Module Expr Str Import alias Import alias ImportFrom alias alias ImportFrom alias alias ClassDef bases NameLoad body FunctionDef arguments args NameParam NameParam NameParam defaults body Assert CompareEq SubscriptLoad NameLoad Index Num Str Assign AttributeStore NameLoad attr SubscriptLoad Call AttributeLoad Call AttributeLoad NameLoad attr Str attr Str Index Num Assign NameStore SubscriptLoad Call AttributeLoad SubscriptLoad Call AttributeLoad NameLoad attr Str Index Num attr Str Index Num Assign TupleStore NameStore NameStore Call AttributeLoad NameLoad attr Assign AttributeStore NameLoad attr NameLoad Assign AttributeStore NameLoad attr Call NameLoad NameLoad Assign AttributeStore NameLoad attr Call NameLoad NameLoad If CompareGt AttributeLoad NameLoad attr AttributeLoad NameLoad attr body Assign TupleStore AttributeStore NameLoad attr AttributeStore NameLoad attr TupleLoad AttributeLoad NameLoad attr AttributeLoad NameLoad attr Assign AttributeStore NameLoad attr IfExp CompareIn Str NameLoad Str Str decorator_list FunctionDef arguments args NameParam defaults body Return 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 Str AttributeLoad NameLoad attr decorator_list NameLoad Assign NameStore NameLoad decorator_list ClassDef bases NameLoad body FunctionDef arguments args NameParam NameParam defaults body Assert CompareEq SubscriptLoad NameLoad Slice Num Str Assign AttributeStore NameLoad attr SubscriptLoad Call AttributeLoad Call AttributeLoad NameLoad attr Str attr Index Num Assign AttributeStore NameLoad attr ListLoad decorator_list FunctionDef arguments args NameParam defaults body Return Call AttributeLoad Str attr TupleLoad AttributeLoad NameLoad attr Call NameLoad AttributeLoad NameLoad attr decorator_list Assign NameStore NameLoad decorator_list ClassDef bases NameLoad body FunctionDef arguments args NameParam NameParam defaults body Expr Call AttributeLoad Call NameLoad NameLoad NameLoad attr NameLoad Assign AttributeStore NameLoad attr Call NameLoad NameLoad decorator_list FunctionDef arguments args NameParam defaults body Assign NameStore NameLoad For TupleStore NameStore NameStore Call NameLoad AttributeLoad NameLoad attr Str body If CompareEq SubscriptLoad NameLoad Slice Num Str body If NameLoad body Expr Yield NameLoad Assign NameStore Call NameLoad NameLoad orelse Expr Call AttributeLoad AttributeLoad NameLoad attr attr Call NameLoad NameLoad AttributeLoad NameLoad attr If NameLoad body Expr Yield NameLoad decorator_list decorator_list FunctionDef arguments args defaults body Assign NameStore TupleLoad 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 ImportFrom alias ImportFrom alias 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 NameStore NameLoad Assign NameStore SubscriptLoad Call AttributeLoad NameLoad attr Str Num Index Num Assign NameStore BinOpAdd NameLoad Str Assign NameStore BinOpAdd NameLoad Str Assign NameStore Call NameLoad NameLoad Assign NameStore Call NameLoad NameLoad Assign NameStore Call NameLoad NameLoad Assign NameStore Str Assign NameStore Call NameLoad NameLoad Str Assign NameStore Call NameLoad NameLoad Str For TupleStore NameStore NameStore Call AttributeLoad NameLoad attr body Assign NameStore SubscriptLoad NameLoad Index NameLoad Assign NameStore Call AttributeLoad Str attr NameLoad Call NameLoad NameLoad Call NameLoad NameLoad NameLoad Print NameLoad NameLoad Print NameLoad NameLoad Print NameLoad Call NameLoad AttributeLoad NameLoad attr For NameStore NameLoad body Assign NameStore AttributeLoad NameLoad attr Assign NameStore AttributeLoad NameLoad attr Assign NameStore SubscriptLoad NameLoad Index NameLoad Assign NameStore IfExp CompareEq NameLoad Str Str Str Assign NameStore Call NameLoad NameLoad Assign TupleStore NameStore NameStore TupleLoad Num NameLoad If CompareEq NameLoad Str body Assign TupleStore NameStore NameStore TupleLoad NameLoad NameLoad Assign NameStore Call AttributeLoad Str attr NameLoad NameLoad Assign NameStore Call AttributeLoad Str attr AttributeLoad NameLoad attr AttributeLoad NameLoad attr Assign NameStore Call AttributeLoad Str attr NameLoad NameLoad NameLoad NameLoad NameLoad NameLoad Print NameLoad NameLoad Print NameLoad Call NameLoad AttributeLoad NameLoad attr Expr Call AttributeLoad NameLoad attr Call AttributeLoad Str attr NameLoad Expr Call AttributeLoad NameLoad attr Call AttributeLoad Str attr NameLoad decorator_list FunctionDef arguments args NameParam defaults body Expr Str Assign NameStore Call NameLoad AttributeLoad NameLoad attr 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 BinOpAdd SubscriptLoad Call AttributeLoad NameLoad attr Str Num Index Num Str Assign NameStore Call NameLoad NameLoad Str Assign NameStore Call NameLoad NameLoad For NameStore Call AttributeLoad NameLoad attr body For NameStore AttributeLoad NameLoad attr body Print NameLoad AttributeLoad NameLoad attr Expr Call AttributeLoad NameLoad attr Call AttributeLoad Str attr NameLoad Return NameLoad decorator_list If CompareEq NameLoad Str body Expr Call NameLoad
N/A N/A 
TIGR contig format, see spec:

<http://www.cbcb.umd.edu/research/contig_representation.shtml#contig>
 N/A sys N/A logging jcvi.formats.base BaseFile read_block jcvi.apps.base OptionParser ActionDispatcher ReadLine N/A object N/A __init__ N/A N/A self row contig N/A N/A N/A N/A N/A row N/A 0 # N/A N/A self id N/A N/A N/A N/A N/A row strip # split ( N/A 0 N/A coords N/A N/A N/A N/A N/A N/A row split < N/A 1 split > N/A 0 N/A N/A start end N/A N/A coords split N/A N/A self contig contig N/A N/A self start N/A int start N/A N/A self end N/A int end N/A N/A N/A self start N/A self end N/A N/A N/A N/A self start N/A self end N/A N/A self end N/A self start N/A N/A self orientation N/A N/A [RC] row - + N/A __str__ N/A N/A self N/A N/A N/A N/A self id 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 contig N/A N/A self start 1 N/A self end N/A self id 0 N/A self orientation N/A property N/A __repr__ __str__ N/A ContigLine N/A object N/A __init__ N/A N/A self row N/A N/A N/A N/A N/A row N/A 2 ## N/A N/A self id N/A N/A N/A N/A N/A row strip # split N/A 0 N/A N/A self reads N/A N/A __str__ N/A N/A self N/A N/A N/A N/A N/A : join N/A N/A self id N/A str N/A self reads N/A N/A __repr__ __str__ N/A ContigFile N/A BaseFile N/A __init__ N/A N/A self filename N/A N/A N/A N/A N/A N/A super ContigFile self __init__ filename N/A N/A self fp N/A open filename N/A iter_records N/A N/A self N/A N/A N/A c None N/A N/A a b N/A read_block N/A self fp # N/A N/A N/A N/A a N/A 2 ## N/A N/A c N/A N/A N/A c N/A c N/A ContigLine a N/A N/A N/A N/A N/A c reads append N/A ReadLine a N/A c id N/A c N/A N/A N/A c N/A N/A main N/A N/A N/A N/A N/A actions N/A N/A bed convert read membership to bed format N/A frombed convert read placement to contig format N/A p N/A ActionDispatcher actions N/A N/A N/A p dispatch N/A globals N/A frombed N/A N/A args N/A N/A N/A 
    %prog frombed bedfile contigfasta readfasta

    Convert read placement to contig format. This is useful before running BAMBUS.
     jcvi.formats.fasta Fasta jcvi.formats.bed Bed jcvi.utils.cbook fill N/A p N/A OptionParser N/A frombed __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 bedfile contigfasta readfasta args N/A prefix N/A N/A N/A bedfile rsplit . 1 N/A 0 N/A contigfile N/A prefix .contig N/A idsfile N/A prefix .ids N/A contigfasta N/A Fasta contigfasta N/A readfasta N/A Fasta readfasta N/A bed N/A Bed bedfile N/A checksum 00000000 checksum. N/A fw_ids N/A open idsfile w N/A fw N/A open contigfile w N/A N/A ctg reads N/A N/A bed sub_beds N/A N/A ctgseq N/A contigfasta N/A ctg N/A ctgline N/A N/A ##{0} {1} {2} bases, {3} format ctg N/A len reads N/A len ctgseq checksum N/A fw_ids ctg N/A fw ctgline N/A fw N/A fill N/A ctgseq seq N/A b reads N/A N/A read N/A b accn N/A strand N/A b strand N/A readseq N/A readfasta N/A read N/A rc N/A N/A strand -  [RC] N/A readlen N/A len readseq N/A N/A rstart rend N/A 1 readlen N/A N/A strand - N/A N/A N/A rstart rend N/A rend rstart N/A readrange N/A N/A {{{0} {1}}} format rstart rend N/A conrange N/A N/A <{0} {1}> format N/A b start N/A b end N/A readline N/A N/A #{0}(0){1} {2} bases, {3} {4} {5} format read rc readlen checksum readrange conrange N/A fw readline N/A fw N/A fill N/A readseq seq N/A N/A N/A logging debug N/A N/A Mapped contigs written to `{0}`. format contigfile N/A N/A N/A logging debug N/A N/A Contig IDs written to `{0}`. format idsfile N/A bed N/A N/A args N/A N/A N/A 
    %prog bed contigfile

    Prints out the contigs and their associated reads.
     N/A p N/A OptionParser N/A main __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 contigfile args N/A bedfile N/A N/A N/A N/A contigfile rsplit . 1 N/A 0 .bed N/A fw N/A open bedfile w N/A c N/A ContigFile contigfile N/A rec N/A N/A c iter_records N/A N/A r N/A rec reads N/A N/A fw N/A r bedline N/A N/A N/A logging debug N/A N/A File written to `{0}`. format bedfile N/A bedfile N/A N/A N/A __name__ __main__ N/A N/A N/A main