N/A p N/A ActionDispatcher actions N/A N/A N/A p dispatch N/A globals N/A compute_score N/A N/A markers bonus penalty N/A N/A N/A 
    Compute chain score using dynamic programming. If a marker is the same
    linkage group as a previous one, we add bonus; otherwise, we penalize the
    chain switching.
     N/A nmarkers N/A len markers N/A s N/A N/A bonus nmarkers N/A f N/A N/A -1 nmarkers N/A i N/A xrange 1 nmarkers N/A N/A j N/A xrange i N/A N/A N/A mi mj N/A N/A markers N/A i N/A markers N/A j N/A t N/A N/A N/A mi mlg N/A mj mlg bonus N/A penalty bonus N/A N/A N/A s N/A i N/A N/A s N/A j t N/A N/A N/A s N/A i N/A N/A s N/A j t N/A N/A f N/A i j N/A highest_score N/A max s N/A si N/A N/A s index highest_score N/A onchain N/A set N/A True N/A N/A N/A si 0 N/A N/A N/A si N/A f N/A si N/A N/A N/A onchain add si N/A N/A x N/A N/A i x N/A enumerate markers N/A i onchain N/A split N/A N/A args N/A N/A N/A 
    %prog split input.bed

    Split suspicious scaffolds. Suspicious scaffolds are those that contain
    chunks that map to more than one linkage group. The chunk size can be
    modified through --chunk option.
     N/A p N/A OptionParser N/A split __doc__ N/A N/A N/A p add_option --chunk default 4 type int help Split chunks of at least N markers N/A N/A N/A p add_option --splitsingle default False action store_true help Split breakpoint range right in the middle N/A N/A opts args N/A N/A p parse_args args N/A N/A N/A len args 1 N/A N/A N/A N/A sys exit N/A N/A N/A p print_help N/A N/A inputbed args N/A bonus 2 N/A nchunk N/A opts chunk N/A nbreaks 0 N/A penalty N/A N/A N/A nchunk bonus 1 N/A bed N/A Bed inputbed N/A N/A seqid bb N/A N/A bed sub_beds N/A N/A markers N/A N/A Marker x N/A x bb N/A markers N/A compute_score markers bonus penalty N/A N/A mi mj N/A pairwise markers N/A N/A N/A N/A mi mlg N/A mj mlg N/A N/A N/A N/A N/A mi seqid N/A mj seqid N/A N/A start end N/A N/A mi pos N/A mj pos N/A N/A start end N/A N/A N/A start end N/A end start N/A N/A opts splitsingle N/A N/A start end N/A N/A start end 2 N/A N/A N/A join N/A N/A str x N/A x N/A N/A mi seqid N/A start 1 end N/A nbreaks 1 N/A N/A N/A logging debug N/A N/A A total of {} breakpoints inferred (--chunk={}) format nbreaks nchunk N/A animation N/A N/A args N/A N/A N/A 
    %prog animation input.bed scaffolds.fasta chr1

    Visualize history of scaffold OO. The history is contained within the
    tourfile, generated by path(). For each historical scaffold OO, the program
    plots a separate PDF file. The plots can be combined to show the progression
    as a little animation. The third argument limits the plotting to a
    specific pseudomolecule, for example `chr1`.
     N/A p N/A OptionParser N/A animation __doc__ N/A N/A N/A p add_option --gapsize default 100 type int help Insert gaps of size between scaffolds N/A N/A add_allmaps_plot_options p N/A N/A opts args N/A N/A p parse_args args N/A N/A N/A len args 3 N/A N/A N/A N/A sys exit N/A N/A N/A p print_help N/A N/A inputbed scaffoldsfasta seqid args N/A gapsize N/A opts gapsize N/A pf N/A N/A N/A inputbed rsplit . 1 N/A 0 N/A agpfile N/A pf .chr.agp N/A tourfile N/A pf .tour N/A fp N/A open tourfile N/A sizes N/A N/A Sizes scaffoldsfasta mapping N/A ffmpeg ffmpeg N/A N/A mkdir ffmpeg N/A score cur_score None N/A i 1 N/A N/A header block N/A read_block fp > N/A N/A N/A s tag label N/A N/A N/A header N/A 1 split N/A N/A s seqid N/A N/A N/A tour N/A N/A N/A block N/A 0 split N/A tour N/A N/A N/A x N/A -1 N/A x N/A -1 N/A x tour N/A N/A N/A label startswith GA N/A N/A cur_score N/A N/A N/A label split - N/A -1 N/A N/A cur_score score N/A N/A i 1 N/A N/A score cur_score N/A image_name N/A N/A . join N/A seqid N/A N/A {0:04d} format i label pdf N/A N/A need_update tourfile image_name N/A N/A fwagp N/A must_open agpfile w N/A N/A order_to_agp seqid tour sizes fwagp gapsize gapsize gaptype map N/A N/A N/A fwagp close N/A N/A N/A logging debug N/A N/A {0} written to `{1}` format header agpfile N/A N/A build N/A inputbed scaffoldsfasta --cleanup N/A pdf_name N/A plot N/A inputbed seqid N/A N/A --title={0} format label N/A N/A sh N/A N/A mv {0} {1} format pdf_name image_name N/A N/A label N/A INIT FLIP TSP FINAL N/A N/A j N/A xrange 5 N/A N/A image_delay N/A N/A N/A N/A image_name rsplit . 1 N/A 0 N/A N/A .d{0}.pdf format j N/A N/A sh N/A N/A cp {0} {1}/{2} format image_name ffmpeg image_delay N/A N/A N/A sh N/A N/A cp {0} {1}/ format image_name ffmpeg N/A i 1 N/A N/A N/A os chdir ffmpeg N/A cmd parallel convert -density 300 {} {.}.png ::: *.pdf N/A N/A sh cmd N/A cmd N/A N/A ffmpeg -framerate 1 -pattern_type glob -i '*.png' {0}.mp4 format pf N/A N/A sh cmd N/A estimategaps N/A N/A args N/A N/A N/A 
    %prog estimategaps input.bed

    Estimate sizes of inter-scaffold gaps. The AGP file generated by path()
    command has unknown gap sizes with a generic number of Ns (often 100 Ns).
    The AGP file `input.chr.agp` will be modified in-place.
     N/A p N/A OptionParser N/A estimategaps __doc__ N/A N/A N/A p add_option --minsize default 100 type int help Minimum gap size N/A N/A N/A p add_option --maxsize default 500000 type int help Maximum gap size N/A N/A N/A p add_option --links default 10 type int help Only use linkage grounds with matchings more than N/A N/A N/A p set_verbose help Print details for each gap calculation N/A N/A opts args N/A N/A p parse_args args N/A N/A N/A len args 1 N/A N/A N/A N/A sys exit N/A N/A N/A p print_help N/A N/A inputbed args N/A pf N/A N/A N/A inputbed rsplit . 1 N/A 0 N/A agpfile N/A pf .chr.agp N/A bedfile N/A pf .lifted.bed N/A cc N/A Map bedfile scaffold_info True N/A agp N/A AGP agpfile N/A N/A minsize maxsize N/A N/A opts minsize N/A opts maxsize N/A links N/A opts links N/A verbose N/A opts verbose N/A outagpfile N/A pf .estimategaps.agp N/A fw N/A must_open outagpfile w N/A N/A ob components N/A N/A agp iter_object N/A N/A components N/A list components N/A s N/A Scaffold ob cc N/A mlg_counts N/A s mlg_counts N/A gaps N/A x N/A x components N/A x is_gap N/A gapsizes N/A N/A None N/A len gaps N/A N/A mlg count N/A N/A mlg_counts items N/A N/A N/A count links N/A N/A N/A g N/A GapEstimator cc agp ob mlg N/A N/A N/A g compute_all_gaps minsize minsize maxsize maxsize verbose verbose N/A N/A N/A len N/A g gapsizes N/A len gaps N/A N/A i gs N/A enumerate gapsizes N/A N/A gg N/A N/A g gapsizes N/A i N/A N/A gs None N/A N/A N/A gapsizes N/A i gg N/A N/A gg N/A N/A N/A gapsizes N/A i N/A min gs gg N/A gapsizes N/A i 0 N/A x components N/A N/A N/A x is_gap N/A N/A N/A x gap_length N/A N/A gapsizes N/A i minsize N/A N/A x component_type N/A N/A N/A x gap_length 100 U N N/A i 1 N/A fw x N/A N/A N/A fw close N/A N/A reindex N/A outagpfile --inplace N/A filename_to_mapname N/A N/A filename N/A N/A N/A mapname N/A N/A N/A N/A N/A op basename filename split . N/A 0 N/A N/A N/A N/A N/A mapname replace - _ replace : _ N/A merge N/A N/A args N/A N/A N/A 
    %prog merge map1 map2 map3 ...

    Convert csv maps to bed format.

    Each input map is csv formatted, for example:

    ScaffoldID,ScaffoldPosition,LinkageGroup,GeneticPosition
    scaffold_2707,11508,1,0
    scaffold_2707,11525,1,1.2
    scaffold_759,81336,1,9.7
     N/A p N/A OptionParser N/A merge __doc__ N/A N/A N/A p add_option -w --weightsfile default weights.txt help Write weights to file N/A N/A N/A p set_outfile out.bed N/A N/A opts args N/A N/A p parse_args args N/A N/A N/A len args 1 N/A N/A N/A N/A sys exit N/A N/A N/A p print_help N/A maps args N/A outfile N/A opts outfile N/A fp N/A must_open maps N/A b N/A Bed N/A mapnames N/A set N/A row fp N/A N/A mapname N/A filename_to_mapname N/A N/A fp filename N/A N/A N/A mapnames add mapname N/A N/A N/A m N/A CSVMapLine row mapname mapname N/A N/A N/A m cm 0 N/A N/A N/A N/A logging error Ignore marker with negative genetic distance N/A N/A sys stderr N/A N/A row strip N/A N/A N/A N/A b append N/A BedLine N/A m bedline N/A N/A N/A N/A IndexError ValueError N/A N/A N/A N/A N/A b print_to_file filename outfile sorted True N/A N/A N/A logging debug N/A N/A A total of {0} markers written to `{1}`. format N/A len b outfile N/A N/A N/A len maps N/A len mapnames You have a collision in map names N/A N/A write_weightsfile mapnames weightsfile N/A opts weightsfile N/A mergebed N/A N/A args N/A N/A N/A 
    %prog mergebed map1.bed map2.bed map3.bed ...

    Combine bed maps to bed format, adding the map name.
     N/A p N/A OptionParser N/A mergebed __doc__ N/A N/A N/A p add_option -w --weightsfile default weights.txt help Write weights to file N/A N/A N/A p set_outfile out.bed N/A N/A opts args N/A N/A p parse_args args N/A N/A N/A len args 1 N/A N/A N/A N/A sys exit N/A N/A N/A p print_help N/A maps args N/A outfile N/A opts outfile N/A fp N/A must_open maps N/A b N/A Bed N/A mapnames N/A set N/A row fp N/A N/A mapname N/A filename_to_mapname N/A N/A fp filename N/A N/A N/A mapnames add mapname N/A N/A N/A m N/A BedLine row N/A N/A m accn N/A N/A {0}-{1} format mapname N/A m accn N/A N/A m extra N/A N/A N/A {0}:{1} format N/A m seqid N/A m start N/A N/A N/A b append m N/A N/A N/A N/A IndexError ValueError N/A N/A N/A N/A N/A b print_to_file filename outfile sorted True N/A N/A N/A logging debug N/A N/A A total of {0} markers written to `{1}`. format N/A len b outfile N/A N/A N/A len maps N/A len mapnames You have a collision in map names N/A N/A write_weightsfile mapnames weightsfile N/A opts weightsfile N/A write_weightsfile N/A N/A mapnames weightsfile N/A weights.txt N/A N/A N/A N/A op exists weightsfile N/A N/A N/A N/A logging debug N/A N/A Weights file `{0}` found. Will not overwrite. format weightsfile N/A N/A fw N/A open weightsfile w N/A mapname N/A sorted mapnames N/A N/A weight 1 N/A fw mapname weight N/A N/A N/A logging debug N/A N/A Weights file written to `{0}`. format weightsfile N/A best_no_ambiguous N/A N/A d label N/A N/A N/A N/A best best_value N/A max N/A N/A d items key N/A N/A N/A x N/A N/A x N/A 1 N/A N/A N/A N/A N/A N/A d values count best_value 1 N/A N/A N/A sys stderr AMBIGUOUS label d N/A N/A None None N/A N/A best best_value N/A get_function N/A N/A field N/A N/A N/A N/A field distance_choices N/A N/A N/A field cM N/A N/A N/A x N/A N/A x cm N/A N/A N/A x N/A N/A x rank N/A print_tour N/A N/A fw object tag label tour recode N/A False N/A N/A recode N/A N/A tour N/A recode_tour tour N/A fw N/A N/A fw N/A N/A >{0} ({1}) {2} format object tag label N/A fw N/A N/A join N/A N/A N/A join x N/A x tour N/A recode_tour N/A N/A tour N/A N/A N/A recode N/A 0 1 -1 ? + - N/A N/A N/A x N/A recode N/A o N/A N/A x o tour N/A path N/A N/A args N/A N/A N/A 
    %prog path input.bed scaffolds.fasta

    Construct golden path given a set of genetic maps. The respective weight for
    each map is given in file `weights.txt`. The map with the highest weight is
    considered the pivot map. The final output is an AGP file that contains
    ordered scaffolds.
     N/A oargs args N/A p N/A OptionParser N/A path __doc__ N/A N/A N/A p add_option -b --bedfile help SUPPRESS_HELP N/A N/A N/A p add_option -s --fastafile help SUPPRESS_HELP N/A N/A N/A p add_option -w --weightsfile default weights.txt help Use weights from file N/A N/A N/A p add_option --compress default 1e-06 type float help Compress markers with distance <= N/A N/A N/A p add_option --noremoveoutliers default False action store_true help Don't remove outlier markers N/A N/A N/A p add_option --distance default rank choices distance_choices help Distance function when building initial consensus N/A N/A N/A p add_option --linkage default double choices linkage_choices help Linkage function when building initial consensus N/A N/A N/A p add_option --gapsize default 100 type int help Insert gaps of size between scaffolds N/A N/A N/A p add_option --seqid help Only run partition with this seqid N/A N/A N/A p add_option --partitions help Use predefined partitions of LGs N/A N/A N/A p add_option --links default 10 type int help Only plot matchings more than N/A N/A N/A p add_option --mincount default 1 type int help Minimum markers on a contig N/A N/A N/A p add_option --noplot default False action store_true help Do not visualize the alignments N/A N/A N/A p add_option --skipconcorde default False action store_true help Skip TSP optimizer, can speed up large cases N/A N/A N/A p add_option --renumber default False action store_true help Renumber chromosome based on decreasing sizes N/A N/A N/A p set_cpus cpus 16 N/A q N/A OptionGroup p Genetic algorithm options N/A N/A N/A p add_option_group q N/A N/A N/A q add_option --ngen default 500 type int help Iterations in GA, higher ~ slower N/A N/A N/A q add_option --npop default 100 type int help Population size in GA, higher ~ slower N/A N/A N/A q add_option --seed default 666 type int help Random seed number N/A N/A opts args iopts N/A N/A p set_image_options args figsize 10x6 N/A N/A N/A len args 2 N/A N/A N/A N/A sys exit N/A N/A N/A p print_help N/A N/A inputbed fastafile args N/A inputbed N/A N/A opts bedfile inputbed N/A fastafile N/A N/A opts fastafile fastafile N/A pf N/A N/A N/A inputbed rsplit . 1 N/A 0 N/A bedfile N/A pf .bed N/A weightsfile N/A opts weightsfile N/A partitionsfile N/A opts partitions N/A gapsize N/A opts gapsize N/A mincount N/A opts mincount N/A skipconcorde N/A opts skipconcorde N/A ngen N/A opts ngen N/A npop N/A opts npop N/A cpus N/A opts cpus N/A seed N/A opts seed N/A N/A N/A N/A sys version_info N/A 2 N/A 2 7 N/A N/A N/A N/A logging debug N/A N/A Python version: {0}. CPUs set to 1. format N/A N/A N/A N/A N/A N/A sys version splitlines N/A 0 strip N/A cpus 1 N/A function N/A get_function N/A opts distance N/A cc N/A Map bedfile function function compress N/A opts compress remove_outliers N/A N/A opts noremoveoutliers N/A mapnames N/A cc mapnames N/A allseqids N/A cc seqids N/A weights N/A Weights weightsfile mapnames N/A pivot N/A weights pivot N/A ref N/A weights ref N/A linkage N/A opts linkage N/A oseqid N/A opts seqid N/A N/A N/A logging debug N/A N/A Linkage function: {0}-linkage format linkage N/A linkage N/A N/A single double complete average median min double_linkage max N/A np mean N/A np median N/A linkage N/A C N/A Grouper N/A mlg N/A cc mlgs N/A N/A N/A N/A C join mlg N/A partitionsfile N/A N/A N/A N/A logging debug N/A N/A Partition LGs based on `{}` format partitionsfile N/A fp N/A open partitionsfile N/A row fp N/A N/A N/A N/A C join N/A N/A N/A N/A row strip split , N/A N/A N/A N/A logging debug N/A N/A Partition LGs based on {0} format ref N/A mapname mapnames N/A N/A N/A mapname ref N/A N/A N/A G N/A defaultdict int N/A s allseqids N/A N/A s N/A Scaffold s cc N/A N/A N/A s add_LG_pairs G N/A ref mapname N/A nodes N/A defaultdict list N/A N/A N/A a b w N/A N/A G items N/A N/A N/A N/A N/A nodes N/A a append N/A b w N/A N/A n neighbors N/A N/A nodes items N/A N/A N/A N/A N/A N/A n split - N/A 0 ref N/A N/A N/A neighbors N/A dict neighbors N/A N/A best_neighbor best_value N/A best_no_ambiguous neighbors n N/A N/A best_neighbor None N/A N/A N/A N/A N/A C join n best_neighbor N/A partitions N/A defaultdict list N/A s allseqids N/A N/A s N/A Scaffold s cc N/A seqid N/A s seqid N/A counts N/A N/A N/A mlg count N/A N/A N/A s mlg_counts items N/A N/A consensus N/A C N/A mlg N/A mapname N/A N/A N/A mlg split - N/A 0 N/A mw N/A weights N/A mapname N/A N/A consensus counts N/A N/A N/A counts N/A consensus 0 N/A N/A count mincount N/A N/A N/A N/A counts N/A consensus N/A count mw N/A N/A best_consensus best_value N/A best_no_ambiguous counts seqid N/A N/A best_consensus None N/A N/A N/A N/A N/A N/A partitions N/A best_consensus append seqid N/A agpfile N/A pf .chr.agp N/A tourfile N/A pf .tour N/A sizes N/A N/A Sizes fastafile mapping N/A fwagp N/A must_open agpfile w N/A fwtour N/A must_open tourfile w N/A solutions N/A N/A N/A lgs scaffolds N/A natsorted N/A N/A partitions items N/A N/A N/A oseqid N/A oseqid lgs N/A N/A N/A tag N/A N/A | join lgs N/A lgs_maps N/A set N/A N/A N/A N/A x split - N/A 0 N/A x lgs N/A N/A pivot lgs_maps N/A N/A N/A N/A logging debug N/A N/A Skipping {0} ... format tag N/A N/A N/A N/A logging debug N/A N/A Working on {0} ... format tag N/A s N/A ScaffoldOO lgs scaffolds cc pivot weights sizes function function linkage linkage fwtour fwtour skipconcorde skipconcorde ngen ngen npop npop cpus cpus seed seed N/A N/A N/A solutions append s N/A N/A N/A fwtour close N/A N/A opts renumber N/A N/A chrsizes N/A N/A conversion N/A N/A s solutions N/A N/A N/A chrsizes N/A N/A s object N/A N/A sum N/A N/A sizes N/A x N/A N/A x o N/A s tour N/A N/A N/A len N/A s tour 1 gapsize N/A N/A i N/A c size N/A enumerate N/A sorted N/A N/A chrsizes items key N/A N/A N/A x N/A N/A N/A x N/A 1 N/A N/A newc N/A N/A chr{0} format N/A i 1 N/A N/A N/A logging debug N/A N/A {0}: {1} => {2} format c size newc N/A N/A conversion N/A c newc N/A s solutions N/A N/A N/A s object N/A conversion N/A N/A s object N/A command N/A N/A # COMMAND: python -m jcvi.assembly.allmaps path {0} format N/A N/A join oargs N/A comment N/A N/A Generated by ALLMAPS v{0} ({1})
{2} format version N/A get_today command N/A N/A N/A AGP print_header fwagp comment comment N/A s N/A natsorted solutions key N/A N/A N/A x N/A N/A x object N/A N/A N/A order_to_agp N/A s object N/A s tour sizes fwagp gapsize gapsize gaptype map N/A N/A N/A fwagp close N/A N/A N/A logging debug N/A N/A AGP file written to `{0}`. format agpfile N/A N/A N/A logging debug N/A N/A Tour file written to `{0}`. format tourfile N/A N/A build N/A inputbed fastafile N/A summaryfile N/A pf .summary.txt N/A N/A summary N/A inputbed fastafile N/A N/A --outfile={0} format summaryfile N/A N/A N/A opts noplot N/A N/A N/A plotall N/A inputbed N/A N/A --links={0} format N/A opts links N/A N/A --figsize={0} format N/A opts figsize N/A write_unplaced_agp N/A N/A agpfile scaffolds unplaced_agp N/A N/A N/A agp N/A AGP agpfile N/A scaffolds_seen N/A set N/A N/A x component_id N/A x agp N/A sizes N/A N/A Sizes scaffolds mapping N/A fwagp N/A must_open unplaced_agp w N/A s N/A natsorted N/A N/A sizes keys N/A N/A N/A s scaffolds_seen N/A N/A N/A N/A order_to_agp s N/A N/A s ? sizes fwagp N/A N/A N/A logging debug N/A N/A Write unplaced AGP to `{0}`. format unplaced_agp N/A summary N/A N/A args N/A N/A N/A 
    %prog summary input.bed scaffolds.fasta

    Print out summary statistics per map, followed by consensus summary of
    scaffold anchoring based on multiple maps.
     N/A p N/A OptionParser N/A summary __doc__ N/A N/A N/A p set_table sep | align True N/A N/A N/A p set_outfile N/A N/A opts args N/A N/A p parse_args args N/A N/A N/A len args 2 N/A N/A N/A N/A sys exit N/A N/A N/A p print_help N/A N/A inputbed scaffolds args N/A pf N/A N/A N/A inputbed rsplit . 1 N/A 0 N/A mapbed N/A pf .bed N/A chr_agp N/A pf .chr.agp N/A sep N/A opts sep N/A align N/A opts align N/A cc N/A Map mapbed N/A mapnames N/A cc mapnames N/A s N/A Sizes scaffolds N/A N/A total l50 n50 N/A s summary N/A r N/A N/A maps N/A N/A fw N/A must_open N/A opts outfile w N/A fw *** Summary for each individual map *** N/A mapname mapnames N/A N/A markers N/A x N/A x cc N/A N/A x mapname mapname N/A ms N/A MapSummary markers l50 s N/A N/A r N/A N/A Linkage Groups mapname N/A ms num_lgs N/A N/A N/A ms export_table r mapname total N/A N/A N/A maps append ms N/A fw N/A tabulate r sep sep align align N/A r N/A N/A agp N/A AGP chr_agp N/A fw *** Summary for consensus map *** N/A consensus_scaffolds N/A set N/A N/A x component_id N/A x agp N/A N/A x is_gap N/A oriented_scaffolds N/A set N/A N/A x component_id N/A x agp N/A N/A N/A x is_gap N/A N/A x orientation ? N/A unplaced_scaffolds N/A N/A set N/A N/A N/A s mapping keys consensus_scaffolds N/A N/A mapname sc N/A N/A Anchored consensus_scaffolds N/A Oriented oriented_scaffolds N/A Unplaced unplaced_scaffolds N/A N/A markers N/A x N/A x cc N/A N/A x seqid sc N/A ms N/A MapSummary markers l50 s scaffolds sc N/A N/A N/A ms export_table r mapname total N/A fw N/A tabulate r sep sep align align N/A build N/A N/A args N/A N/A N/A 
    %prog build input.bed scaffolds.fasta

    Build associated genome FASTA file and CHAIN file that can be used to lift
    old coordinates to new coordinates. The CHAIN file will be used to lift the
    original marker positions to new positions in the reconstructed genome. The
    new positions of the markers will be reported in *.lifted.bed.
     N/A p N/A OptionParser N/A build __doc__ N/A N/A N/A p add_option --cleanup default False action store_true help Clean up bulky FASTA files, useful for plotting N/A N/A opts args N/A N/A p parse_args args N/A N/A N/A len args 2 N/A N/A N/A N/A sys exit N/A N/A N/A p print_help N/A N/A inputbed scaffolds args N/A pf N/A N/A N/A inputbed rsplit . 1 N/A 0 N/A mapbed N/A pf .bed N/A chr_agp N/A pf .chr.agp N/A chr_fasta N/A pf .chr.fasta N/A N/A need_update N/A chr_agp scaffolds chr_fasta N/A N/A N/A agp_build N/A chr_agp scaffolds chr_fasta N/A unplaced_agp N/A pf .unplaced.agp N/A N/A need_update N/A chr_agp scaffolds unplaced_agp N/A N/A N/A write_unplaced_agp chr_agp scaffolds unplaced_agp N/A unplaced_fasta N/A pf .unplaced.fasta N/A N/A need_update N/A unplaced_agp scaffolds unplaced_fasta N/A N/A N/A agp_build N/A unplaced_agp scaffolds unplaced_fasta N/A combined_agp N/A pf .agp N/A N/A need_update N/A chr_agp unplaced_agp combined_agp N/A N/A N/A N/A N/A FileMerger N/A chr_agp unplaced_agp combined_agp merge N/A combined_fasta N/A pf .fasta N/A N/A need_update N/A chr_fasta unplaced_fasta combined_fasta N/A N/A N/A N/A N/A FileMerger N/A chr_fasta unplaced_fasta combined_fasta merge N/A chainfile N/A pf .chain N/A N/A need_update N/A combined_agp scaffolds combined_fasta chainfile N/A N/A N/A fromagp N/A combined_agp scaffolds combined_fasta N/A liftedbed N/A N/A N/A N/A mapbed rsplit . 1 N/A 0 .lifted.bed N/A N/A need_update N/A mapbed chainfile liftedbed N/A N/A cmd N/A N/A liftOver -minMatch=1 {0} {1} {2} unmapped format mapbed chainfile liftedbed N/A N/A sh cmd N/A N/A opts cleanup N/A N/A N/A FileShredder N/A chr_fasta unplaced_fasta combined_fasta chainfile unplaced_agp N/A combined_fasta .sizes unmapped N/A N/A sort N/A liftedbed -i N/A add_allmaps_plot_options N/A N/A p N/A N/A N/A N/A N/A p add_option -w --weightsfile default weights.txt help Use weights from file N/A N/A N/A p add_option --distance default cM choices distance_choices help Plot markers based on distance N/A N/A N/A p add_option --links default 10 type int help Only plot matchings more than N/A N/A N/A p add_option --panels default False action store_true help Add panel labels A/B N/A plot N/A N/A args N/A N/A N/A 
    %prog plot input.bed seqid

    Plot the matchings between the reconstructed pseudomolecules and the maps.
    Two types of visualizations are available in one canvas:

    1. Parallel axes, and matching markers are shown in connecting lines;
    2. Scatter plot.
     jcvi.graphics.base plt savefig normalize_axes set2 panel_labels shorten jcvi.graphics.chromosome Chromosome GeneticMap HorizontalChromosome N/A p N/A OptionParser N/A plot __doc__ N/A N/A N/A p add_option --title help Title of the plot N/A N/A add_allmaps_plot_options p N/A N/A opts args iopts N/A N/A p set_image_options args figsize 10x6 N/A N/A N/A len args 2 N/A N/A N/A N/A sys exit N/A N/A N/A p print_help N/A N/A inputbed seqid args N/A pf N/A N/A N/A inputbed rsplit . 1 N/A 0 N/A bedfile N/A pf .lifted.bed N/A agpfile N/A pf .agp N/A weightsfile N/A opts weightsfile N/A links N/A opts links N/A function N/A get_function N/A opts distance N/A cc N/A Map bedfile function function N/A allseqids N/A cc seqids N/A mapnames N/A cc mapnames N/A weights N/A Weights weightsfile mapnames N/A N/A seqid allseqids N/A N/A {0} not in {1} format seqid allseqids N/A s N/A Scaffold seqid cc N/A mlgs N/A k N/A N/A k v N/A N/A N/A s mlg_counts items N/A v links N/A N/A mlgs N/A N/A links 2 N/A N/A N/A logging error N/A N/A No markers to plot, --links reset to {0} format links N/A mlgs N/A k N/A N/A k v N/A N/A N/A s mlg_counts items N/A v links N/A mlgsizes N/A N/A mlg mlgs N/A N/A mm N/A N/A cc extract_mlg mlg N/A mlgsize N/A max N/A N/A function x N/A x mm N/A N/A mlgsizes N/A mlg mlgsize N/A fig N/A N/A plt figure 1 N/A N/A iopts w N/A iopts h N/A root N/A N/A fig add_axes N/A 0 0 1 1 N/A bbox N/A dict boxstyle round fc darkslategray ec darkslategray N/A N/A opts title N/A N/A N/A N/A root text 0.5 0.95 N/A opts title color w bbox bbox size 16 N/A ax1 N/A N/A fig add_axes N/A 0 0 0.5 1 N/A ax2 N/A N/A fig add_axes N/A 0.5 0 0.5 1 N/A N/A ystart ystop N/A 0.9 0.1 N/A L N/A Layout mlgsizes N/A coords N/A L coords N/A tip 0.02 N/A marker_pos N/A N/A colors N/A dict N/A N/A mapname N/A set2 N/A i N/A N/A i mapname N/A enumerate mapnames N/A colors N/A dict N/A N/A mlg N/A colors N/A N/A N/A N/A mlg split - N/A 0 N/A mlg mlgs N/A rhos N/A N/A N/A mlg N/A x y1 y2 N/A N/A coords items N/A N/A mm N/A N/A cc extract_mlg mlg N/A markers N/A N/A N/A m accn N/A function m N/A m mm N/A xy N/A N/A N/A m pos N/A function m N/A m mm N/A N/A m seqid seqid N/A N/A mx my N/A zip xy N/A rho N/A spearmanr mx my N/A N/A rhos N/A mlg rho N/A flip N/A rho 0 N/A g N/A GeneticMap ax1 x y1 y2 markers tip tip flip flip N/A extra N/A N/A x 0.5 N/A -3 tip N/A 3 tip N/A ha N/A N/A x 0.5 right left N/A mapname N/A N/A N/A mlg split - N/A 0 N/A tlg N/A shorten N/A N/A mlg replace _ . N/A label N/A N/A {0} (w={1}) format tlg N/A weights N/A mapname N/A N/A N/A ax1 text N/A x extra N/A N/A y1 y2 2 label color N/A colors N/A mlg ha ha va center rotation 90 N/A N/A N/A marker_pos update N/A g marker_pos N/A agp N/A AGP agpfile N/A agp N/A x N/A x agp N/A N/A x object seqid N/A chrsize N/A max N/A N/A x object_end N/A x agp N/A r N/A ystart ystop N/A ratio N/A r chrsize N/A f N/A N/A N/A x N/A N/A ystart N/A ratio x N/A patchstart N/A N/A f N/A x object_beg N/A x agp N/A N/A x is_gap N/A N/A Chromosome ax1 0.5 ystart ystop width N/A 2 tip patch patchstart lw 2 N/A label N/A N/A {0} ({1}) format seqid N/A human_size chrsize precision 0 N/A N/A N/A ax1 text 0.5 N/A ystart tip label ha center N/A scatter_data N/A defaultdict list N/A b N/A s markers N/A N/A marker_name N/A b accn N/A N/A marker_name marker_pos N/A N/A N/A cx 0.5 N/A cy N/A f N/A b pos N/A mx N/A N/A coords N/A N/A b mlg N/A 0 N/A my N/A marker_pos N/A marker_name N/A extra N/A N/A mx cx N/A tip tip N/A extra 1.25 N/A cx extra N/A mx extra N/A N/A N/A ax1 plot N/A cx mx N/A cy my - color N/A colors N/A N/A b mlg N/A N/A N/A N/A scatter_data N/A N/A b mlg append N/A N/A b pos N/A function b N/A N/A xstart xstop N/A sorted N/A ystart ystop N/A f N/A N/A N/A x N/A N/A xstart N/A ratio x N/A pp N/A N/A x object_beg N/A x agp N/A N/A x is_gap N/A patchstart N/A N/A f x N/A x pp N/A N/A HorizontalChromosome ax2 xstart xstop ystop height N/A 2 tip patch patchstart lw 2 N/A N/A draw_gauge ax2 xstart chrsize N/A gap 0.03 N/A ratio N/A N/A N/A r N/A gap N/A len mlgs tip N/A sum N/A N/A mlgsizes values N/A tlgs N/A N/A N/A mlg mlgsize N/A sorted N/A N/A mlgsizes items N/A N/A height N/A ratio mlgsize N/A ystart height N/A xx N/A 0.5 N/A xstart 2 N/A width N/A r 2 N/A color N/A colors N/A mlg N/A ax N/A N/A fig add_axes N/A xx ystart width height N/A ypos N/A ystart N/A height 2 N/A ystart gap N/A sd N/A scatter_data N/A mlg N/A N/A xx yy N/A zip sd N/A N/A N/A ax vlines pp 0 N/A 2 mlgsize colors beige N/A N/A N/A ax plot xx yy . color color N/A rho N/A rhos N/A mlg N/A N/A N/A ax text 0.5 N/A 1 N/A N/A 0.4 gap height N/A N/A $\rho$={0:.3f} format rho ha center va top transform N/A ax transAxes color gray N/A tlg N/A shorten N/A N/A mlg replace _ . N/A N/A N/A tlgs append N/A tlg ypos color N/A N/A N/A ax set_xlim 0 chrsize N/A N/A N/A ax set_ylim 0 mlgsize N/A N/A N/A ax set_xticks N/A N/A N/A N/A N/A height N/A len N/A N/A ax get_yticks 0.03 N/A N/A len N/A N/A ax get_yticks 2 N/A N/A N/A N/A ax set_yticks N/A N/A N/A ax get_yticks N/A 2 N/A yticklabels N/A N/A int x N/A x N/A N/A ax get_yticks N/A N/A N/A ax set_yticklabels yticklabels family Helvetica N/A N/A rho 0 N/A N/A N/A N/A ax invert_yaxis N/A N/A i N/A tlg ypos color N/A enumerate tlgs N/A N/A ha center N/A N/A N/A len tlgs 4 N/A N/A ha N/A N/A i 2 right left N/A N/A N/A root text 0.5 ypos tlg color color rotation 90 ha ha va center N/A N/A opts panels N/A N/A labels N/A N/A 0.04 0.96 A N/A 0.48 0.96 B N/A N/A panel_labels root labels N/A N/A normalize_axes N/A ax1 ax2 root N/A image_name N/A N/A seqid . N/A iopts format N/A N/A savefig image_name dpi N/A iopts dpi iopts iopts N/A N/A N/A plt close fig N/A image_name N/A plotall N/A N/A xargs N/A N/A N/A 
    %prog plotall input.bed

    Plot the matchings between the reconstructed pseudomolecules and the maps.
    This command will plot each reconstructed object (non-singleton).
     N/A p N/A OptionParser N/A plotall __doc__ N/A N/A add_allmaps_plot_options p N/A N/A opts args iopts N/A N/A p set_image_options xargs figsize 10x6 N/A N/A N/A len args 1 N/A N/A N/A N/A sys exit N/A N/A N/A p print_help N/A N/A inputbed args N/A pf N/A N/A N/A inputbed rsplit . 1 N/A 0 N/A agpfile N/A pf .agp N/A agp N/A AGP agpfile N/A objects N/A ob N/A N/A ob lines N/A N/A agp iter_object N/A N/A len lines 1 N/A seqid N/A natsorted objects N/A N/A N/A plot N/A xargs N/A seqid N/A N/A N/A __name__ __main__ N/A N/A N/A main