Module Expr Str Import alias Import alias ImportFrom alias ImportFrom alias alias alias alias ImportFrom alias alias ImportFrom alias ImportFrom alias ImportFrom alias alias alias Assign NameStore Str ClassDef bases NameLoad NameLoad body FunctionDef arguments args NameParam NameParam defaults body Expr Call AttributeLoad Call NameLoad NameLoad NameLoad attr NameLoad Assign NameStore Call NameLoad NameLoad For TupleStore NameStore NameStore Call NameLoad NameLoad Str body Assign NameStore SubscriptLoad Call AttributeLoad NameLoad attr Index Num Assign SubscriptStore NameLoad Index NameLoad ListLoad For NameStore NameLoad body If BoolOpOr CompareEq Call AttributeLoad NameLoad attr Str CompareEq SubscriptLoad NameLoad Index Num Str body Continue Assign TupleStore NameStore NameStore Call AttributeLoad NameLoad attr Assign NameStore Call NameLoad BinOpMult Call NameLoad NameLoad Num Expr Call AttributeLoad SubscriptLoad NameLoad Index NameLoad attr TupleLoad NameLoad NameLoad decorator_list FunctionDef arguments args NameParam NameParam NameParam defaults Str NameLoad body Assign NameStore Call NameLoad NameLoad Str For TupleStore NameStore NameStore Call NameLoad Call AttributeLoad NameLoad attr body For TupleStore NameStore NameStore NameLoad body If UnaryOpNot NameLoad body Assign NameStore TupleLoad NameLoad NameLoad BinOpAdd NameLoad Num NameLoad orelse Assign TupleStore NameStore NameStore Call AttributeLoad NameLoad attr Str Assign NameStore Call NameLoad NameLoad Assign NameStore Call AttributeLoad Str attr NameLoad BinOpDiv NameLoad Num Assign NameStore TupleLoad NameLoad BinOpSub NameLoad Num NameLoad NameLoad Print NameLoad Call AttributeLoad Str attr GeneratorExp Call NameLoad NameLoad comprehension NameStore NameLoad Expr Call AttributeLoad NameLoad attr decorator_list decorator_list ClassDef bases NameLoad body FunctionDef arguments args NameParam NameParam NameParam defaults Num body Assign NameStore Call AttributeLoad NameLoad attr Assign AttributeStore NameLoad attr SubscriptLoad NameLoad Index Num Assign TupleStore AttributeStore NameLoad attr NameStore Call AttributeLoad AttributeLoad NameLoad attr attr Str Assign AttributeStore NameLoad attr Call NameLoad NameLoad Assign AttributeStore NameLoad attr Call AttributeLoad Str attr SubscriptLoad NameLoad Slice NameLoad decorator_list FunctionDef arguments args NameParam defaults body Return Call NameLoad AttributeLoad NameLoad attr decorator_list FunctionDef arguments args NameParam defaults body Return Call AttributeLoad Str attr AttributeLoad NameLoad attr AttributeLoad NameLoad attr 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 decorator_list NameLoad decorator_list ClassDef bases NameLoad body FunctionDef arguments args NameParam NameParam defaults body Expr Call AttributeLoad Call NameLoad NameLoad NameLoad attr NameLoad Assign NameStore Call NameLoad NameLoad Assign NameStore Num For NameStore NameLoad body If Call AttributeLoad NameLoad attr Str body If CompareEq SubscriptLoad Call AttributeLoad NameLoad attr Index Num Str body Assign NameStore Num Assign AttributeStore NameLoad attr Call AttributeLoad NameLoad attr Break For NameStore NameLoad body Expr Call AttributeLoad NameLoad attr Call NameLoad NameLoad keyword NameLoad Assign AttributeStore NameLoad attr Call NameLoad NameLoad Assign AttributeStore NameLoad attr Call NameLoad AttributeLoad SubscriptLoad NameLoad Index Num attr Expr Call AttributeLoad NameLoad attr Call AttributeLoad Str attr AttributeLoad NameLoad attr AttributeLoad NameLoad attr decorator_list decorator_list ClassDef bases NameLoad body FunctionDef arguments args NameParam NameParam NameParam NameParam NameParam defaults body Assign AttributeStore NameLoad attr NameLoad Assign AttributeStore NameLoad attr NameLoad Assign AttributeStore NameLoad attr NameLoad Assign AttributeStore NameLoad attr NameLoad Assign AttributeStore NameLoad attr Call NameLoad NameLoad Assign AttributeStore NameLoad attr BinOpSub Call NameLoad NameLoad Num Assert CompareEq AttributeLoad NameLoad attr BinOpSub Call NameLoad SubscriptLoad NameLoad Index Num Num Expr Call AttributeLoad NameLoad attr Call AttributeLoad Str attr AttributeLoad NameLoad attr AttributeLoad NameLoad attr decorator_list FunctionDef arguments args NameParam NameParam NameParam defaults Str NameLoad body Assign NameStore Call NameLoad NameLoad Str If NameLoad body Print NameLoad Call AttributeLoad NameLoad attr AttributeLoad NameLoad attr AttributeLoad NameLoad attr AttributeLoad NameLoad attr AttributeLoad NameLoad attr Print NameLoad Call AttributeLoad Str attr AttributeLoad NameLoad attr For NameStore AttributeLoad NameLoad attr body Print NameLoad Call AttributeLoad Str attr NameLoad decorator_list 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 Assign NameStore Call NameLoad NameLoad Expr Call AttributeLoad NameLoad attr Call NameLoad decorator_list FunctionDef arguments args NameParam NameParam defaults body Assert CompareEq Call NameLoad NameLoad Call NameLoad NameLoad Call AttributeLoad Str attr NameLoad NameLoad Assign NameStore Call NameLoad Call NameLoad NameLoad NameLoad Assign NameStore SubscriptLoad NameLoad Index TupleLoad Str Str Assign NameStore SubscriptLoad NameLoad Index TupleLoad Str Str Assign NameStore SubscriptLoad NameLoad Index TupleLoad Str Str Assign NameStore SubscriptLoad NameLoad Index TupleLoad Str Str Assign NameStore BinOpAdd BinOpAdd BinOpAdd NameLoad NameLoad NameLoad NameLoad If CompareEq NameLoad Num body Return Num Assign NameStore BinOpDiv Num NameLoad Assign NameStore BinOpMult NameLoad NameLoad Assign NameStore BinOpMult NameLoad NameLoad Assign NameStore BinOpMult NameLoad NameLoad Assign NameStore BinOpMult NameLoad NameLoad Assign NameStore BinOpAdd NameLoad NameLoad Assign NameStore BinOpAdd NameLoad NameLoad Assign NameStore BinOpAdd NameLoad NameLoad Assign NameStore BinOpAdd NameLoad NameLoad Assign NameStore BinOpSub NameLoad BinOpMult NameLoad NameLoad Assign NameStore BinOpMult BinOpMult BinOpMult NameLoad NameLoad NameLoad NameLoad If CompareEq NameLoad Num body Return Num Assign NameStore BinOpDiv BinOpMult NameLoad NameLoad NameLoad Return NameLoad decorator_list NameLoad FunctionDef arguments args NameParam defaults body Expr Str Import alias identifier ImportFrom alias ImportFrom alias Assign NameStore Call NameLoad AttributeLoad NameLoad attr 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 NameLoad Assign NameStore AttributeLoad NameLoad attr Assign NameStore Call NameLoad NameLoad Assign NameStore BinOpAdd NameLoad Str Assign NameStore BinOpAdd NameLoad Str If CompareLt NameLoad AttributeLoad NameLoad attr body Assign NameStore ListComp SubscriptLoad NameLoad Index NameLoad comprehension NameStore Call NameLoad Call NameLoad Call NameLoad Call NameLoad NameLoad NameLoad orelse Expr Call AttributeLoad NameLoad attr Str Assign NameStore Call NameLoad NameLoad If Call NameLoad NameLoad TupleLoad NameLoad NameLoad body Assign NameStore Call NameLoad NameLoad Str Print NameLoad Call AttributeLoad Str attr GeneratorExp AttributeLoad NameLoad attr comprehension NameStore NameLoad Expr Call AttributeLoad NameLoad attr Call AttributeLoad Str attr NameLoad NameLoad Expr Call AttributeLoad NameLoad attr Assign NameStore Call AttributeLoad NameLoad attr TupleLoad NameLoad NameLoad keyword NameLoad For TupleStore NameStore NameStore Call NameLoad Call NameLoad NameLoad Num body Assign NameStore SubscriptLoad NameLoad Index NameLoad Assign NameStore SubscriptLoad NameLoad Index NameLoad Assign SubscriptStore NameLoad Index TupleLoad NameLoad NameLoad Call NameLoad AttributeLoad NameLoad attr AttributeLoad NameLoad attr Assign NameStore Call NameLoad NameLoad Expr Call AttributeLoad NameLoad attr Call AttributeLoad Str attr NameLoad Expr Call AttributeLoad NameLoad attr NameLoad orelse Assign NameStore Call NameLoad Call NameLoad NameLoad Assign NameStore Call AttributeLoad Call AttributeLoad NameLoad attr NameLoad keyword Str attr NameLoad NameLoad Expr Call AttributeLoad NameLoad attr Call AttributeLoad Str attr NameLoad NameLoad ImportFrom alias alias alias alias Assign SubscriptStore AttributeLoad NameLoad attr Index Str Num 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 AttributeLoad NameLoad attr ListLoad Num Num Num Num Expr Call AttributeLoad NameLoad attr NameLoad keyword AttributeLoad NameLoad attr Assign NameStore Call NameLoad NameLoad Assign NameStore Call NameLoad NameLoad Assign NameStore TupleLoad Num NameLoad Assign NameStore ListLoad Assign NameStore Num For TupleStore NameStore NameStore NameStore Call AttributeLoad NameLoad attr body Assign NameStore CompareLt Call NameLoad BinOpSub NameLoad NameLoad NameLoad Assign NameStore BinOpDiv BinOpAdd NameLoad NameLoad Num Expr Call AttributeLoad NameLoad attr TupleLoad NameLoad NameLoad NameLoad If NameLoad body Continue Expr Call AttributeLoad NameLoad attr TupleLoad NameLoad NameLoad NameLoad Str keyword Num Expr Call AttributeLoad NameLoad attr NameLoad TupleLoad NameLoad NameLoad Str keyword Num For TupleStore NameStore NameStore NameStore NameLoad body Assign NameStore BinOpAdd Num BinOpDiv BinOpMult NameLoad Num NameLoad If UnaryOpNot NameLoad body Expr Call AttributeLoad NameLoad attr NameLoad Num NameLoad keyword Str keyword Str keyword Num keyword Str Expr Call AttributeLoad NameLoad attr Num NameLoad NameLoad keyword Str keyword Str keyword Str Expr Call AttributeLoad NameLoad attr NameLoad Expr Call AttributeLoad NameLoad attr NameLoad Expr Call AttributeLoad NameLoad attr Expr Call NameLoad NameLoad Str Num Num keyword AttributeLoad NameLoad attr Expr Call AttributeLoad NameLoad attr Call NameLoad TupleLoad Num Num Num Num keyword NameLoad keyword Str keyword Num Assign NameStore SubscriptLoad Call AttributeLoad NameLoad attr Str Index Num Expr Call AttributeLoad NameLoad attr Num Num Call AttributeLoad Str attr NameLoad keyword Str Expr Call AttributeLoad NameLoad attr Num Num Expr Call AttributeLoad NameLoad attr Num Num Expr Call AttributeLoad NameLoad attr Assign NameStore BinOpAdd BinOpAdd BinOpAdd NameLoad Str Str AttributeLoad NameLoad attr Expr Call NameLoad NameLoad keyword AttributeLoad NameLoad attr keyword 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 Str keyword Str Expr Call AttributeLoad NameLoad attr 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 NameLoad NameLoad Assign NameStore AttributeLoad NameLoad attr Assign NameStore Call NameLoad NameLoad Assign NameStore ListComp BinOpAdd AttributeLoad NameLoad attr Call AttributeLoad NameLoad attr NameLoad NameLoad comprehension NameStore NameLoad Print Call AttributeLoad Str attr NameLoad Print Str Print Call AttributeLoad Str attr NameLoad Assign NameStore AttributeLoad NameLoad attr If NameLoad body Assign NameStore Call NameLoad NameLoad Str Print NameLoad Call AttributeLoad Str attr 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 NameLoad Assign NameStore Call NameLoad NameLoad Assign NameStore AttributeLoad NameLoad attr Assign NameStore Call NameLoad NameLoad Assign NameStore AttributeLoad NameLoad attr Assign NameStore BinOpAdd BinOpAdd ListLoad SubscriptLoad NameLoad Index Num ListLoad Str Str SubscriptLoad NameLoad Slice Num Assign NameStore ListLoad For NameStore NameLoad body Assign TupleStore NameStore NameStore TupleLoad AttributeLoad NameLoad attr AttributeLoad NameLoad attr Assign NameStore NameLoad If CompareNotIn NameLoad NameLoad body Assign NameStore SubscriptLoad Call AttributeLoad NameLoad attr Str Num Index Num If CompareNotIn NameLoad NameLoad body Continue Assign TupleStore NameStore NameStore SubscriptLoad NameLoad Index NameLoad Expr Call AttributeLoad NameLoad attr ListLoad NameLoad AttributeLoad NameLoad attr AttributeLoad NameLoad attr Call AttributeLoad Str attr Call NameLoad NameLoad Expr Call AttributeLoad NameLoad attr keyword Lambda arguments args NameParam defaults TupleLoad SubscriptLoad NameLoad Index Num SubscriptLoad NameLoad Index Num Assign NameStore Call NameLoad AttributeLoad NameLoad attr Str Print NameLoad Call AttributeLoad Str attr NameLoad For NameStore NameLoad body Print NameLoad 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 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 ListLoad NameLoad Assign NameStore Call NameLoad NameLoad Assign NameStore AttributeLoad NameLoad attr Assign NameStore Call NameLoad NameLoad keyword NameLoad For NameStore NameLoad body Assign NameStore AttributeLoad NameLoad attr If CompareNotIn NameLoad NameLoad body Continue Assign TupleStore NameStore NameStore SubscriptLoad NameLoad Index NameLoad Assign NameStore Call AttributeLoad Str attr AttributeLoad NameLoad attr AttributeLoad NameLoad attr AttributeLoad NameLoad attr Assign AttributeStore NameLoad attr NameLoad Print 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 NameLoad Assign NameStore SubscriptLoad Call AttributeLoad NameLoad attr Str Index Num Assign NameStore BinOpAdd NameLoad Str Assign NameStore Call NameLoad NameLoad Expr Call AttributeLoad NameLoad attr NameLoad keyword AttributeLoad NameLoad attr Return 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 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 SubscriptLoad Call AttributeLoad NameLoad attr Str Index Num Assign NameStore BinOpAdd NameLoad Str Assign NameStore Call NameLoad NameLoad Expr Call AttributeLoad NameLoad attr NameLoad Assign NameStore Call NameLoad NameLoad keyword NameLoad Assign NameStore BinOpAdd NameLoad Str Assign NameStore Call NameLoad NameLoad Str Assign NameStore AttributeLoad Call NameLoad NameLoad attr For NameStore NameLoad body Assign NameStore AttributeLoad NameLoad attr Assign TupleStore NameStore NameStore Call AttributeLoad NameLoad attr Str Assign NameStore Call NameLoad NameLoad Assign NameStore Call NameLoad Num BinOpSub NameLoad NameLoad Assign NameStore Call NameLoad BinOpAdd NameLoad NameLoad SubscriptLoad NameLoad Index NameLoad Print NameLoad Call AttributeLoad Str attr GeneratorExp Call NameLoad NameLoad comprehension NameStore TupleLoad NameLoad NameLoad NameLoad NameLoad Expr Call AttributeLoad NameLoad attr Expr Call NameLoad NameLoad NameLoad keyword NameLoad decorator_list FunctionDef arguments args NameParam NameParam NameParam defaults NameLoad body Assign NameStore Num For TupleStore NameStore NameStore Call NameLoad NameLoad NameLoad body If BoolOpAnd NameLoad CompareIn NameLoad TupleLoad NameLoad NameLoad body Continue If CompareNotEq NameLoad NameLoad body AugAssignAdd NameStore Num Return NameLoad decorator_list Assign TupleStore NameStore NameStore NameStore Call NameLoad Num FunctionDef arguments args NameParam NameParam NameParam defaults body If CompareNotEq AttributeLoad NameLoad attr AttributeLoad NameLoad attr body Return TupleLoad NameLoad NameLoad Assign NameStore Call NameLoad AttributeLoad NameLoad attr AttributeLoad NameLoad attr keyword Str Assign NameStore BinOpMult Call NameLoad NameLoad NameLoad If CompareLtE NameLoad NameLoad body Return TupleLoad NameLoad NameLoad Return TupleLoad NameLoad TupleLoad AttributeLoad NameLoad attr AttributeLoad NameLoad attr 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 keyword Num 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 NameLoad Assign NameStore ListLoad Assign NameStore Num For NameStore Call NameLoad Num BinOpSub Call NameLoad NameLoad Num body Assign NameStore SubscriptLoad NameLoad Index NameLoad Assign TupleStore NameStore NameStore Call NameLoad SubscriptLoad NameLoad Index BinOpSub NameLoad Num NameLoad NameLoad Assign TupleStore NameStore NameStore Call NameLoad NameLoad SubscriptLoad NameLoad Index BinOpAdd NameLoad Num NameLoad If BoolOpAnd CompareEq NameLoad NameLoad CompareEq NameLoad NameLoad body AugAssignAdd NameStore Num Continue Expr Call AttributeLoad NameLoad attr NameLoad Expr Call AttributeLoad NameLoad attr Call AttributeLoad Str attr NameLoad For TupleStore NameStore NameStore Call NameLoad NameLoad body Assign TupleStore NameStore NameStore Call NameLoad NameLoad NameLoad NameLoad If CompareEq NameLoad NameLoad body Print Call AttributeLoad Str attr GeneratorExp Call NameLoad NameLoad comprehension NameStore NameLoad decorator_list If CompareEq NameLoad Str body Expr Call NameLoad
N/A N/A 
Use genetic map to break chimeric scaffolds, order and orient scaffolds onto
chromosomes.
 N/A sys N/A logging itertools combinations jcvi.formats.base BaseFile LineFile must_open read_block jcvi.formats.bed Bed fastaFromBed jcvi.utils.cbook memoized jcvi.utils.counter Counter jcvi.apps.base OptionParser ActionDispatcher need_update N/A MSTheader population_type {0}
population_name LG
distance_function kosambi
cut_off_p_value 0.000001
no_map_dist 10.0
no_map_size 0
missing_threshold {1}
estimation_before_clustering no
detect_bad_data yes
objective_function ML
number_of_loci {2}
number_of_individual {3}
 BinMap N/A BaseFile dict N/A __init__ N/A N/A self filename N/A N/A N/A N/A N/A N/A super BinMap self __init__ filename N/A fp N/A open filename N/A N/A header seq N/A read_block fp group  N/A N/A lg N/A N/A N/A header split N/A -1 N/A N/A self N/A lg N/A N/A s seq N/A N/A N/A N/A N/A N/A s strip N/A N/A s N/A 0 ; N/A N/A N/A N/A marker pos N/A N/A s split N/A pos N/A int N/A N/A float pos 1000 N/A N/A N/A N/A self N/A lg append N/A marker pos N/A print_to_bed N/A N/A self filename switch N/A stdout False N/A N/A fw N/A must_open filename w N/A N/A lg markers N/A sorted N/A N/A self items N/A N/A N/A marker pos markers N/A N/A N/A switch N/A N/A line N/A lg pos N/A pos 1 marker N/A N/A N/A seqid spos N/A N/A marker split . N/A spos N/A int spos N/A marker N/A N/A {0}:{1} format lg N/A pos 1000.0 N/A line N/A seqid N/A spos 1 spos marker N/A fw N/A N/A join N/A N/A str x N/A x line N/A N/A N/A fw close N/A N/A MSTMapLine N/A object N/A __init__ N/A N/A self row startidx N/A 3 N/A N/A args N/A N/A row split N/A N/A self id N/A args N/A 0 N/A N/A N/A self seqid pos N/A N/A N/A self id split . N/A N/A self pos N/A int pos N/A N/A self genotype N/A N/A join N/A args N/A startidx N/A __len__ N/A N/A self N/A N/A N/A N/A len N/A self genotype N/A __str__ N/A N/A self N/A N/A N/A N/A N/A {0}: {1} format N/A self id N/A self genotype N/A bedline 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 id N/A property N/A MSTMap N/A LineFile N/A __init__ N/A N/A self filename N/A N/A N/A N/A N/A N/A super MSTMap self __init__ filename N/A fp N/A open filename N/A startidx 1 N/A row fp N/A N/A N/A N/A row startswith locus_name N/A N/A N/A N/A N/A N/A row split N/A 1 seqid N/A N/A startidx 3 N/A N/A self header N/A N/A row split N/A N/A row fp N/A N/A N/A N/A self append N/A MSTMapLine row startidx startidx N/A N/A self nmarkers N/A len self N/A N/A self nind N/A len N/A N/A self N/A 0 genotype N/A N/A N/A logging debug N/A N/A Map contains {0} markers in {1} individuals format N/A self nmarkers N/A self nind N/A N/A MSTMatrix N/A object N/A __init__ N/A N/A self matrix markerheader population_type missing_threshold N/A N/A N/A N/A self matrix matrix N/A N/A self markerheader markerheader N/A N/A self population_type population_type N/A N/A self missing_threshold missing_threshold N/A N/A self ngenotypes N/A len matrix N/A N/A self nind N/A N/A len markerheader 1 N/A N/A N/A self nind N/A N/A len N/A matrix N/A 0 1 N/A N/A N/A logging debug N/A N/A Imported {0} markers and {1} individuals. format N/A self ngenotypes N/A self nind N/A write N/A N/A self filename header N/A stdout True N/A N/A fw N/A must_open filename w N/A header N/A N/A fw N/A N/A MSTheader format N/A self population_type N/A self missing_threshold N/A self ngenotypes N/A self nind N/A fw N/A N/A join N/A self markerheader N/A m N/A self matrix N/A N/A fw N/A N/A join m N/A N/A main N/A N/A N/A N/A N/A actions N/A N/A breakpoint find scaffold breakpoints using genetic map N/A ld calculate pairwise linkage disequilibrium N/A bed convert MSTmap output to bed format N/A fasta extract markers based on map N/A anchor anchor scaffolds based on map N/A rename rename markers according to the new mapping locations N/A header rename lines in the map header N/A p N/A ActionDispatcher actions N/A N/A N/A p dispatch N/A globals N/A calc_ldscore N/A N/A a b N/A N/A N/A N/A N/A len a N/A len b N/A N/A {0}
{1} format a b N/A c N/A Counter N/A zip a b N/A c_aa N/A c N/A N/A A A N/A c_ab N/A c N/A N/A A B N/A c_ba N/A c N/A N/A B A N/A c_bb N/A c N/A N/A B B N/A n N/A N/A N/A c_aa c_ab c_ba c_bb N/A N/A n 0 N/A N/A 0 N/A f N/A 1.0 n N/A x_aa N/A c_aa f N/A x_ab N/A c_ab f N/A x_ba N/A c_ba f N/A x_bb N/A c_bb f N/A p_a N/A x_aa x_ab N/A p_b N/A x_ba x_bb N/A q_a N/A x_aa x_ba N/A q_b N/A x_ab x_bb N/A D N/A x_aa N/A p_a q_a N/A denominator N/A N/A N/A p_a p_b q_a q_b N/A N/A denominator 0 N/A N/A 0 N/A r2 N/A N/A D D denominator N/A r2 N/A memoized ld N/A N/A args N/A N/A N/A 
    %prog ld map

    Calculate pairwise linkage disequilibrium given MSTmap.
     N/A numpy np random sample jcvi.algorithms.matrix symmetrize N/A p N/A OptionParser N/A ld __doc__ N/A N/A N/A p add_option --subsample default 1000 type int help Subsample markers to speed up [default: %default] N/A N/A opts args iopts N/A N/A p set_image_options args figsize 8x8 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 mstmap args N/A subsample N/A opts subsample N/A data N/A MSTMap mstmap N/A markerbedfile N/A mstmap .subsample.bed N/A ldmatrix N/A mstmap .subsample.matrix N/A N/A subsample N/A data nmarkers N/A N/A data N/A N/A data N/A x N/A x N/A sorted N/A sample N/A xrange N/A len data subsample N/A N/A N/A N/A logging debug Use all markers, --subsample ignored N/A nmarkers N/A len data N/A N/A need_update mstmap N/A ldmatrix markerbedfile N/A N/A fw N/A open markerbedfile w N/A fw N/A N/A join N/A N/A x bedline N/A x data N/A N/A N/A logging debug N/A N/A Write marker set of size {0} to file `{1}`. format nmarkers markerbedfile N/A N/A N/A fw close N/A M N/A N/A np zeros N/A nmarkers nmarkers dtype float N/A N/A i j N/A combinations N/A range nmarkers 2 N/A N/A a N/A data N/A i N/A b N/A data N/A j N/A N/A M N/A N/A i j N/A calc_ldscore N/A a genotype N/A b genotype N/A M N/A symmetrize M N/A N/A N/A logging debug N/A N/A Write LD matrix to file `{0}`. format ldmatrix N/A N/A N/A M tofile ldmatrix N/A N/A nmarkers N/A len N/A Bed markerbedfile N/A M N/A N/A N/A N/A np fromfile ldmatrix dtype float reshape nmarkers nmarkers N/A N/A N/A logging debug N/A N/A LD matrix `{0}` exists ({1}x{1}). format ldmatrix nmarkers jcvi.graphics.base plt savefig Rectangle draw_cmap N/A N/A N/A plt rcParams N/A axes.linewidth 0 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 ax N/A N/A fig add_axes N/A 0.1 0.1 0.8 0.8 N/A N/A N/A ax matshow M cmap N/A iopts cmap N/A bed N/A Bed markerbedfile N/A xsize N/A len bed N/A extent N/A 0 nmarkers N/A chr_labels N/A N/A ignore_size 20 N/A N/A seqid beg end N/A N/A bed get_breaks N/A N/A ignore N/A N/A abs N/A end beg ignore_size N/A pos N/A N/A beg end 2 N/A N/A N/A chr_labels append N/A seqid pos ignore N/A ignore N/A N/A N/A N/A N/A ax plot N/A end end extent w- lw 1 N/A N/A N/A ax plot extent N/A end end w- lw 1 N/A N/A label pos ignore chr_labels N/A N/A pos N/A 0.1 N/A N/A pos 0.8 xsize N/A N/A ignore N/A N/A N/A N/A root text pos 0.91 label ha center va bottom rotation 45 color grey N/A N/A N/A root text 0.09 pos label ha right va center color grey N/A N/A N/A ax set_xlim extent N/A N/A N/A ax set_ylim extent N/A N/A N/A ax set_axis_off N/A N/A draw_cmap root Pairwise LD (r2) 0 1 cmap N/A iopts cmap N/A N/A N/A root add_patch N/A Rectangle N/A 0.1 0.1 0.8 0.8 fill False ec k lw 2 N/A m N/A N/A N/A mstmap split . N/A 0 N/A N/A N/A root text 0.5 0.06 N/A N/A Linkage Disequilibrium between {0} markers format m ha center N/A N/A N/A root set_xlim 0 1 N/A N/A N/A root set_ylim 0 1 N/A N/A N/A root set_axis_off N/A image_name N/A N/A N/A m .subsample . N/A iopts format N/A N/A savefig image_name dpi N/A iopts dpi iopts iopts N/A header N/A N/A args N/A N/A N/A 
    %prog header map conversion_table

    Rename lines in the map header. The mapping of old names to new names are
    stored in two-column `conversion_table`.
     jcvi.formats.base DictFile N/A p N/A OptionParser N/A header __doc__ N/A N/A N/A p add_option --prefix default help Prepend text to line number [default: %default] N/A N/A N/A p add_option --ids help Write ids to file [default: %default] 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 mstmap conversion_table args N/A data N/A MSTMap mstmap N/A hd N/A data header N/A conversion N/A DictFile conversion_table N/A newhd N/A N/A N/A opts prefix N/A N/A conversion get x x N/A x hd N/A N/A N/A join hd N/A ---> N/A N/A N/A join newhd N/A ids N/A opts ids N/A ids N/A N/A fw N/A open ids w N/A fw N/A N/A join newhd N/A N/A N/A fw close N/A rename N/A N/A args N/A N/A N/A 
    %prog rename map markers.bed > renamed.map

    Rename markers according to the new mapping locations.
     N/A p N/A OptionParser N/A rename __doc__ 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 mstmap bedfile args N/A markersbed N/A Bed bedfile N/A markers N/A markersbed order N/A data N/A MSTMap mstmap N/A header N/A data header N/A header N/A N/A N/A N/A header N/A 0 N/A seqid start N/A header N/A 1 N/A renamed N/A N/A b data N/A N/A N/A m geno N/A N/A b id N/A b genotype N/A om m N/A N/A m markers N/A N/A m N/A N/A N/A m rsplit . 1 N/A 0 N/A N/A m markers N/A N/A N/A N/A i mb N/A markers N/A m N/A N/A N/A renamed append N/A om N/A mb seqid N/A mb start N/A N/A join N/A list geno N/A N/A N/A renamed sort key N/A N/A N/A x N/A N/A N/A x N/A 1 N/A x N/A 2 N/A fw N/A must_open N/A opts outfile w N/A fw N/A N/A join header N/A d renamed N/A N/A fw N/A N/A join N/A N/A str x N/A x d N/A anchor N/A N/A args N/A N/A N/A 
    %prog anchor map.bed markers.blast > anchored.bed

    Anchor scaffolds based on map.
     jcvi.formats.blast bed N/A p N/A OptionParser N/A anchor __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 mapbed blastfile args N/A bedfile N/A bed N/A blastfile N/A markersbed N/A Bed bedfile N/A markers N/A markersbed order N/A mapbed N/A Bed mapbed sorted False N/A b mapbed N/A N/A m N/A b accn N/A N/A m markers N/A N/A N/A N/A i mb N/A markers N/A m N/A new_accn N/A N/A {0}:{1}-{2} format N/A mb seqid N/A mb start N/A mb end N/A N/A b accn new_accn N/A b N/A bed N/A N/A args N/A N/A N/A 
    %prog fasta map.out

    Convert MSTMAP output into bed format.
     N/A p N/A OptionParser N/A bed __doc__ N/A N/A N/A p add_option --switch default False action store_true help Switch reference and aligned map elements [default: %default] 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 mapout args N/A pf N/A N/A N/A mapout split . N/A 0 N/A mapbed N/A pf .bed N/A bm N/A BinMap mapout N/A N/A N/A bm print_to_bed mapbed switch N/A opts switch N/A mapbed N/A fasta N/A N/A args N/A N/A N/A 
    %prog fasta map.out scaffolds.fasta

    Extract marker sequences based on map.
     jcvi.formats.sizes Sizes N/A p N/A OptionParser N/A fasta __doc__ N/A N/A N/A p add_option --extend default 1000 type int help Extend seq flanking the gaps [default: %default] 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 mapout sfasta args N/A Flank N/A opts extend N/A pf N/A N/A N/A mapout split . N/A 0 N/A mapbed N/A pf .bed N/A bm N/A BinMap mapout N/A N/A N/A bm print_to_bed mapbed N/A bed N/A Bed mapbed sorted False N/A markersbed N/A pf .markers.bed N/A fw N/A open markersbed w N/A sizes N/A N/A Sizes sfasta mapping N/A b bed N/A N/A accn N/A b accn N/A N/A scf pos N/A N/A accn split . N/A pos N/A int pos N/A start N/A max 0 N/A pos Flank N/A end N/A min N/A pos Flank N/A sizes N/A scf N/A fw N/A N/A join N/A N/A str x N/A x N/A scf start end accn N/A N/A N/A fw close N/A N/A fastaFromBed markersbed sfasta name True N/A hamming_distance N/A N/A a b ignore N/A None N/A N/A dist 0 N/A N/A x y N/A zip a b N/A N/A N/A ignore N/A ignore N/A x y N/A N/A N/A N/A x y N/A N/A dist 1 N/A dist N/A N/A N/A OK BREAK END N/A range 3 check_markers N/A N/A a b maxdiff N/A N/A N/A N/A N/A a seqid N/A b seqid N/A N/A N/A END None N/A diff N/A hamming_distance N/A a genotype N/A b genotype ignore - N/A max_allowed N/A N/A len a maxdiff N/A N/A diff max_allowed N/A N/A N/A OK None N/A N/A BREAK N/A N/A a seqid N/A a pos N/A b pos N/A breakpoint N/A N/A args N/A N/A N/A 
    %prog breakpoint mstmap.input > breakpoints.bed

    Find scaffold breakpoints using genetic map. Use variation.vcf.mstmap() to
    generate the input for this routine.
     jcvi.utils.iter pairwise N/A p N/A OptionParser N/A breakpoint __doc__ N/A N/A N/A p add_option --diff default 0.1 type float help Maximum ratio of differences allowed [default: %default] 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 mstmap args N/A diff N/A opts diff N/A data N/A MSTMap mstmap N/A good N/A N/A nsingletons 0 N/A i N/A xrange 1 N/A N/A len data 1 N/A N/A a N/A data N/A i N/A N/A left_label left_rr N/A check_markers N/A data N/A N/A i 1 a diff N/A N/A right_label right_rr N/A check_markers a N/A data N/A N/A i 1 diff N/A N/A N/A left_label BREAK N/A right_label BREAK N/A N/A nsingletons 1 N/A N/A N/A N/A good append a N/A N/A N/A logging debug N/A N/A A total of {0} singleton markers removed. format nsingletons N/A N/A a b N/A pairwise good N/A N/A N/A label rr N/A check_markers a b diff N/A N/A label BREAK N/A N/A N/A N/A join N/A N/A str x N/A x rr N/A N/A N/A __name__ __main__ N/A N/A N/A main