Module Expr Str Import alias Import alias Import alias identifier Import alias Import alias Import alias Import alias Import alias identifier Import alias identifier ImportFrom alias alias ImportFrom alias alias ImportFrom alias ImportFrom alias alias ImportFrom alias ImportFrom alias ImportFrom alias alias ImportFrom alias alias alias alias ImportFrom alias alias alias alias alias Assign NameStore Num Assign NameStore Num Assign NameStore Call AttributeLoad Str attr Assign NameStore Call AttributeLoad Str attr Assign NameStore Call AttributeLoad Str attr Assign NameStore Call AttributeLoad Str attr Assign NameStore Call AttributeLoad Str attr Assign NameStore Call AttributeLoad Str attr ClassDef bases NameLoad body FunctionDef arguments args NameParam NameParam defaults body Assign NameStore Call AttributeLoad NameLoad attr Assign AttributeStore NameLoad attr SubscriptLoad NameLoad Index Num Assign AttributeStore NameLoad attr Call NameLoad SubscriptLoad NameLoad Index Num Assign AttributeStore NameLoad attr Call NameLoad 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 Call NameLoad 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 SubscriptLoad NameLoad Index Num Assign AttributeStore NameLoad attr SubscriptLoad NameLoad Index Num Assign AttributeStore NameLoad attr 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 SubscriptLoad NameLoad Index Num Assert CompareEq AttributeLoad NameLoad attr Call NameLoad AttributeLoad NameLoad attr Assign AttributeStore NameLoad attr IfExp CompareGt Call NameLoad NameLoad Num SubscriptLoad NameLoad Index Num NameLoad decorator_list FunctionDef arguments args NameParam defaults body Assign NameStore ListLoad AttributeLoad NameLoad attr AttributeLoad NameLoad attr AttributeLoad NameLoad attr AttributeLoad NameLoad attr AttributeLoad NameLoad attr AttributeLoad NameLoad attr AttributeLoad NameLoad attr AttributeLoad NameLoad attr AttributeLoad NameLoad attr AttributeLoad NameLoad attr AttributeLoad NameLoad attr AttributeLoad NameLoad attr AttributeLoad NameLoad attr Call AttributeLoad Str attr AttributeLoad NameLoad attr AttributeLoad NameLoad attr If CompareIsNot AttributeLoad NameLoad attr NameLoad body AugAssignAdd NameStore ListLoad AttributeLoad NameLoad attr Return Call AttributeLoad Str attr GeneratorExp Call NameLoad NameLoad comprehension NameStore NameLoad decorator_list FunctionDef arguments args NameParam defaults body Return Call AttributeLoad Str attr GeneratorExp Call NameLoad NameLoad comprehension NameStore TupleLoad AttributeLoad NameLoad attr AttributeLoad NameLoad attr AttributeLoad NameLoad attr decorator_list NameLoad FunctionDef arguments args NameParam NameParam NameParam NameParam defaults Num NameLoad NameLoad body Return BoolOpAnd CompareLtELtE Num AttributeLoad NameLoad attr NameLoad CompareLtE BinOpAdd BinOpSub AttributeLoad NameLoad attr AttributeLoad NameLoad attr Num NameLoad CompareGtE AttributeLoad NameLoad attr NameLoad decorator_list FunctionDef arguments args NameParam defaults body Assign NameStore BinOpAdd BinOpAdd BinOpAdd AttributeLoad NameLoad attr AttributeLoad NameLoad attr AttributeLoad NameLoad attr AttributeLoad NameLoad attr If CompareEq NameLoad Num body Return Num Assign NameStore ListComp BinOpDiv BinOpMult NameLoad Num NameLoad comprehension NameStore ListLoad AttributeLoad NameLoad attr AttributeLoad NameLoad attr AttributeLoad NameLoad attr AttributeLoad NameLoad attr Assign NameStore Call NameLoad ListComp BinOpMult BinOpMult Num NameLoad Call NameLoad NameLoad Num comprehension NameStore NameLoad CompareNotEq NameLoad Num Return NameLoad decorator_list FunctionDef arguments args NameParam NameParam defaults body Assign NameStore Call AttributeLoad NameLoad attr Call AttributeLoad Str attr AttributeLoad NameLoad attr Assign NameStore AttributeLoad NameLoad attr Assign NameStore Call AttributeLoad SubscriptLoad SubscriptLoad NameLoad Index AttributeLoad NameLoad attr Slice BinOpSub AttributeLoad NameLoad attr Num AttributeLoad NameLoad attr attr For NameStore Call AttributeLoad NameLoad attr NameLoad NameLoad body Assign AttributeStore NameLoad attr BinOpAdd NameLoad Call AttributeLoad NameLoad attr Assign NameStore BinOpSub Call AttributeLoad NameLoad attr Call AttributeLoad NameLoad attr Assign NameStore Call AttributeLoad NameLoad attr Num Assert CompareEq BinOpMod NameLoad AttributeLoad NameLoad attr Num Assert Call AttributeLoad NameLoad attr AttributeLoad NameLoad attr Assign AttributeStore NameLoad attr BinOpAdd BinOpSub AttributeLoad NameLoad attr Num NameLoad Assign AttributeStore NameLoad attr BinOpDiv NameLoad AttributeLoad NameLoad attr Assign AttributeStore NameLoad attr Num Assign AttributeStore NameLoad attr Num Assign AttributeStore NameLoad attr BinOpMult Num NameLoad Expr Call AttributeLoad NameLoad attr NameLoad Expr Yield NameLoad decorator_list FunctionDef arguments args NameParam NameParam defaults body Assign NameStore Call NameLoad Call NameLoad BinOpMult AttributeLoad NameLoad attr Call NameLoad AttributeLoad NameLoad attr Assign AttributeStore NameLoad attr Call NameLoad AttributeLoad NameLoad attr BinOpSub BinOpAdd AttributeLoad NameLoad attr NameLoad Num Assign AttributeStore NameLoad attr Call AttributeLoad NameLoad attr Str Assign AttributeStore NameLoad attr Call AttributeLoad NameLoad attr Str Assign AttributeStore NameLoad attr Call AttributeLoad NameLoad attr Str Assign AttributeStore NameLoad attr Call AttributeLoad NameLoad attr Str Assign AttributeStore NameLoad attr Call AttributeLoad NameLoad attr decorator_list decorator_list ClassDef bases NameLoad body FunctionDef arguments args NameParam NameParam NameParam defaults Str body Assign NameStore Call AttributeLoad NameLoad attr NameLoad Call AttributeLoad Str attr NameLoad Expr Call AttributeLoad Call NameLoad NameLoad NameLoad attr NameLoad Assign NameStore Call NameLoad NameLoad For NameStore NameLoad body Expr Call AttributeLoad NameLoad attr Call NameLoad NameLoad decorator_list FunctionDef arguments args NameParam defaults body Return ListComp AttributeLoad NameLoad attr comprehension NameStore NameLoad decorator_list NameLoad FunctionDef arguments args NameParam defaults body Return Call NameLoad GeneratorExp TupleLoad TupleLoad AttributeLoad NameLoad attr AttributeLoad NameLoad attr AttributeLoad NameLoad attr comprehension NameStore NameLoad decorator_list NameLoad decorator_list ClassDef bases NameLoad body FunctionDef arguments args NameParam NameParam defaults Str body Assign AttributeStore NameLoad attr NameLoad Assign NameStore Call NameLoad NameLoad Assign AttributeStore NameLoad attr ListComp Call AttributeLoad NameLoad attr comprehension NameStore NameLoad Assign AttributeStore NameLoad attr Dict Expr Call AttributeLoad NameLoad attr Call AttributeLoad Str attr Call NameLoad AttributeLoad NameLoad attr NameLoad decorator_list FunctionDef arguments args NameParam NameParam NameParam NameParam NameParam defaults NameLoad NameLoad NameLoad body Assign AttributeStore NameLoad attr SubscriptLoad Call AttributeLoad Call AttributeLoad NameLoad attr NameLoad attr Str Index Num Expr Call AttributeLoad NameLoad attr Call AttributeLoad Str attr NameLoad NameLoad NameLoad Assign NameStore Call NameLoad NameLoad Assign NameStore Call AttributeLoad NameLoad attr NameLoad For NameStore NameLoad body If BoolOpAnd NameLoad CompareNotEq AttributeLoad NameLoad attr Str body Continue If BoolOpAnd NameLoad AttributeLoad NameLoad attr body Continue Assign NameStore AttributeLoad NameLoad attr Assign NameStore Call NameLoad SubscriptLoad NameLoad Index Str Assign NameStore Call AttributeLoad NameLoad attr Str NameLoad Assign NameStore SubscriptLoad NameLoad Index Str Assign NameStore Call AttributeLoad Str attr GeneratorExp Call NameLoad NameLoad comprehension NameStore TupleLoad AttributeLoad NameLoad attr AttributeLoad NameLoad attr NameLoad For NameStore AttributeLoad NameLoad attr body If NameLoad body Assign NameStore Call NameLoad SubscriptLoad NameLoad Index Str If CompareLt NameLoad Num body Break Assign NameStore SubscriptLoad NameLoad Index Str Assign NameStore ListLoad For NameStore Call AttributeLoad NameLoad attr Str body Assign TupleStore NameStore NameStore Call AttributeLoad NameLoad attr Str Expr Call AttributeLoad NameLoad attr Call NameLoad NameLoad Assign NameStore Call NameLoad NameLoad Assign NameStore BinOpSub NameLoad NameLoad If CompareGt BinOpDiv BinOpMult NameLoad Num NameLoad Num body Break Assign SubscriptStore AttributeLoad NameLoad attr Index NameLoad Call AttributeLoad Str attr NameLoad NameLoad Break Assign NameStore SubscriptLoad NameLoad Index Str If BoolOpAnd NameLoad CompareNotEq SubscriptLoad NameLoad Index Str Str body Continue If CompareEq NameLoad Str body Assign NameStore TupleLoad NameLoad NameLoad orelse If CompareIn NameLoad TupleLoad Str Str body Assign NameStore TupleLoad NameLoad SubscriptLoad NameLoad Index Num orelse If CompareEq NameLoad Str body Assign NameStore TupleLoad SubscriptLoad NameLoad Index Num SubscriptLoad NameLoad Index Num orelse If CompareEq NameLoad Str body Assign NameStore NameLoad Assign SubscriptStore NameLoad Index NameLoad Call AttributeLoad Str attr GeneratorExp Call NameLoad Call NameLoad NameLoad comprehension NameStore Call NameLoad NameLoad Assign NameStore Call NameLoad NameLoad Assign NameStore ListComp BinOpMult BinOpSub NameLoad NameLoad NameLoad comprehension NameStore NameLoad Assign NameStore NameStore Num Assign NameStore SubscriptLoad NameLoad Index Str For NameStore Call AttributeLoad NameLoad attr Str body Assign TupleStore NameStore NameStore Call AttributeLoad NameLoad attr Str Assign TupleStore NameStore NameStore TupleLoad Call NameLoad NameLoad Call NameLoad NameLoad Assign NameStore Call NameLoad ListComp Call NameLoad BinOpSub NameLoad NameLoad comprehension NameStore NameLoad If CompareLtLt BinOpMult NameLoad Num NameLoad BinOpMult NameLoad Num body AugAssignAdd NameStore NameLoad AugAssignAdd NameStore NameLoad Assign SubscriptStore AttributeLoad NameLoad attr Index NameLoad Call AttributeLoad Str attr NameLoad NameLoad If NameLoad body Expr Call NameLoad Call AttributeLoad Str attr Call AttributeLoad NameLoad attr NameLoad decorator_list FunctionDef arguments args NameParam defaults body Return Call AttributeLoad Str attr ListComp Call AttributeLoad NameLoad attr NameLoad Str comprehension NameStore AttributeLoad NameLoad attr decorator_list NameLoad FunctionDef arguments args NameParam defaults body Return Call AttributeLoad Str attr ListComp Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad Str comprehension NameStore AttributeLoad NameLoad attr decorator_list NameLoad 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 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 defaults body Expr Str Assign NameStore Call NameLoad 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 NameLoad Assign NameStore SubscriptLoad Call AttributeLoad Call AttributeLoad NameLoad attr NameLoad attr Str Index Num Assign TupleStore NameStore NameStore Call AttributeLoad NameLoad attr Str Assign NameStore Str AugAssignAdd NameStore Call AttributeLoad Str attr NameLoad NameLoad AugAssignAdd NameStore Call AttributeLoad Str attr NameLoad Assign NameStore BinOpAdd NameLoad Str If Call NameLoad NameLoad NameLoad body Assign NameStore BinOpAdd NameLoad Str Expr Call NameLoad NameLoad Assign NameStore BinOpAdd NameLoad Str If Call NameLoad NameLoad NameLoad body Assign NameStore BinOpAdd NameLoad Str Expr Call NameLoad NameLoad Assign NameStore BinOpAdd NameLoad Str If Call NameLoad NameLoad NameLoad body Assign NameStore BinOpAdd NameLoad Str Expr Call NameLoad NameLoad Assign NameStore BinOpAdd NameLoad Str If Call NameLoad TupleLoad NameLoad NameLoad NameLoad NameLoad body Assign NameStore Call AttributeLoad Str attr NameLoad AugAssignAdd NameStore Str AugAssignAdd NameStore Call AttributeLoad Str attr NameLoad NameLoad AugAssignAdd NameStore Str Expr Call NameLoad NameLoad keyword NameLoad decorator_list FunctionDef arguments args NameParam NameParam NameParam defaults NameLoad body If Call AttributeLoad NameLoad attr Str body Assign NameStore Call NameLoad NameLoad Assign NameStore Call AttributeLoad Call AttributeLoad NameLoad attr NameLoad attr Str Str Assign NameStore Call AttributeLoad Str attr NameLoad AugAssignAdd NameStore Call AttributeLoad Str attr NameLoad AugAssignAdd NameStore Str Expr Call NameLoad NameLoad keyword NameLoad If NameLoad body Expr Call NameLoad NameLoad NameLoad Return NameLoad decorator_list FunctionDef arguments args NameParam defaults body Assign TupleStore NameStore NameStore NameStore NameLoad Assign NameStore Call AttributeLoad NameLoad attr Str Str TryExcept body If Call AttributeLoad NameLoad attr Str body If Call NameLoad NameLoad body Expr Call AttributeLoad NameLoad attr Call AttributeLoad Str attr NameLoad orelse Expr Call NameLoad NameLoad NameLoad keyword NameLoad Expr Call AttributeLoad NameLoad attr Call AttributeLoad Str attr NameLoad orelse If Call NameLoad NameLoad NameLoad body Expr Call NameLoad NameLoad NameLoad keyword NameLoad handlers ExceptHandler type NameLoad name NameStore body 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 Str keyword Str Expr Call AttributeLoad NameLoad attr keyword Str 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 NameLoad Assign NameStore AttributeLoad NameLoad attr Assign NameStore AttributeLoad NameLoad attr If BoolOpOr Call AttributeLoad NameLoad attr Str Call AttributeLoad NameLoad attr Str body Assign NameStore ListLoad NameLoad orelse Assign NameStore ListComp Call AttributeLoad NameLoad attr comprehension NameStore Call NameLoad NameLoad Assign NameStore ListComp NameLoad comprehension NameStore NameLoad CompareNotIn Str NameLoad Assign NameStore ListComp TupleLoad NameLoad NameLoad BoolOpAnd Call AttributeLoad NameLoad attr Str NameLoad comprehension NameStore NameLoad Assign NameStore Call NameLoad AttributeLoad NameLoad attr Call NameLoad NameLoad Assign NameStore Call NameLoad keyword NameLoad For NameStore Call AttributeLoad Call AttributeLoad NameLoad attr NameLoad NameLoad attr body Continue decorator_list FunctionDef arguments args NameParam defaults body Expr Str Assign NameStore Call NameLoad 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 NameStore NameStore NameLoad Assign TupleStore NameStore NameStore NameStore NameStore Call NameLoad NameLoad NameLoad NameLoad Assign NameStore Call AttributeLoad NameLoad attr NameLoad keyword Num keyword Str For TupleStore NameStore NameStore Call NameLoad NameLoad body Assign NameStore SubscriptLoad NameLoad ExtSlice Slice Index NameLoad Print NameLoad NameLoad Assign NameStore Call NameLoad NameLoad Assign NameStore Call NameLoad SubscriptLoad SubscriptLoad AttributeLoad NameLoad attr Index NameLoad Index Str Print Str NameLoad Expr Call AttributeLoad NameLoad attr NameLoad Assign NameStore Call NameLoad NameLoad Print Str NameLoad If CompareGt NameLoad Num body Return decorator_list FunctionDef arguments args NameParam defaults body Assign NameStore Call NameLoad Assign NameStore BinOpDiv NameLoad Num Assign NameStore BinOpMod NameLoad Num Expr Call AttributeLoad NameLoad attr NameLoad Expr Call AttributeLoad NameLoad attr NameLoad Delete SubscriptDel NameLoad Index Num Delete SubscriptDel NameLoad Index Num Return NameLoad decorator_list FunctionDef arguments args NameParam defaults body Return BinOpAdd BinOpAdd Str Call AttributeLoad Str attr GeneratorExp Call AttributeLoad Str attr NameLoad NameLoad comprehension TupleStore NameStore NameStore Call NameLoad Call AttributeLoad NameLoad attr Str decorator_list FunctionDef arguments args NameParam defaults body Assign NameStore ListComp NameLoad comprehension NameStore Call AttributeLoad Call AttributeLoad NameLoad attr Str attr Str NameLoad Assign NameStore Dict For NameStore NameLoad body Assign TupleStore NameStore NameStore Call AttributeLoad NameLoad attr Str Assign SubscriptStore NameLoad Index Call NameLoad NameLoad Call NameLoad NameLoad Return 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 TupleLoad Str 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 AttributeLoad NameLoad attr If CompareIs NameLoad NameLoad body Assign NameStore IfExp CompareIn Str NameLoad AttributeLoad NameLoad attr AttributeLoad NameLoad attr orelse Assign NameStore IfExp CompareEq NameLoad Str AttributeLoad NameLoad attr AttributeLoad NameLoad attr Print AttributeLoad NameLoad attr Call AttributeLoad Str attr NameLoad Assign NameStore Call NameLoad NameLoad Expr Call AttributeLoad NameLoad attr Assign NameStore ListLoad For TupleStore NameStore NameStore Call NameLoad NameLoad body Assign NameStore Call AttributeLoad NameLoad attr NameLoad keyword Str keyword NameLoad Assign NameStore SubscriptLoad NameLoad Slice Num Expr Call AttributeLoad NameLoad attr NameLoad Print AttributeLoad NameLoad attr NameLoad NameLoad Print AttributeLoad NameLoad attr Str Assign NameStore Call AttributeLoad NameLoad attr NameLoad Print AttributeLoad NameLoad attr Call AttributeLoad Str attr AttributeLoad NameLoad attr Assign NameStore BinOpAdd SubscriptLoad Call AttributeLoad NameLoad attr Str Num Index Num Str Expr Call AttributeLoad NameLoad attr NameLoad decorator_list FunctionDef arguments args NameParam defaults body Assign NameStore Dict Assign NameStore Num For TupleStore NameStore NameStore Call NameLoad Call AttributeLoad NameLoad attr keyword NameLoad body AugAssignAdd NameStore NameLoad Assign SubscriptStore NameLoad Index NameLoad NameLoad For TupleStore NameStore NameStore Call AttributeLoad NameLoad attr body Assign NameStore Call AttributeLoad Str attr BinOpDiv BinOpMult NameLoad Num NameLoad Assign SubscriptStore NameLoad Index NameLoad NameLoad Return NameLoad decorator_list FunctionDef arguments args NameParam defaults body Assign TupleStore NameStore NameStore NameStore NameLoad Assign NameStore BinOpMod NameLoad Num Assign NameStore Call AttributeLoad NameLoad attr ListComp Call AttributeLoad NameLoad attr NameLoad Str comprehension NameStore NameLoad keyword Str If CompareEq BinOpMod NameLoad Num Num body Print AttributeLoad NameLoad attr NameLoad Print AttributeLoad NameLoad attr NameLoad Print AttributeLoad NameLoad attr NameLoad Return TupleLoad NameLoad NameLoad decorator_list FunctionDef arguments args NameParam NameParam NameParam NameParam NameParam NameParam defaults Str Str body Assign NameStore Call NameLoad NameLoad Str Print NameLoad Call AttributeLoad Str attr BinOpAdd ListLoad NameLoad NameLoad For TupleStore NameStore NameStore Call NameLoad NameLoad body Print NameLoad BinOpAdd BinOpAdd SubscriptLoad NameLoad Index NameLoad Str Call AttributeLoad Str attr GeneratorExp Call NameLoad NameLoad comprehension NameStore NameLoad Expr Call 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 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 NameStore NameStore NameStore NameLoad Assign TupleStore NameStore NameStore NameStore NameStore Call NameLoad NameLoad NameLoad NameLoad Assign NameStore ListComp Call AttributeLoad NameLoad attr comprehension NameStore Call NameLoad NameLoad Assign NameStore Call NameLoad NameLoad Assign NameStore ListComp Call AttributeLoad NameLoad attr comprehension NameStore Call NameLoad NameLoad Assert CompareEq Call NameLoad NameLoad BinOpAdd Call NameLoad NameLoad Call NameLoad NameLoad Assign NameStore Call NameLoad NameLoad Assign NameStore Dict For NameStore NameLoad body Assign TupleStore NameStore NameStore Call AttributeLoad NameLoad attr Assign NameStore Call NameLoad NameLoad Assign NameStore Call NameLoad NameLoad Assign SubscriptStore NameLoad Index NameLoad NameLoad Assign NameStore ListLoad For TupleStore NameStore NameStore Call NameLoad NameLoad body If CompareIn NameLoad NameLoad body Continue Assign NameStore SubscriptLoad NameLoad ExtSlice Slice Index NameLoad Assign NameStore SubscriptLoad NameLoad Index NameLoad Expr Call AttributeLoad NameLoad attr TupleLoad NameLoad NameLoad NameLoad Assign NameStore Call NameLoad AttributeLoad NameLoad attr Call NameLoad NameLoad Assign NameStore Call NameLoad keyword NameLoad Assign NameStore ListLoad For NameStore Call AttributeLoad Call AttributeLoad NameLoad attr NameLoad NameLoad attr body Expr Call AttributeLoad NameLoad attr NameLoad Expr Call AttributeLoad NameLoad attr Assign TupleStore NameStore NameStore Call NameLoad NameLoad Assign NameStore AttributeLoad Call AttributeLoad NameLoad attr NameLoad attr Expr Call NameLoad Str NameLoad NameLoad NameLoad Expr Call AttributeLoad NameLoad attr NameLoad keyword NameLoad keyword Num Assign AttributeStore NameLoad attr NameLoad Assign NameStore Str Assign NameStore Call AttributeLoad NameLoad attr Assign SubscriptStore NameLoad Index CompareLt NameLoad Num Num Expr Call AttributeLoad NameLoad attr NameLoad Expr Call AttributeLoad NameLoad attr Call AttributeLoad Str attr NameLoad Expr Call AttributeLoad NameLoad attr Str keyword Str keyword Str decorator_list FunctionDef arguments args NameParam defaults body Expr Str Assign NameStore Call NameLoad 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 NameStore NameLoad Assign NameStore Call NameLoad ListComp Call AttributeLoad NameLoad attr comprehension NameStore Call NameLoad NameLoad Assign NameStore BinOpMult NameLoad Num Expr Call AttributeLoad NameLoad attr Call AttributeLoad Str attr NameLoad NameLoad NameLoad Expr Call AttributeLoad NameLoad attr Call AttributeLoad Str attr NameLoad Assign NameStore Call NameLoad NameLoad Assign NameStore Call NameLoad NameLoad For NameStore NameLoad body Assign TupleStore NameStore NameStore NameStore NameStore NameStore NameStore NameStore NameStore Call AttributeLoad NameLoad attr AugAssignBitOr SubscriptStore NameLoad Index TupleLoad NameLoad NameLoad Call NameLoad Call AttributeLoad NameLoad attr Str For TupleStore NameStore NameStore Call AttributeLoad NameLoad attr body Assign NameStore Call NameLoad GeneratorExp NameLoad comprehension NameStore NameLoad UnaryOpNot Call AttributeLoad NameLoad attr Str Assign NameStore Call NameLoad GeneratorExp SubscriptLoad Call AttributeLoad NameLoad attr Str Num Index Num comprehension NameStore NameLoad Call AttributeLoad NameLoad attr Str Assign SubscriptStore NameLoad Index NameLoad Call AttributeLoad Str attr BinOpAdd NameLoad NameLoad Expr Call AttributeLoad NameLoad attr Call AttributeLoad Str attr NameLoad Assign NameStore Call NameLoad NameLoad Assign NameStore Call NameLoad NameLoad Assign NameStore ListLoad Assign NameStore Call NameLoad Str Str Assign NameStore Call AttributeLoad Str attr Str Str Print NameLoad NameLoad Assign NameStore Str Assign NameStore Str For NameStore NameLoad body Assign TupleStore NameStore NameStore Call AttributeLoad NameLoad attr Assign NameStore SubscriptLoad Call AttributeLoad NameLoad attr Str Num Index Num Assign TupleStore NameStore NameStore NameStore Call AttributeLoad NameLoad attr Str Assign NameStore ListComp NameLoad comprehension NameStore Call AttributeLoad Call AttributeLoad NameLoad attr Str attr Str NameLoad Assign NameStore Dict For NameStore NameLoad body Assign TupleStore NameStore NameStore Call AttributeLoad NameLoad attr Str Assign SubscriptStore NameLoad Index Call NameLoad NameLoad Call NameLoad NameLoad If Call NameLoad NameLoad NameLoad NameLoad body Expr Call AttributeLoad NameLoad attr NameLoad Continue If CompareIn NameLoad NameLoad body Expr Call AttributeLoad NameLoad attr NameLoad Continue Expr Call AttributeLoad NameLoad attr NameLoad Assign NameStore Call AttributeLoad NameLoad attr TupleLoad NameLoad NameLoad Str Print NameLoad Call AttributeLoad Str attr TupleLoad NameLoad Call AttributeLoad NameLoad attr NameLoad NameLoad NameLoad NameLoad NameLoad Expr Call AttributeLoad NameLoad attr Assign NameStore Str Assign NameStore Call NameLoad NameLoad Str Print NameLoad Call AttributeLoad Str attr NameLoad Expr Call AttributeLoad NameLoad attr Expr Call AttributeLoad NameLoad attr Call AttributeLoad Str attr Call NameLoad NameLoad NameLoad decorator_list FunctionDef arguments args NameParam NameParam NameParam defaults body If CompareLt Call NameLoad NameLoad Num body Return NameLoad Assign NameStore Call NameLoad Call AttributeLoad NameLoad attr Assign NameStore BinOpDiv BinOpMult NameLoad Num NameLoad If CompareLt NameLoad Num body If UnaryOpNot BoolOpAnd CompareEq NameLoad Str CompareGtE NameLoad Num body Return NameLoad decorator_list FunctionDef arguments args NameParam NameParam NameParam NameParam defaults AttributeLoad NameLoad attr body Assign NameStore Call AttributeLoad NameLoad attr NameLoad keyword NameLoad Assign NameStore ListComp Call AttributeLoad NameLoad attr comprehension NameStore Call NameLoad NameLoad Assign NameStore ListComp Call AttributeLoad NameLoad attr comprehension NameStore Call NameLoad NameLoad Assign TupleStore NameStore NameStore TupleLoad Call NameLoad NameLoad Call NameLoad NameLoad Print AttributeLoad NameLoad attr Call AttributeLoad Str attr NameLoad NameLoad Expr Call AttributeLoad NameLoad attr NameLoad NameLoad Assign NameStore Call AttributeLoad NameLoad attr NameLoad keyword NameLoad keyword NameLoad Return TupleLoad NameLoad NameLoad NameLoad NameLoad decorator_list FunctionDef arguments args NameParam defaults body Expr Str Assign NameStore Call NameLoad AttributeLoad NameLoad attr 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 ListLoad Assign NameStore ListLoad For NameStore NameLoad body Assign NameStore SubscriptLoad Call AttributeLoad Call AttributeLoad NameLoad attr NameLoad attr Str Index Num Assign NameStore Call AttributeLoad NameLoad attr NameLoad keyword Str keyword AttributeLoad NameLoad attr Assign NameStore SubscriptLoad NameLoad Slice Num Assign NameStore SubscriptLoad NameLoad Slice Num Num Assign NameStore BinOpAdd BinOpMult NameLoad Num NameLoad Assign SubscriptStore NameLoad Index CompareLt NameLoad Num Num Expr Call AttributeLoad NameLoad attr NameLoad Expr Call AttributeLoad NameLoad attr NameLoad Print AttributeLoad NameLoad attr NameLoad NameLoad Print AttributeLoad NameLoad attr Str Assign NameStore Call AttributeLoad NameLoad attr NameLoad Expr Call AttributeLoad NameLoad attr Str Assign NameStore Call NameLoad Str Str Print NameLoad Call AttributeLoad Str attr NameLoad Expr Call AttributeLoad NameLoad attr decorator_list FunctionDef arguments args NameParam NameParam NameParam NameParam NameParam defaults NameLoad NameLoad body Assign NameStore Call NameLoad Expr Call AttributeLoad NameLoad attr NameLoad keyword NameLoad keyword NameLoad keyword NameLoad Assign NameStore BinOpAdd Call AttributeLoad NameLoad attr NameLoad Str Assign NameStore BinOpAdd Call AttributeLoad NameLoad attr NameLoad Str If NameLoad body Assign NameStore Call NameLoad NameLoad Str Print NameLoad AttributeLoad NameLoad attr Expr Call AttributeLoad NameLoad attr Return Assign NameStore Call NameLoad NameLoad Str Print NameLoad AttributeLoad NameLoad attr Expr Call AttributeLoad NameLoad attr Assign NameStore Call NameLoad NameLoad Str Print NameLoad AttributeLoad NameLoad attr Expr Call AttributeLoad NameLoad attr If NameLoad body Expr Call NameLoad NameLoad NameLoad Expr Call NameLoad NameLoad NameLoad decorator_list FunctionDef arguments args NameParam defaults body Assign TupleStore NameStore NameStore NameStore NameStore NameStore NameLoad Assign NameStore BinOpAdd NameLoad Str TryExcept body If Call AttributeLoad NameLoad attr Str body If Call NameLoad NameLoad body Expr Call AttributeLoad NameLoad attr Call AttributeLoad Str attr NameLoad orelse Expr Call NameLoad NameLoad NameLoad NameLoad keyword NameLoad keyword NameLoad Expr Call AttributeLoad NameLoad attr Call AttributeLoad Str attr NameLoad orelse If Call NameLoad NameLoad NameLoad body Expr Call NameLoad NameLoad NameLoad NameLoad keyword NameLoad keyword NameLoad handlers ExceptHandler type NameLoad name NameStore body 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 Str 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 Expr Call AttributeLoad NameLoad attr 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 AttributeLoad NameLoad attr Assign NameStore AttributeLoad NameLoad attr Assign NameStore AttributeLoad NameLoad attr Assign NameStore UnaryOpNot AttributeLoad NameLoad attr Assign NameStore UnaryOpNot AttributeLoad NameLoad attr Assign NameStore Call AttributeLoad AttributeLoad NameLoad attr attr Str Assign NameStore Call AttributeLoad NameLoad attr Expr Call NameLoad NameLoad Expr Call AttributeLoad NameLoad attr NameLoad Assign NameStore Call AttributeLoad NameLoad attr NameLoad NameLoad Assign NameStore Str Assign NameStore ListComp Call AttributeLoad NameLoad attr comprehension NameStore Call NameLoad NameLoad If UnaryOpNot Call AttributeLoad NameLoad attr NameLoad body Assign NameStore ListLoad For NameStore NameLoad body Expr Call AttributeLoad NameLoad attr AttributeLoad Call NameLoad AttributeLoad NameLoad attr keyword NameLoad attr Assign NameStore Call NameLoad NameLoad Expr Call AttributeLoad NameLoad attr Call AttributeLoad Str attr Call NameLoad NameLoad Call NameLoad NameLoad Assign NameStore Call NameLoad NameLoad Str Print NameLoad Call AttributeLoad Str attr NameLoad Expr Call AttributeLoad NameLoad attr Assign NameStore ListComp TupleLoad NameLoad NameLoad NameLoad NameLoad NameLoad comprehension NameStore NameLoad Assign NameStore Call NameLoad AttributeLoad NameLoad attr Call NameLoad NameLoad Assign NameStore Call NameLoad keyword NameLoad For NameStore Call AttributeLoad Call AttributeLoad NameLoad attr NameLoad NameLoad attr body Continue decorator_list FunctionDef arguments args NameParam NameParam defaults ListLoad Str Str Str body Assign NameStore Str Assign NameStore ListLoad For TupleStore NameStore NameStore Call NameLoad NameLoad NameLoad body Assign NameStore Call AttributeLoad NameLoad attr NameLoad Str If BoolOpOr CompareIn Str NameLoad CompareIn NameLoad NameLoad body Assign NameStore Str Assign NameStore Call AttributeLoad Str attr NameLoad NameLoad Expr Call AttributeLoad NameLoad attr NameLoad Print BinOpAdd NameLoad Call AttributeLoad Str attr NameLoad decorator_list FunctionDef arguments args NameParam NameParam NameParam defaults ListLoad Str body Assign NameStore ListLoad For NameStore NameLoad body Assign NameStore Call AttributeLoad NameLoad attr NameLoad Str If CompareIn NameLoad NameLoad body Assign NameStore Str Expr Call AttributeLoad NameLoad attr NameLoad Print Call AttributeLoad Str attr GeneratorExp Call NameLoad NameLoad comprehension NameStore NameLoad decorator_list FunctionDef arguments args NameParam defaults body Expr Str ImportFrom alias Assign NameStore Call NameLoad AttributeLoad NameLoad attr Expr Call AttributeLoad NameLoad attr 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 Call NameLoad AttributeLoad NameLoad attr keyword Str Assign NameStore AttributeLoad NameLoad attr Assign NameStore Call AttributeLoad Str attr Str Assign NameStore ListLoad Assign NameStore Call NameLoad NameLoad Assign NameStore Call AttributeLoad NameLoad attr NameLoad Assign NameStore Dict For NameStore NameLoad body Assign NameStore SubscriptLoad NameLoad Index TupleLoad AttributeLoad NameLoad attr AttributeLoad NameLoad attr Assign NameStore AttributeLoad NameLoad attr Assign NameStore Call NameLoad Call NameLoad SubscriptLoad NameLoad Index Str Assign NameStore Call AttributeLoad NameLoad attr Str NameLoad If Call NameLoad NameLoad NameLoad body Assign NameStore Call AttributeLoad Str attr GeneratorExp Call NameLoad Call NameLoad Call NameLoad NameLoad comprehension NameStore NameLoad Assign NameStore SubscriptLoad NameLoad Index Str Assign SubscriptStore NameLoad Index NameLoad NameLoad For NameStore AttributeLoad NameLoad attr body Expr Call AttributeLoad NameLoad attr TupleLoad NameLoad SubscriptLoad NameLoad Index Str NameLoad NameLoad NameLoad Assign TupleStore NameStore NameStore NameStore TupleLoad Str Str Str If BoolOpAnd CompareIn NameLoad NameLoad CompareIn NameLoad NameLoad body Assign SubscriptStore NameLoad Index NameLoad BinOpAdd Call NameLoad SubscriptLoad NameLoad Index NameLoad Call NameLoad SubscriptLoad NameLoad Index NameLoad Assign NameStore ListLoad Str Str Str For NameStore NameLoad body Assign TupleStore NameStore NameStore TupleLoad BinOpAdd NameLoad Str BinOpAdd NameLoad Str If BoolOpOr CompareNotIn NameLoad NameLoad CompareNotIn NameLoad NameLoad body Assign SubscriptStore NameLoad Index NameLoad SubscriptStore NameLoad Index NameLoad NameLoad Delete SubscriptDel NameLoad Index NameLoad Delete SubscriptDel NameLoad Index NameLoad Continue If CompareGt SubscriptLoad NameLoad Index NameLoad SubscriptLoad NameLoad Index NameLoad body Assign TupleStore SubscriptStore NameLoad Index NameLoad SubscriptStore NameLoad Index NameLoad TupleLoad SubscriptLoad NameLoad Index NameLoad SubscriptLoad NameLoad Index NameLoad Expr Call NameLoad NameLoad NameLoad keyword Str Print Str Expr Call NameLoad NameLoad Print Str Expr Call NameLoad NameLoad keyword NameLoad Print Str Expr Call NameLoad NameLoad keyword NameLoad Print Str Expr Call NameLoad NameLoad keyword NameLoad decorator_list FunctionDef arguments args NameParam NameParam defaults body Assign NameStore Call NameLoad NameLoad Assign NameStore Call NameLoad For NameStore Call NameLoad BinOpSub NameLoad NameLoad body Assign NameStore SubscriptLoad NameLoad Slice NameLoad BinOpAdd NameLoad NameLoad Expr Call AttributeLoad NameLoad attr NameLoad Assign NameStore ListLoad For NameStore NameLoad body Expr Call AttributeLoad NameLoad attr TupleLoad Call AttributeLoad NameLoad attr NameLoad UnaryOpUSub Call AttributeLoad NameLoad attr NameLoad NameLoad Return SubscriptLoad SubscriptLoad Call NameLoad NameLoad keyword NameLoad Index Num Index Num 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 Call AttributeLoad NameLoad attr NameLoad Assign NameStore ListLoad Assign NameStore Call NameLoad NameLoad For TupleStore NameStore NameStore Call NameLoad NameLoad body Assign NameStore Call NameLoad NameLoad Assign NameStore Call AttributeLoad SubscriptLoad SubscriptLoad NameLoad Index AttributeLoad NameLoad attr Slice BinOpSub AttributeLoad NameLoad attr Num AttributeLoad NameLoad attr attr Assign AttributeStore NameLoad attr Call NameLoad NameLoad Call NameLoad AttributeLoad NameLoad attr Expr Call AttributeLoad NameLoad attr NameLoad If BoolOpAnd AttributeLoad NameLoad attr UnaryOpNot Call AttributeLoad NameLoad attr body Continue Expr Call AttributeLoad NameLoad attr NameLoad If CompareEq BinOpMod NameLoad Num Num body Print AttributeLoad NameLoad attr NameLoad Str Assign NameStore Call NameLoad NameLoad keyword Lambda arguments args NameParam defaults TupleLoad AttributeLoad NameLoad attr AttributeLoad NameLoad attr For NameStore NameLoad body Print Call NameLoad NameLoad decorator_list FunctionDef arguments args NameParam defaults body Expr Str ImportFrom alias 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 Expr Call AttributeLoad NameLoad attr Str keyword Num keyword Str keyword Str Expr Call AttributeLoad NameLoad attr Str keyword BinOpDiv NameLoad 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 AttributeLoad NameLoad attr Assign NameStore Call NameLoad If AttributeLoad NameLoad attr body Assign TupleStore AttributeStore NameLoad attr AttributeStore NameLoad attr TupleLoad Num Num Assign NameStore Call AttributeLoad Call AttributeLoad Str attr AttributeLoad NameLoad attr AttributeLoad NameLoad attr AttributeLoad NameLoad attr attr Assign NameStore ListLoad For NameStore Call NameLoad Call NameLoad NameLoad Str body Assign NameStore SubscriptLoad Call AttributeLoad Call AttributeLoad NameLoad attr NameLoad attr Str Index Num Assign NameStore Call AttributeLoad Str attr NameLoad Call AttributeLoad Str attr NameLoad Assign NameStore BinOpAdd BinOpAdd BinOpAdd Call AttributeLoad NameLoad attr NameLoad Str Call AttributeLoad Str attr NameLoad Str Assign NameStore Call AttributeLoad Str attr NameLoad Assign NameStore Call AttributeLoad Str attr NameLoad NameLoad BinOpSub NameLoad NameLoad AugAssignAdd NameStore Str AugAssignAdd NameStore Call AttributeLoad Str attr NameLoad NameLoad Expr Call AttributeLoad NameLoad attr NameLoad NameLoad NameLoad Expr Call AttributeLoad NameLoad attr NameLoad NameLoad NameLoad Expr Call AttributeLoad NameLoad attr NameLoad Assign NameStore Str Assign NameStore Call AttributeLoad Str attr Call AttributeLoad Str attr Call NameLoad NameLoad NameLoad Expr Call AttributeLoad NameLoad attr NameLoad NameLoad NameLoad Expr Call 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 keyword Str keyword Str Expr Call AttributeLoad NameLoad attr 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 AttributeLoad NameLoad attr Assign NameStore Call NameLoad NameLoad Assign NameStore Call NameLoad NameLoad Assign NameStore NameStore Num For NameStore NameLoad body AugAssignAdd NameStore Num Assign TupleStore NameStore NameStore SubscriptLoad Call AttributeLoad Call AttributeLoad NameLoad attr attr Str Slice Num Assign TupleStore NameStore NameStore Call AttributeLoad NameLoad attr Str Assign NameStore Call AttributeLoad Call AttributeLoad NameLoad attr Str Str attr Str Str Assign NameStore BinOpAdd NameLoad Call AttributeLoad Str attr Str If CompareIn NameLoad NameLoad body AugAssignAdd NameStore Num Continue Print Call AttributeLoad AttributeLoad NameLoad attr attr BinOpAdd Call AttributeLoad Str attr ListLoad Str Str NameLoad Str NameLoad Str NameLoad Str NameLoad Str AttributeLoad NameLoad attr Str AttributeLoad NameLoad attr Expr Call AttributeLoad NameLoad attr Expr Call AttributeLoad NameLoad attr Call AttributeLoad Str attr Call NameLoad 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 Str Expr Call AttributeLoad NameLoad attr Str keyword Str Expr Call AttributeLoad NameLoad attr Expr Call AttributeLoad NameLoad attr keyword Str Assign TupleStore NameStore NameStore Call AttributeLoad NameLoad attr NameLoad Assign NameStore AttributeLoad NameLoad attr If BoolOpOr CompareLt Call NameLoad NameLoad Num CompareIs NameLoad NameLoad body Expr Call AttributeLoad NameLoad attr UnaryOpNot Call AttributeLoad NameLoad attr Assign NameStore NameLoad Assign NameStore Call AttributeLoad NameLoad attr Str Assign NameStore AttributeLoad NameLoad attr Assign NameStore UnaryOpNot AttributeLoad NameLoad attr Assign NameStore AttributeLoad NameLoad attr Expr Call NameLoad NameLoad Expr Call AttributeLoad NameLoad attr NameLoad Assign NameStore AttributeLoad NameLoad attr If Call AttributeLoad NameLoad attr Str body Assign NameStore Call NameLoad NameLoad keyword NameLoad Assign TupleStore NameStore NameStore TupleLoad AttributeLoad NameLoad attr AttributeLoad NameLoad attr Assign NameStore ListComp NameLoad comprehension NameStore TupleLoad NameLoad NameLoad NameLoad If NameLoad body Assign NameStore Call AttributeLoad Str attr NameLoad orelse Assign NameStore SubscriptLoad Call AttributeLoad SubscriptLoad Call AttributeLoad NameLoad attr Str Index Num attr Str Index Num If NameLoad body Assign NameStore BinOpAdd NameLoad Call AttributeLoad Str attr SubscriptLoad NameLoad Index Num Assign NameStore Call AttributeLoad Str attr NameLoad NameLoad If Call NameLoad NameLoad body Expr Call AttributeLoad NameLoad attr Call AttributeLoad Str attr NameLoad Return Assign NameStore BinOpAdd NameLoad Str Assign NameStore BinOpAdd NameLoad Str If Call AttributeLoad NameLoad attr NameLoad body Expr Call AttributeLoad NameLoad attr Str orelse Expr Call NameLoad NameLoad NameLoad If Call AttributeLoad NameLoad attr NameLoad body Expr Call AttributeLoad NameLoad attr Str orelse Assign NameStore BinOpAdd NameLoad Str If Call NameLoad NameLoad body Expr Call NameLoad NameLoad NameLoad orelse Assign NameStore BinOpAdd SubscriptLoad Call AttributeLoad NameLoad attr Str Index Num Str If Call NameLoad NameLoad body Expr Call NameLoad NameLoad NameLoad orelse Expr Call AttributeLoad NameLoad attr Str Expr Call NameLoad Call AttributeLoad Str attr NameLoad Assign NameStore NameLoad Assign NameStore IfExp AttributeLoad NameLoad attr ListLoad AttributeLoad NameLoad attr BinOpAdd Call NameLoad Num Num ListLoad Str Str For NameStore NameLoad body Assign NameStore Call AttributeLoad Str attr NameLoad Assign NameStore Call NameLoad keyword NameLoad Assign NameStore ListLoad For NameStore NameLoad body Assign TupleStore NameStore NameStore Call NameLoad NameLoad NameLoad NameLoad NameLoad Expr Call AttributeLoad NameLoad attr NameLoad NameLoad NameLoad Assign NameStore Call AttributeLoad NameLoad attr Str Str Assign NameStore Call AttributeLoad Str attr NameLoad AugAssignAdd NameStore Call AttributeLoad Str attr NameLoad Expr Call AttributeLoad NameLoad attr NameLoad NameLoad NameLoad Expr Call AttributeLoad NameLoad attr NameLoad Assign NameStore BinOpAdd SubscriptLoad Call AttributeLoad NameLoad attr Str Index Num Call AttributeLoad Str attr NameLoad Assign NameStore Call AttributeLoad Str attr Call AttributeLoad Str attr NameLoad AugAssignAdd NameStore Call AttributeLoad Str attr NameLoad Expr Call AttributeLoad NameLoad attr NameLoad NameLoad NameLoad Expr Call AttributeLoad NameLoad attr keyword AttributeLoad NameLoad attr If NameLoad body Expr Call NameLoad NameLoad NameLoad If NameLoad body Expr Call AttributeLoad NameLoad attr Expr Call NameLoad Call AttributeLoad Str attr NameLoad AttributeLoad NameLoad attr decorator_list FunctionDef arguments args NameParam NameParam NameParam NameParam defaults body Assign NameStore Call AttributeLoad Str attr SubscriptLoad Call AttributeLoad NameLoad attr Str Index Num NameLoad Assign NameStore Call AttributeLoad Str attr NameLoad AugAssignAdd NameStore Call AttributeLoad Str attr NameLoad AugAssignAdd NameStore Call AttributeLoad Str attr NameLoad NameLoad AugAssignAdd NameStore Call AttributeLoad Str attr NameLoad NameLoad AugAssignAdd NameStore Call AttributeLoad Str attr NameLoad NameLoad NameLoad AugAssignAdd NameStore Call AttributeLoad Str attr NameLoad AugAssignAdd NameStore Str AugAssignAdd NameStore Str Return TupleLoad NameLoad Call AttributeLoad Str attr TupleLoad NameLoad NameLoad Str decorator_list FunctionDef arguments args NameParam defaults body Expr Str Assign NameStore Call NameLoad 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 Call NameLoad NameLoad Expr Call AttributeLoad NameLoad attr For NameStore NameLoad body Assign TupleStore NameStore NameStore NameStore NameStore NameStore Call AttributeLoad Call AttributeLoad NameLoad attr attr Str Expr Call NameLoad ListLoad NameLoad NameLoad Expr Call AttributeLoad NameLoad attr decorator_list FunctionDef arguments args NameParam defaults body Expr Str ImportFrom alias Assign NameStore Call NameLoad AttributeLoad NameLoad attr Expr Call AttributeLoad NameLoad attr 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 AttributeLoad NameLoad attr Assign NameStore Call NameLoad NameLoad NameLoad Assign NameStore Call AttributeLoad SubscriptLoad Call AttributeLoad NameLoad attr Str Index Num attr Str Str Assign TupleStore NameStore NameStore Call NameLoad NameLoad NameLoad NameLoad Str 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 NameLoad keyword Str keyword Str Expr Call AttributeLoad NameLoad attr 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 Index Num Assign NameStore AttributeLoad NameLoad attr Expr Call NameLoad NameLoad If AttributeLoad NameLoad attr body Assign NameStore BinOpAdd NameLoad Str Assign NameStore Call NameLoad NameLoad Str Assign NameStore Call NameLoad NameLoad Assign NameStore NameStore Num Assign NameStore Call NameLoad For NameStore NameLoad body Assign NameStore Call NameLoad NameLoad AugAssignAdd NameStore Num Assign NameStore AttributeLoad NameLoad attr If CompareIn NameLoad NameLoad body Continue Expr Call AttributeLoad NameLoad attr NameLoad Print NameLoad NameLoad AugAssignAdd NameStore Num Expr Call AttributeLoad NameLoad attr Expr Call AttributeLoad NameLoad attr Call AttributeLoad Str attr Call NameLoad NameLoad NameLoad orelse Assign NameStore NameLoad Assign NameStore Call NameLoad Assign NameStore Call AttributeLoad Str attr NameLoad AugAssignAdd NameStore Call AttributeLoad Str attr NameLoad NameLoad NameLoad Expr Call AttributeLoad NameLoad attr TupleLoad NameLoad NameLoad Call AttributeLoad NameLoad attr NameLoad Str NameLoad Assign NameStore Call AttributeLoad Str attr NameLoad Assign NameStore Call AttributeLoad Str attr NameLoad AugAssignAdd NameStore Call AttributeLoad Str attr NameLoad NameLoad NameLoad Expr Call AttributeLoad NameLoad attr TupleLoad NameLoad NameLoad NameLoad NameLoad Assign NameStore Call AttributeLoad Str attr NameLoad Assign NameStore Call AttributeLoad Str attr NameLoad NameLoad Expr Call AttributeLoad NameLoad attr NameLoad NameLoad NameLoad Expr Call AttributeLoad NameLoad attr decorator_list If CompareEq NameLoad Str body Expr Call NameLoad
N/A N/A 
Identify repeat numbers in STR repeats.
 N/A re N/A os N/A os.path op N/A sys N/A vcf N/A logging N/A pyfasta N/A numpy np N/A pandas pd math log ceil collections Counter defaultdict multiprocessing Pool jcvi.utils.cbook percentage uniqify jcvi.formats.bed natsorted jcvi.apps.grid MakeManager jcvi.formats.base LineFile must_open jcvi.utils.aws push_to_s3 pull_from_s3 check_exists_s3 ls_s3 jcvi.apps.base OptionParser ActionDispatcher mkdir need_update sh N/A READLEN 150 N/A MINSCORE 36 N/A YSEARCH_HAPLOTYPE N/A N/A 
DYS393  DYS390 DYS19/DYS394  DYS19b        DYS391        DYS385a       DYS385b DYS426  DYS388  DYS439
DYS389I DYS392 DYS389B       DYS458        DYS459a/b     DYS459a/b     DYS455  DYS454  DYS447  DYS437
DYS448  DYS449 DYS464a/b/c/d DYS464a/b/c/d DYS464a/b/c/d DYS464a/b/c/d DYS464e DYS464f DYS464g DYS460
GATA-H4 YCAIIa YCAIIb        DYS456        DYS607        DYS576        DYS570  CDYa    CDYb    DYS442
DYS438  DYS531 DYS578        DYS395S1a/b   DYS395S1a/b   DYS590        DYS537  DYS641  DYS472  DYS406S1
DYS511  DYS425 DYS413a       DYS413b       DYS557        DYS594        DYS436  DYS490  DYS534  DYS450
DYS444  DYS481 DYS520        DYS446        DYS617        DYS568        DYS487  DYS572  DYS640  DYS492
DYS565  DYS461 DYS462        GATA-A10      DYS635        GAAT1B07      DYS441  DYS445  DYS452  DYS463
DYS434  DYS435 DYS485        DYS494        DYS495        DYS505        DYS522  DYS533  DYS549  DYS556
DYS575  DYS589 DYS636        DYS638        DYS643        DYS714        DYS716  DYS717  DYS726  DXYS156-Y
 split N/A YSEARCH_LL N/A N/A 
L1  L2  L3  L4  L5  L6  L7  L8  L9  L10
L11 L12 L13 L14 L15 L16 L17 L18 L19 L20
L21 L22 L23 L24 L25 L26 L27 L28 L29 L30
L31 L32 L33 L34 L35 L36 L37 L38 L39 L40
L41 L54 L55 L56 L57 L58 L59 L60 L61 L62
L63 L42 L64 L65 L66 L67 L68 L69 L70 L71
L49 L72 L73 L51 L74 L75 L76 L77 L78 L79
L80 L43 L44 L45 L46 L47 L48 L50 L52 L53
L81 L82 L83 L84 L85 L86 L87 L88 L89 L90
L91 L92 L93 L94 L95 L96 L97 L98 L99 L100
 split N/A YHRD_YFILER N/A N/A 
DYS456 DYS389I DYS390 DYS389B DYS458 DYS19/DYS394 DYS385
DYS393 DYS391 DYS439 DYS635 DYS392 GATA-H4 DYS437 DYS438 DYS448
 split N/A YHRD_YFILERPLUS N/A N/A 
DYS576 DYS389I DYS635 DYS389B DYS627 DYS460 DYS458 DYS19/DYS394 GATA-H4 DYS448 DYS391
DYS456 DYS390 DYS438 DYS392 DYS518 DYS570 DYS437 DYS385a DYS449
DYS393 DYS439 DYS481 DYF387S1 DYS533
 split N/A USYSTR_ALL N/A N/A 
DYF387S1 DYS19/DYS394 DYS385 DYS389I
DYS389B DYS390 DYS391 DYS392
DYS393 DYS437 DYS438 DYS439
DYS448 DYS449 DYS456 DYS458
DYS460 DYS481 DYS518 DYS533
DYS549 DYS570 DYS576 DYS627
DYS635 DYS643 GATA-H4
 split N/A TREDS N/A N/A chr19_45770205_CAG
chr6_170561926_CAG
chrX_67545318_CAG
chr9_69037287_GAA
chrX_147912051_CGG
chr4_3074877_CAG
chrX_148500639_CCG
chr12_6936729_CAG
chr13_70139384_CTG
chr6_16327636_CTG
chr14_92071011_CTG
chr12_111598951_CTG
chr3_63912686_CAG
chr19_13207859_CTG split STRLine N/A object N/A __init__ N/A N/A self line N/A N/A N/A args N/A N/A line split N/A N/A self seqid N/A args N/A 0 N/A N/A self start N/A int N/A args N/A 1 N/A N/A self end N/A int N/A args N/A 2 N/A N/A self period N/A int N/A args N/A 3 N/A N/A self copynum N/A args N/A 4 N/A N/A self consensusSize N/A int N/A args N/A 5 N/A N/A self pctmatch N/A int N/A args N/A 6 N/A N/A self pctindel N/A int N/A args N/A 7 N/A N/A self score N/A args N/A 8 N/A N/A self A N/A args N/A 9 N/A N/A self C N/A args N/A 10 N/A N/A self G N/A args N/A 11 N/A N/A self T N/A args N/A 12 N/A N/A self entropy N/A float N/A args N/A 13 N/A N/A self motif N/A args N/A 14 N/A N/A N/A self period N/A len N/A self motif N/A N/A self name N/A N/A N/A len args 15 N/A args N/A 15 None N/A __str__ N/A N/A self N/A N/A N/A fields N/A N/A self seqid N/A self start N/A self end N/A self period N/A self copynum N/A self consensusSize N/A self pctmatch N/A self pctindel N/A self score N/A self A N/A self C N/A self G N/A self T N/A N/A {0:.2f} format N/A self entropy N/A self motif N/A N/A N/A self name None N/A N/A fields N/A N/A self name N/A N/A N/A join N/A N/A str x N/A x fields N/A longname 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 self start N/A self motif N/A property is_valid N/A N/A self maxperiod maxlength minscore N/A 6 READLEN MINSCORE N/A N/A N/A N/A 1 N/A self period maxperiod N/A N/A N/A N/A self end N/A self start 1 maxlength N/A N/A self score minscore N/A calc_entropy N/A N/A self N/A N/A N/A total N/A N/A N/A N/A self A N/A self C N/A self G N/A self T N/A N/A total 0 N/A N/A 0 N/A fractions N/A N/A N/A x 1.0 total N/A x N/A N/A self A N/A self C N/A self G N/A self T N/A entropy N/A sum N/A N/A N/A -1.0 x N/A log x 2 N/A x fractions N/A x 0 N/A entropy N/A iter_exact_str N/A N/A self genome N/A N/A N/A pat N/A N/A re compile N/A N/A (({0}){{2,}}) format N/A self motif N/A start N/A self start N/A s N/A N/A N/A N/A genome N/A N/A self seqid N/A N/A N/A self start 1 N/A self end upper N/A m N/A N/A re finditer pat s N/A N/A N/A self start N/A start N/A N/A m start N/A length N/A N/A N/A m end N/A N/A m start N/A subseq N/A N/A m group 0 N/A N/A N/A length N/A self period 0 N/A N/A N/A subseq startswith N/A self motif N/A N/A self end N/A N/A N/A self start 1 length N/A N/A self copynum N/A length N/A self period N/A N/A self pctmatch 100 N/A N/A self pctindel 0 N/A N/A self score N/A 2 length N/A N/A N/A self fix_counts subseq N/A N/A self N/A fix_counts N/A N/A self subseq N/A N/A N/A length N/A int N/A ceil N/A N/A self period N/A float N/A self copynum N/A N/A self end N/A max N/A self end N/A N/A N/A self start length 1 N/A N/A self A N/A N/A subseq count A N/A N/A self C N/A N/A subseq count C N/A N/A self G N/A N/A subseq count G N/A N/A self T N/A N/A subseq count T N/A N/A self entropy N/A N/A self calc_entropy N/A N/A STRFile N/A LineFile N/A __init__ N/A N/A self lobstr_home db N/A hg38 N/A N/A filename N/A N/A op join lobstr_home N/A N/A {0}/index.info format db N/A N/A N/A N/A super STRFile self __init__ filename N/A fp N/A open filename N/A row fp N/A N/A N/A N/A self append N/A STRLine row N/A ids N/A N/A self N/A N/A N/A N/A N/A s longname N/A s self N/A property register N/A N/A self N/A N/A N/A N/A dict N/A N/A N/A N/A s seqid N/A s start N/A s name N/A s self N/A property N/A LobSTRvcf N/A dict N/A __init__ N/A N/A self columnidsfile N/A STR.ids N/A N/A N/A self samplekey None N/A fp N/A open columnidsfile N/A N/A self columns N/A N/A N/A x strip N/A x fp N/A N/A self evidence N/A N/A N/A N/A logging debug N/A N/A A total of {} markers imported from `{}` format N/A len N/A self columns columnidsfile N/A parse N/A N/A self filename filtered cleanup stutter N/A True False False N/A N/A N/A self samplekey N/A N/A N/A N/A N/A op basename filename split . N/A 0 N/A N/A N/A logging debug N/A N/A Parse `{}` (filtered={} stutter={}) format filename filtered stutter N/A fp N/A must_open filename N/A reader N/A N/A vcf Reader fp N/A record reader N/A N/A N/A stutter N/A N/A record CHROM chrY N/A N/A N/A N/A filtered N/A record FILTER N/A N/A N/A info N/A record INFO N/A ref N/A float N/A info N/A REF N/A rpa N/A N/A info get RPA ref N/A motif N/A info N/A MOTIF N/A name N/A N/A _ join N/A N/A str x N/A x N/A N/A record CHROM N/A record POS motif N/A sample N/A record samples N/A N/A stutter N/A N/A dp N/A int N/A sample N/A DP N/A N/A dp 10 N/A N/A N/A allreads N/A sample N/A ALLREADS N/A counts N/A N/A r N/A N/A allreads split ; N/A N/A N/A k v N/A N/A r split | N/A N/A N/A counts append N/A int v N/A mode N/A max counts N/A st N/A dp mode N/A N/A N/A N/A st 1.0 dp 0.2 N/A N/A N/A N/A N/A self evidence N/A name N/A N/A {},{} format st dp N/A N/A gt N/A sample N/A GT N/A N/A filtered N/A N/A sample N/A FT PASS N/A N/A N/A N/A gt 0/0 N/A N/A alleles N/A ref ref N/A N/A N/A gt N/A 0/1 1/0 N/A N/A alleles N/A ref N/A rpa N/A 0 N/A N/A N/A gt 1/1 N/A N/A alleles N/A N/A rpa N/A 0 N/A rpa N/A 0 N/A N/A N/A gt 1/2 N/A N/A alleles rpa N/A N/A self N/A name N/A N/A , join N/A N/A str N/A int x N/A x N/A sorted alleles N/A motif_length N/A len motif N/A adjusted_alleles N/A N/A N/A x ref motif_length N/A x alleles N/A support stutters 0 N/A allreads N/A sample N/A ALLREADS N/A r N/A N/A allreads split ; N/A N/A N/A k v N/A N/A r split | N/A N/A k v N/A N/A int k N/A int v N/A min_dist N/A min N/A N/A abs N/A k x N/A x adjusted_alleles N/A N/A N/A motif_length 0.5 min_dist N/A motif_length 1.5 N/A N/A stutters v N/A support v N/A N/A N/A self evidence N/A name N/A N/A {},{} format stutters support N/A cleanup N/A N/A N/A sh N/A N/A rm -f {} format N/A N/A op basename filename N/A csvline N/A N/A self N/A N/A N/A N/A N/A , join N/A N/A N/A self get c -1,-1 N/A c N/A self columns N/A property evline N/A N/A self N/A N/A N/A N/A N/A , join N/A N/A N/A N/A self evidence get c -1,-1 N/A c N/A self columns N/A property N/A main N/A N/A N/A N/A N/A actions N/A N/A bin convert tsv to binary format N/A mask compute P-values based on meta and data N/A filterloci select subset of loci based on allele counts N/A filterdata select subset of data based on filtered loci N/A filtervcf filter lobSTR VCF N/A compilevcf compile vcf results into master spreadsheet N/A mergecsv combine csv into binary array N/A lobstrindex make lobSTR index N/A batchlobstr run batch lobSTR N/A lobstr run lobSTR on a big BAM N/A batchhtt run batch HTT caller N/A htt extract HTT region and run lobSTR N/A stutter extract info from lobSTR vcf file N/A liftover liftOver CODIS/Y-STR markers N/A trf run TRF on FASTA files N/A ystr print out Y-STR info given VCF N/A p N/A ActionDispatcher actions N/A N/A N/A p dispatch N/A globals N/A stutter N/A N/A args N/A N/A N/A 
    %prog stutter a.vcf.gzi sample_id

    Extract info from lobSTR vcf file. Generates a file that has the following
    fields:

    CHR, POS, MOTIF, RL, ALLREADS, Q
     N/A p N/A OptionParser N/A stutter __doc__ 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 vcf args N/A pf N/A N/A N/A N/A N/A op basename vcf split . N/A 0 N/A N/A execid sampleid N/A N/A pf split _ N/A C vcftools --remove-filtered-all --min-meanDP 10 N/A C N/A N/A  --gzvcf {} --out {} format vcf pf N/A C N/A N/A  --indv {} format sampleid N/A info N/A pf .INFO N/A N/A need_update vcf info N/A N/A cmd N/A C  --get-INFO MOTIF --get-INFO RL N/A N/A sh cmd N/A allreads N/A pf .ALLREADS.FORMAT N/A N/A need_update vcf allreads N/A N/A cmd N/A C  --extract-FORMAT-info ALLREADS N/A N/A sh cmd N/A q N/A pf .Q.FORMAT N/A N/A need_update vcf q N/A N/A cmd N/A C  --extract-FORMAT-info Q N/A N/A sh cmd N/A outfile N/A pf .STUTTER N/A N/A need_update N/A info allreads q outfile N/A N/A cmd N/A N/A cut -f1,2,5,6 {} format info N/A cmd  | sed -e 's/\t/_/g' N/A cmd N/A N/A  | paste - {} {} format allreads q N/A cmd  | cut -f1,4,7 N/A N/A sh cmd outfile outfile N/A write_filtered N/A N/A vcffile lhome store N/A None N/A N/A N/A N/A vcffile startswith s3:// N/A N/A vcffile N/A pull_from_s3 vcffile N/A filteredvcf N/A N/A N/A N/A op basename vcffile replace .vcf .filtered.vcf N/A cmd N/A N/A python {}/scripts/lobSTR_filter_vcf.py format lhome N/A cmd N/A N/A  --vcf {} format vcffile N/A cmd  --loc-cov 5 --loc-log-score 0.8 N/A N/A sh cmd outfile filteredvcf N/A store N/A N/A N/A push_to_s3 store filteredvcf N/A filteredvcf N/A run_filter N/A N/A arg N/A N/A N/A N/A vcffile lhome store arg N/A filteredvcf N/A N/A vcffile replace .vcf .filtered.vcf N/A N/A N/A N/A N/A vcffile startswith s3:// N/A N/A N/A check_exists_s3 filteredvcf N/A N/A N/A N/A logging debug N/A N/A {} exists. Skipped. format filteredvcf N/A N/A N/A write_filtered vcffile lhome store store N/A N/A N/A logging debug N/A N/A {} written and uploaded. format filteredvcf N/A N/A N/A need_update vcffile filteredvcf N/A N/A N/A write_filtered vcffile lhome store None N/A N/A N/A Exception N/A e N/A N/A N/A N/A logging debug N/A N/A Thread failed! Error: {} format e N/A filtervcf N/A N/A args N/A N/A N/A 
    %prog filtervcf NA12878.hg38.vcf.gz

    Filter lobSTR VCF using script shipped in lobSTR. Input file can be a list
    of vcf files.
     N/A p N/A OptionParser N/A filtervcf __doc__ N/A N/A N/A p set_home lobstr default /mnt/software/lobSTR N/A N/A N/A p set_aws_opts store hli-mv-data-science/htang/str N/A N/A N/A p set_cpus 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 samples args N/A lhome N/A opts lobstr_home N/A store N/A opts output_path N/A N/A N/A N/A samples endswith .vcf N/A N/A samples endswith .vcf.gz N/A N/A vcffiles N/A samples N/A N/A vcffiles N/A N/A N/A x strip N/A x N/A must_open samples N/A vcffiles N/A x N/A x vcffiles N/A .filtered. x N/A run_args N/A N/A x lhome N/A N/A N/A x startswith s3:// store N/A x vcffiles N/A cpus N/A min N/A opts cpus N/A len run_args N/A p N/A Pool processes cpus N/A res N/A N/A N/A N/A p map_async run_filter run_args get N/A N/A N/A mask N/A N/A args N/A N/A N/A 
    %prog mask meta.tsv data.bin samples.ids STR.ids

    Compute P-values based on meta and data. Write mask.bin and a new meta.tsv
    with updated counts.
     N/A p N/A OptionParser N/A mask __doc__ N/A N/A opts args N/A N/A p parse_args args N/A N/A N/A len args 4 N/A N/A N/A N/A sys exit N/A N/A N/A p print_help N/A N/A metafile databin sampleids strids args N/A N/A df m samples loci N/A read_binfile databin sampleids strids N/A sf N/A N/A pd read_csv metafile index_col 0 sep N/A N/A i locus N/A enumerate loci N/A N/A a N/A m N/A N/A N/A i N/A locus a N/A counts N/A alleles_to_counts a N/A p_counts N/A af_to_counts N/A N/A N/A sf ix N/A locus N/A allele_frequency N/A before: counts N/A N/A N/A counts update p_counts N/A af N/A counts_to_af counts N/A after: counts N/A N/A i 30 N/A N/A N/A alleles_to_counts N/A N/A a N/A N/A N/A counts N/A Counter N/A xa N/A a 1000 N/A xb N/A a 1000 N/A N/A N/A counts update xa N/A N/A N/A counts update xb N/A N/A counts N/A -1 N/A N/A counts N/A 999 N/A counts N/A counts_to_af N/A N/A counts N/A N/A N/A N/A N/A { N/A N/A , join N/A N/A N/A {}:{} format k v N/A N/A k v N/A sorted N/A N/A counts items } N/A af_to_counts N/A N/A af N/A N/A N/A countst N/A x N/A x N/A N/A N/A N/A af strip {} split , x N/A countsd N/A N/A x countst N/A N/A N/A a b N/A N/A x split : N/A N/A countsd N/A N/A int a N/A int b N/A countsd N/A bin N/A N/A args N/A N/A N/A 
    %prog bin data.tsv

    Conver tsv to binary format.
     N/A p N/A OptionParser N/A bin __doc__ N/A N/A N/A p add_option --dtype choices N/A float32 int32 help dtype of the matrix 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 tsvfile args N/A dtype N/A opts dtype N/A N/A dtype None N/A N/A dtype N/A N/A data tsvfile N/A np int32 N/A np float32 N/A N/A dtype N/A N/A dtype int32 N/A np int32 N/A np float32 N/A N/A sys stderr N/A N/A dtype: {} format dtype N/A fp N/A open tsvfile N/A N/A N/A fp next N/A arrays N/A N/A N/A i row N/A enumerate fp N/A N/A a N/A N/A np fromstring row sep dtype dtype N/A a N/A a N/A 1 N/A N/A N/A arrays append a N/A N/A sys stderr i a N/A N/A sys stderr Merging N/A b N/A N/A np concatenate arrays N/A N/A sys stderr N/A N/A Binary shape: {} format N/A b shape N/A binfile N/A N/A N/A N/A tsvfile rsplit . 1 N/A 0 .bin N/A N/A N/A b tofile binfile N/A counts_to_percentile N/A N/A counts N/A N/A N/A percentile N/A N/A s 0 N/A N/A k v N/A sorted N/A N/A counts items reverse True N/A N/A s v N/A N/A percentile N/A k s N/A N/A k v N/A N/A percentile items N/A N/A v N/A N/A {:.6f} format N/A N/A v 1.0 s N/A N/A percentile N/A k v N/A percentile N/A convert_to_percentile N/A N/A arg N/A N/A N/A N/A i a percentile arg N/A xb N/A a 1000 N/A pp N/A N/A np array N/A N/A N/A percentile get x 1.000000 N/A x xb dtype S8 N/A N/A N/A i 1000 0 N/A N/A N/A sys stderr i N/A N/A sys stderr xb N/A N/A sys stderr pp N/A N/A i pp N/A write_csv N/A N/A csvfile m index columns sep index_label N/A SampleKey N/A N/A fw N/A open csvfile w N/A fw N/A N/A join N/A N/A index_label columns N/A N/A i a N/A enumerate m N/A N/A fw N/A N/A N/A index N/A i N/A N/A join N/A N/A str x N/A x a N/A N/A N/A fw close N/A filterdata N/A N/A args N/A N/A N/A 
    %prog filterdata data.bin samples.ids STR.ids allele_freq remove.ids final.ids

    Filter subset of data after dropping remove.ids.
     N/A p N/A OptionParser N/A filterdata __doc__ N/A N/A N/A p set_cpus N/A N/A opts args N/A N/A p parse_args args N/A N/A N/A len args 6 N/A N/A N/A N/A sys exit N/A N/A N/A p print_help N/A N/A binfile sampleids strids af remove final args N/A N/A df m samples loci N/A read_binfile binfile sampleids strids N/A remove N/A N/A N/A x strip N/A x N/A open remove N/A removes N/A set remove N/A final N/A N/A N/A x strip N/A x N/A open final N/A N/A N/A len loci N/A N/A len remove N/A len final N/A fp N/A open af N/A percentiles N/A N/A row fp N/A N/A N/A sname counts N/A N/A row split N/A countsd N/A af_to_counts counts N/A percentile N/A counts_to_percentile countsd N/A N/A percentiles N/A sname percentile N/A run_args N/A N/A N/A i sname N/A enumerate loci N/A N/A N/A sname removes N/A N/A N/A a N/A m N/A N/A N/A i N/A percentile N/A percentiles N/A sname N/A N/A N/A run_args append N/A i a percentile N/A cpus N/A min N/A opts cpus N/A len run_args N/A p N/A Pool processes cpus N/A res N/A N/A r N/A N/A N/A N/A p map_async convert_to_percentile run_args get N/A N/A N/A N/A res append r N/A N/A N/A res sort N/A N/A ii pvalues N/A zip res N/A m N/A N/A N/A np vstack pvalues T N/A N/A write_csv final.mask.tsv m samples final N/A N/A N/A df drop remove inplace True axis 1 N/A N/A df columns final N/A filtered_bin filtered.bin N/A m N/A N/A df as_matrix N/A N/A m N/A N/A m 0 -1 N/A N/A N/A m tofile filtered_bin N/A N/A N/A logging debug N/A N/A Binary matrix written to `{}` format filtered_bin N/A N/A N/A df to_csv final.data.tsv sep index_label SampleKey N/A filterloci N/A N/A args N/A N/A N/A 
    %prog filterloci allele_freq STR-exons.wo.bed SAMPLES

    Filter subset of loci that satisfy:
    1. no redundancy (unique chr:pos)
    2. variable (n_alleles > 1)
    3. low level of missing data (>= 50% autosomal + X, > 25% for Y)

    Write meta file with the following infor:
    1. id
    2. title
    3. gene_name
    4. variant_type
    5. motif
    6. allele_frequency

    `STR-exons.wo.bed` can be generated like this:
    $ tail -n 854476 /mnt/software/lobSTR/hg38/index.tab | cut -f1-3 > all-STR.bed
    $ intersectBed -a all-STR.bed -b all-exons.bed -wo > STR-exons.wo.bed
     N/A p N/A OptionParser N/A filterloci __doc__ 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 af wobed samples args N/A nsamples N/A len N/A N/A N/A x strip N/A x N/A open samples N/A nalleles N/A nsamples 2 N/A N/A N/A logging debug N/A N/A Load {} samples ({} alleles) from `{}` format nsamples nalleles samples N/A N/A N/A logging debug N/A N/A Load gene intersections from `{}` format wobed N/A fp N/A open wobed N/A gene_map N/A defaultdict set N/A row fp N/A N/A N/A chr1 start1 end1 chr2 start2 end2 name ov N/A N/A row split N/A N/A gene_map N/A N/A chr1 start1 N/A set N/A N/A name split , N/A N/A k v N/A N/A gene_map items N/A N/A non_enst N/A sorted N/A x N/A x v N/A N/A N/A x startswith ENST N/A enst N/A sorted N/A N/A N/A N/A x rsplit . 1 N/A 0 N/A x v N/A N/A x startswith ENST N/A N/A gene_map N/A k N/A N/A , join N/A non_enst enst N/A N/A N/A logging debug N/A N/A Filtering loci from `{}` format af N/A fp N/A open af N/A seen N/A set TREDS N/A remove N/A N/A fw N/A open meta.tsv w N/A header N/A N/A id title gene_name variant_type motif allele_frequency replace N/A fw header N/A variant_type short tandem repeats N/A title Short tandem repeats ({})n N/A row fp N/A N/A N/A sname counts N/A N/A row split N/A name N/A N/A N/A sname rsplit _ 1 N/A 0 N/A N/A seqid pos motif N/A N/A name split _ N/A countst N/A x N/A x N/A N/A N/A N/A counts strip {} split , x N/A countsd N/A N/A x countst N/A N/A N/A a b N/A N/A x split : N/A N/A countsd N/A N/A int a N/A int b N/A N/A counts_filter countsd nalleles seqid N/A N/A N/A N/A remove append sname N/A N/A N/A name seen N/A N/A N/A N/A remove append sname N/A N/A N/A N/A seen add name N/A gene_name N/A N/A gene_map get N/A seqid pos N/A fw N/A N/A join N/A name N/A N/A title format motif gene_name variant_type motif counts N/A N/A N/A fw close N/A removeidsfile remove.ids N/A fw N/A open removeidsfile w N/A fw N/A N/A join remove N/A N/A N/A fw close N/A N/A N/A logging debug N/A N/A A total of {} filtered loci written to `{}` format N/A len remove removeidsfile N/A counts_filter N/A N/A countsd nalleles seqid N/A N/A N/A N/A N/A len countsd 2 N/A N/A True N/A observed N/A sum N/A N/A countsd values N/A observed_pct N/A N/A observed 100 nalleles N/A N/A observed_pct 50 N/A N/A N/A N/A N/A seqid chrY N/A observed_pct 25 N/A N/A True N/A read_binfile N/A N/A binfile sampleids strids dtype N/A N/A np int32 N/A N/A m N/A N/A np fromfile binfile dtype dtype N/A samples N/A N/A N/A x strip N/A x N/A open sampleids N/A loci N/A N/A N/A x strip N/A x N/A open strids N/A N/A nsamples nloci N/A N/A len samples N/A len loci N/A N/A sys stderr N/A N/A {} x {} entries imported format nsamples nloci N/A N/A N/A m resize nsamples nloci N/A df N/A N/A pd DataFrame m index samples columns loci N/A N/A df m samples loci N/A mergecsv N/A N/A args N/A N/A N/A 
    %prog mergecsv *.csv

    Combine CSV into binary array.
     N/A p N/A OptionParser N/A mergecsv __doc__ 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 csvfiles args N/A arrays N/A N/A samplekeys N/A N/A csvfile csvfiles N/A N/A samplekey N/A N/A N/A N/A N/A op basename csvfile split . N/A 0 N/A a N/A N/A np fromfile csvfile sep , dtype N/A np int32 N/A x1 N/A a N/A 2 N/A x2 N/A a N/A 1 2 N/A a N/A N/A x1 1000 x2 N/A N/A a N/A N/A a 0 -1 N/A N/A N/A arrays append a N/A N/A N/A samplekeys append samplekey N/A N/A sys stderr samplekey a N/A N/A sys stderr Merging N/A b N/A N/A np concatenate arrays N/A N/A N/A b tofile data.bin N/A fw N/A open samples w N/A fw N/A N/A join samplekeys N/A N/A N/A fw close N/A write_csv_ev N/A N/A filename filtered cleanup store stutter N/A None False N/A N/A lv N/A LobSTRvcf N/A N/A N/A lv parse filename filtered filtered cleanup cleanup stutter stutter N/A csvfile N/A N/A N/A op basename filename .csv N/A evfile N/A N/A N/A op basename filename .ev N/A stutter N/A N/A fw N/A open evfile w N/A fw N/A lv evline N/A N/A N/A fw close N/A N/A fw N/A open csvfile w N/A fw N/A lv csvline N/A N/A N/A fw close N/A fw N/A open evfile w N/A fw N/A lv evline N/A N/A N/A fw close N/A store N/A N/A N/A push_to_s3 store csvfile N/A N/A push_to_s3 store evfile N/A run_compile N/A N/A arg N/A N/A N/A N/A filename filtered cleanup store stutter arg N/A csvfile N/A filename .csv N/A N/A N/A N/A N/A filename startswith s3:// N/A N/A N/A check_exists_s3 csvfile N/A N/A N/A N/A logging debug N/A N/A {} exists. Skipped. format csvfile N/A N/A N/A write_csv_ev filename filtered cleanup store store stutter stutter N/A N/A N/A logging debug N/A N/A {} written and uploaded. format csvfile N/A N/A N/A need_update filename csvfile N/A N/A N/A write_csv_ev filename filtered cleanup store None stutter stutter N/A N/A N/A Exception N/A e N/A N/A N/A N/A logging debug N/A N/A Thread failed! Error: {} format e N/A compilevcf N/A N/A args N/A N/A N/A 
    %prog compilevcf samples.csv

    Compile vcf results into master spreadsheet.
     N/A p N/A OptionParser N/A compilevcf __doc__ N/A N/A N/A p add_option --db default hg38 help Use these lobSTR db N/A N/A N/A p add_option --stutter default False action store_true help Count stutter reads on chrY N/A N/A N/A p add_option --nofilter default False action store_true help Do not filter the variants N/A N/A N/A p set_home lobstr N/A N/A N/A p set_cpus N/A N/A N/A p set_aws_opts store hli-mv-data-science/htang/str-data 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 samples args N/A workdir N/A opts workdir N/A store N/A opts output_path N/A stutter N/A opts stutter N/A cleanup N/A N/A opts nocleanup N/A filtered N/A N/A opts nofilter N/A dbs N/A N/A N/A opts db split , N/A cwd N/A N/A os getcwd N/A N/A mkdir workdir N/A N/A N/A os chdir workdir N/A samples N/A N/A op join cwd samples N/A stridsfile STR.ids N/A vcffiles N/A N/A N/A x strip N/A x N/A must_open samples N/A N/A N/A N/A op exists stridsfile N/A N/A ids N/A N/A db dbs N/A N/A N/A N/A ids extend N/A N/A STRFile N/A opts lobstr_home db db ids N/A uids N/A uniqify ids N/A N/A N/A logging debug N/A N/A Combined: {} Unique: {} format N/A len ids N/A len uids N/A fw N/A open stridsfile w N/A fw N/A N/A join uids N/A N/A N/A fw close N/A run_args N/A N/A x filtered cleanup store stutter N/A x vcffiles N/A cpus N/A min N/A opts cpus N/A len run_args N/A p N/A Pool processes cpus N/A res N/A N/A N/A N/A p map_async run_compile run_args get N/A N/A N/A build_ysearch_link N/A N/A r ban N/A N/A DYS520 DYS413a DYS413b N/A N/A template http://www.ysearch.org/search_search.asp?fail=2&uid=&freeentry=true& N/A markers N/A N/A N/A i marker N/A zip YSEARCH_LL YSEARCH_HAPLOTYPE N/A N/A z N/A N/A r get marker null N/A N/A N/A a/b marker N/A marker ban N/A N/A z null N/A m N/A N/A {0}={1} format i z N/A N/A N/A markers append m N/A N/A template N/A N/A & join markers N/A build_yhrd_link N/A N/A r panel ban N/A N/A DYS385 N/A N/A L N/A N/A marker panel N/A N/A z N/A N/A r get marker -- N/A N/A marker ban N/A N/A z -- N/A N/A N/A L append z N/A N/A N/A join N/A N/A str x N/A x L N/A ystr N/A N/A args N/A N/A N/A 
    %prog ystr chrY.vcf

    Print out Y-STR info given VCF. Marker name extracted from tabfile.
     jcvi.utils.table write_csv N/A p N/A OptionParser N/A ystr __doc__ N/A N/A N/A p set_home lobstr 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 vcffile args N/A si N/A STRFile N/A opts lobstr_home db hg38-named N/A register N/A si register N/A header N/A N/A Marker|Reads|Ref|Genotype|Motif split | N/A contents N/A N/A fp N/A must_open vcffile N/A reader N/A N/A vcf Reader fp N/A simple_register N/A N/A record reader N/A N/A name N/A register N/A N/A N/A record CHROM N/A record POS N/A info N/A record INFO N/A ref N/A int N/A float N/A info N/A REF N/A rpa N/A N/A info get RPA ref N/A N/A isinstance rpa list N/A N/A rpa N/A N/A | join N/A N/A str N/A int N/A float x N/A x rpa N/A ru N/A info N/A RU N/A N/A simple_register N/A name rpa N/A sample N/A record samples N/A N/A N/A N/A contents append N/A name N/A sample N/A ALLREADS ref rpa ru N/A N/A a b c N/A DYS389I DYS389B.1 DYS389B N/A N/A N/A a simple_register N/A b simple_register N/A N/A N/A simple_register N/A c N/A N/A int N/A simple_register N/A a N/A int N/A simple_register N/A b N/A mm N/A DYS385 DYS413 YCAII N/A m mm N/A N/A N/A ma mb N/A N/A m a N/A m b N/A N/A N/A ma simple_register N/A mb simple_register N/A N/A N/A simple_register N/A ma N/A simple_register N/A mb None N/A N/A simple_register N/A ma N/A N/A simple_register N/A mb N/A N/A N/A N/A simple_register N/A ma N/A simple_register N/A mb N/A N/A N/A N/A simple_register N/A ma N/A simple_register N/A mb N/A N/A simple_register N/A mb N/A simple_register N/A ma N/A N/A write_csv header contents sep N/A [YSEARCH] N/A N/A build_ysearch_link simple_register N/A [YFILER] N/A N/A build_yhrd_link simple_register panel YHRD_YFILER N/A [YFILERPLUS] N/A N/A build_yhrd_link simple_register panel YHRD_YFILERPLUS N/A [YSTR-ALL] N/A N/A build_yhrd_link simple_register panel USYSTR_ALL N/A get_motif N/A N/A s motif_length N/A N/A N/A sl N/A len s N/A kmers N/A set N/A i N/A xrange N/A sl motif_length N/A N/A ss N/A s N/A i N/A i motif_length N/A N/A N/A kmers add ss N/A kmer_counts N/A N/A kmer kmers N/A N/A N/A N/A kmer_counts append N/A N/A N/A s count kmer N/A N/A N/A s index kmer kmer N/A N/A N/A N/A sorted kmer_counts reverse True N/A 0 N/A -1 N/A liftover N/A N/A args N/A N/A N/A 
    %prog liftover lobstr_v3.0.2_hg38_ref.bed hg38.upper.fa

    LiftOver CODIS/Y-STR markers.
     N/A p N/A OptionParser N/A liftover __doc__ N/A N/A N/A p add_option --checkvalid default False action store_true help Check minscore, period and length 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 refbed fastafile args N/A genome N/A N/A pyfasta Fasta fastafile N/A edits N/A N/A fp N/A open refbed N/A N/A i row N/A enumerate fp N/A N/A s N/A STRLine row N/A seq N/A N/A N/A N/A genome N/A N/A s seqid N/A N/A N/A s start 1 N/A s end upper N/A N/A s motif N/A get_motif seq N/A len N/A s motif N/A N/A N/A s fix_counts seq N/A N/A N/A opts checkvalid N/A N/A N/A s is_valid N/A N/A N/A N/A N/A edits append s N/A N/A N/A i 10000 0 N/A N/A N/A sys stderr i lines read N/A edits N/A natsorted edits key N/A N/A N/A x N/A N/A N/A x seqid N/A x start N/A e edits N/A N/A N/A str e N/A trf N/A N/A args N/A N/A N/A 
    %prog trf outdir

    Run TRF on FASTA files.
     jcvi.apps.base iglob N/A p N/A OptionParser N/A trf __doc__ N/A N/A N/A p add_option --mismatch default 31 type int help Mismatch and gap penalty N/A N/A N/A p add_option --minscore default MINSCORE type int help Minimum score to report N/A N/A N/A p add_option --period default 6 type int help Maximum period to report N/A N/A N/A p add_option --minlength default N/A MINSCORE 2 type int help Minimum length of repeat tract N/A N/A N/A p add_option --telomeres default False action store_true help Run telomere search: minscore=140 period=7 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 outdir args N/A minlength N/A opts minlength N/A mm N/A MakeManager N/A N/A opts telomeres N/A N/A N/A N/A opts minscore N/A opts period N/A 140 7 N/A params N/A N/A N/A N/A 2 {0} {0} 80 10 {1} {2} format N/A opts mismatch N/A opts minscore N/A opts period split N/A bedfiles N/A N/A fastafile N/A natsorted N/A iglob outdir *.fa,*.fasta N/A N/A pf N/A N/A N/A N/A N/A op basename fastafile split . N/A 0 N/A cmd1 N/A N/A trf {0} {1} -d -h format fastafile N/A N/A join params N/A datfile N/A N/A N/A N/A N/A op basename fastafile . N/A N/A . join params .dat N/A bedfile N/A N/A {0}.trf.bed format pf N/A cmd2 N/A N/A cat {} | awk '($8 >= {} && $8 <= {})' format datfile minlength N/A READLEN minlength N/A cmd2  | sed 's/ /\t/g' N/A cmd2 N/A N/A  | awk '{{print "{0}\t" $0}}' > {1} format pf bedfile N/A N/A N/A mm add fastafile datfile cmd1 N/A N/A N/A mm add datfile bedfile cmd2 N/A N/A N/A bedfiles append bedfile N/A bedfile trf.bed N/A cmd N/A N/A cat {0} > {1} format N/A N/A join N/A natsorted bedfiles bedfile N/A N/A N/A mm add bedfiles bedfile cmd N/A N/A N/A mm write N/A batchlobstr N/A N/A args N/A N/A N/A 
    %prog batchlobstr samples.csv

    Run lobSTR sequentially on list of samples. Each line contains:
    sample-name,s3-location
     N/A p N/A OptionParser N/A batchlobstr __doc__ N/A N/A N/A p add_option --sep default , help Separator for building commandline N/A N/A N/A p set_home lobstr default s3://hli-mv-data-science/htang/str-build/lobSTR/ N/A N/A N/A p set_aws_opts store hli-mv-data-science/htang/str-data 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 samplesfile args N/A store N/A opts output_path N/A computed N/A ls_s3 store N/A fp N/A open samplesfile N/A skipped total 0 N/A row fp N/A N/A total 1 N/A N/A sample s3file N/A N/A N/A N/A N/A row strip split , N/A 2 N/A N/A exec_id sample_id N/A N/A sample split _ N/A bamfile N/A N/A N/A N/A s3file replace .gz replace .vcf .bam N/A gzfile N/A sample N/A N/A .{0}.vcf.gz format hg38 N/A N/A gzfile computed N/A N/A skipped 1 N/A N/A N/A N/A N/A opts sep join N/A N/A N/A python -m jcvi.variation.str lobstr split N/A hg38 --input_bam_path bamfile --output_path store --sample_id sample_id --workflow_execution_id exec_id --lobstr_home N/A opts lobstr_home --workdir N/A opts workdir N/A N/A N/A fp close N/A N/A N/A logging debug N/A N/A Total skipped: {0} format N/A percentage skipped total N/A lobstr N/A N/A args N/A N/A N/A 
    %prog lobstr lobstr_index1 lobstr_index2 ...

    Run lobSTR on a big BAM file. There can be multiple lobSTR indices. In
    addition, bamfile can be S3 location and --lobstr_home can be S3 location
    (e.g. s3://hli-mv-data-science/htang/str-build/lobSTR/)
     N/A p N/A OptionParser N/A lobstr __doc__ N/A N/A N/A p add_option --chr help Run only this chromosome N/A N/A N/A p set_home lobstr default s3://hli-mv-data-science/htang/str-build/lobSTR/ N/A N/A N/A p set_cpus N/A N/A N/A p set_aws_opts store hli-mv-data-science/htang/str-data N/A N/A opts args N/A N/A p parse_args args N/A bamfile N/A opts input_bam_path N/A N/A N/A N/A len args 1 N/A bamfile None N/A N/A N/A N/A sys exit N/A N/A N/A p print_help N/A lbindices args N/A s3mode N/A N/A bamfile startswith s3 N/A store N/A opts output_path N/A cleanup N/A N/A opts nocleanup N/A workdir N/A opts workdir N/A N/A mkdir workdir N/A N/A N/A os chdir workdir N/A lhome N/A opts lobstr_home N/A N/A N/A lhome startswith s3:// N/A N/A lhome N/A pull_from_s3 lhome overwrite False N/A N/A exec_id sample_id N/A N/A opts workflow_execution_id N/A opts sample_id N/A prefix N/A x N/A x N/A exec_id sample_id x N/A prefix N/A N/A pf N/A N/A _ join prefix N/A N/A pf N/A N/A N/A N/A N/A N/A bamfile split / N/A -1 split . N/A 0 N/A s3mode N/A N/A gzfile N/A pf N/A N/A .{0}.vcf.gz format N/A lbindices N/A -1 N/A remotegzfile N/A N/A {0}/{1} format store gzfile N/A N/A check_exists_s3 remotegzfile N/A N/A N/A N/A logging debug N/A N/A Object `{0}` exists. Computation skipped. format remotegzfile N/A N/A localbamfile N/A pf .bam N/A localbaifile N/A localbamfile .bai N/A N/A N/A op exists localbamfile N/A N/A N/A N/A logging debug BAM file already downloaded. N/A N/A N/A pull_from_s3 bamfile localbamfile N/A N/A N/A op exists localbaifile N/A N/A N/A N/A logging debug BAM index file already downloaded. N/A N/A remotebaifile N/A bamfile .bai N/A N/A check_exists_s3 remotebaifile N/A N/A N/A pull_from_s3 remotebaifile localbaifile N/A N/A remotebaifile N/A N/A N/A N/A bamfile rsplit . N/A 0 .bai N/A N/A check_exists_s3 remotebaifile N/A N/A N/A pull_from_s3 remotebaifile localbaifile N/A N/A N/A N/A logging debug BAM index cannot be found in S3! N/A N/A sh N/A N/A samtools index {0} format localbamfile N/A bamfile localbamfile N/A chrs N/A N/A opts chr N/A N/A opts chr N/A N/A range 1 23 N/A X Y N/A lbidx lbindices N/A N/A makefile N/A N/A makefile.{0} format lbidx N/A mm N/A MakeManager filename makefile N/A vcffiles N/A N/A chr chrs N/A N/A N/A cmd vcffile N/A allelotype_on_chr bamfile chr lhome lbidx N/A N/A N/A mm add bamfile vcffile cmd N/A filteredvcffile N/A N/A vcffile replace .vcf .filtered.vcf N/A cmd N/A N/A python -m jcvi.variation.str filtervcf {} format vcffile N/A cmd N/A N/A  --lobstr_home {} format lhome N/A N/A N/A mm add vcffile filteredvcffile cmd N/A N/A N/A vcffiles append filteredvcffile N/A gzfile N/A N/A N/A N/A bamfile split . N/A 0 N/A N/A .{0}.vcf.gz format lbidx N/A cmd N/A N/A vcf-concat {0} | vcf-sort format N/A N/A join vcffiles N/A cmd N/A N/A  | bgzip -c > {0} format gzfile N/A N/A N/A mm add vcffiles gzfile cmd N/A N/A N/A mm run cpus N/A opts cpus N/A s3mode N/A N/A N/A push_to_s3 store gzfile N/A cleanup N/A N/A N/A N/A mm clean N/A N/A sh N/A N/A rm -f {} {} *.bai *.stats format bamfile N/A mm makefile N/A allelotype_on_chr N/A N/A bamfile chr lhome lbidx N/A N/A N/A outfile N/A N/A {0}.chr{1} format N/A N/A N/A bamfile split . N/A 0 chr N/A cmd N/A N/A allelotype --command classify --bam {} format bamfile N/A cmd N/A N/A  --noise_model {0}/models/illumina_v3.pcrfree format lhome N/A cmd N/A N/A  --strinfo {0}/{1}/index.tab format lhome lbidx N/A cmd N/A N/A  --index-prefix {0}/{1}/lobSTR_ format lhome lbidx N/A cmd N/A N/A  --chrom chr{0} --out {1}.{2} format chr outfile lbidx N/A cmd N/A N/A  --max-diff-ref {0} format READLEN N/A cmd  --realign N/A cmd  --haploid chrY N/A N/A cmd N/A N/A . join N/A outfile lbidx vcf N/A batchhtt N/A N/A args N/A N/A N/A 
    %prog htt samples.csv chr4:3070000-3080000

    Batch HTT caller. The samples are:
    SampleId,ExecID,Norm VCF,gVCF,BAM
     N/A p N/A OptionParser N/A batchhtt __doc__ 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 samplesfile region args N/A fp N/A open samplesfile N/A N/A N/A fp next N/A row fp N/A N/A N/A sample ex vcf gvcf bam N/A N/A N/A N/A row strip split , N/A N/A htt N/A bam region N/A N/A N/A fp close N/A htt N/A N/A args N/A N/A N/A 
    %prog htt bamfile chr4:3070000-3080000

    Extract HTT region and run lobSTR.
     jcvi.formats.sam get_minibam N/A p N/A OptionParser N/A htt __doc__ N/A N/A N/A p set_home lobstr 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 bamfile region args N/A lhome N/A opts lobstr_home N/A minibamfile N/A get_minibam bamfile region N/A c N/A N/A N/A N/A N/A region split : N/A 0 replace chr N/A N/A cmd vcf N/A allelotype_on_chr minibamfile c lhome hg38 N/A N/A sh cmd N/A lobstrindex N/A N/A args N/A N/A N/A 
    %prog lobstrindex hg38.trf.bed hg38.upper.fa

    Make lobSTR index. Make sure the FASTA contain only upper case (so use
    fasta.format --upper to convert from UCSC fasta). The bed file is generated
    by str().
     N/A p N/A OptionParser N/A lobstrindex __doc__ N/A N/A N/A p add_option --notreds default False action store_true help Remove TREDs from the bed file N/A N/A N/A p set_home lobstr 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 trfbed fastafile args N/A pf N/A N/A N/A fastafile split . N/A 0 N/A lhome N/A opts lobstr_home N/A N/A mkdir pf N/A N/A opts notreds N/A N/A newbedfile N/A trfbed .new N/A newbed N/A open newbedfile w N/A fp N/A open trfbed N/A retained total 0 N/A seen N/A set N/A row fp N/A N/A r N/A STRLine row N/A total 1 N/A name N/A r longname N/A N/A name seen N/A N/A N/A N/A N/A seen add name N/A newbed r N/A retained 1 N/A N/A N/A newbed close N/A N/A N/A logging debug N/A N/A Retained: {0} format N/A percentage retained total N/A N/A newbedfile trfbed N/A mm N/A MakeManager N/A cmd N/A N/A python {0}/scripts/lobstr_index.py format lhome N/A cmd N/A N/A  --str {0} --ref {1} --out {2} format newbedfile fastafile pf N/A N/A N/A mm add N/A newbedfile fastafile N/A N/A op join pf lobSTR_ref.fasta.rsa cmd N/A tabfile N/A N/A {0}/index.tab format pf N/A cmd N/A N/A python {0}/scripts/GetSTRInfo.py format lhome N/A cmd N/A N/A  {0} {1} > {2} format newbedfile fastafile tabfile N/A N/A N/A mm add N/A newbedfile fastafile tabfile cmd N/A infofile N/A N/A {0}/index.info format pf N/A cmd N/A N/A cp {0} {1} format newbedfile infofile N/A N/A N/A mm add trfbed infofile cmd N/A N/A N/A mm write N/A N/A N/A __name__ __main__ N/A N/A N/A main