Module Expr Str Import alias ImportFrom alias alias ImportFrom alias ImportFrom alias alias ClassDef bases NameLoad body FunctionDef arguments args NameParam NameParam NameParam defaults NameLoad body Assign NameStore Call AttributeLoad Call AttributeLoad NameLoad attr attr Str Assign AttributeStore NameLoad attr Call NameLoad NameLoad Assign AttributeStore NameLoad attr SubscriptLoad Call AttributeLoad SubscriptLoad NameLoad Index Num attr 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 Call NameLoad SubscriptLoad NameLoad Index Num Assign AttributeStore NameLoad attr IfExp CompareEq SubscriptLoad NameLoad Index Num Str Str Str 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 SubscriptLoad NameLoad Index Num Assign AttributeStore NameLoad attr Call NameLoad SubscriptLoad NameLoad Index Num If CompareEq AttributeLoad NameLoad attr Str body Assign TupleStore AttributeStore NameLoad attr AttributeStore NameLoad attr TupleLoad AttributeLoad NameLoad attr AttributeLoad NameLoad attr 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 If NameLoad body 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 Call AttributeLoad Str attr GeneratorExp Call NameLoad NameLoad comprehension NameStore TupleLoad AttributeLoad NameLoad attr AttributeLoad NameLoad attr AttributeLoad NameLoad attr orelse Assign AttributeStore NameLoad attr Call NameLoad SubscriptLoad NameLoad Index Num Assign AttributeStore NameLoad attr Call NameLoad SubscriptLoad NameLoad Index Num Assign AttributeStore NameLoad attr IfExp CompareGt Call NameLoad NameLoad Num Call NameLoad SubscriptLoad NameLoad Index Num NameLoad decorator_list FunctionDef arguments args NameParam NameParam defaults body Return Call NameLoad NameLoad NameLoad decorator_list FunctionDef arguments args NameParam defaults body Return Call AttributeLoad Str attr TupleLoad AttributeLoad NameLoad attr BinOpAdd BinOpAdd AttributeLoad NameLoad attr Str AttributeLoad NameLoad attr BinOpMod Str AttributeLoad NameLoad attr Str Str Str BinOpMod Str AttributeLoad NameLoad attr BinOpMod Str AttributeLoad NameLoad attr BinOpMod Str AttributeLoad NameLoad attr BinOpMod Str AttributeLoad NameLoad attr BinOpMod Str AttributeLoad NameLoad attr BinOpMod Str AttributeLoad NameLoad attr decorator_list NameLoad FunctionDef arguments args NameParam NameParam NameParam NameParam NameParam defaults NameLoad Str Str NameLoad body Assign NameStore IfExp UnaryOpNot NameLoad AttributeLoad NameLoad attr NameLoad If CompareNotIn NameLoad NameLoad body Assign NameStore Call AttributeLoad Str attr AttributeLoad NameLoad attr Assign NameStore Call AttributeLoad Str attr GeneratorExp Call NameLoad NameLoad comprehension NameStore ListLoad AttributeLoad NameLoad attr AttributeLoad NameLoad attr AttributeLoad NameLoad attr Assign NameStore Call AttributeLoad Str attr GeneratorExp Call NameLoad NameLoad comprehension NameStore ListLoad BinOpAdd BinOpAdd NameLoad Str NameLoad BinOpAdd Str NameLoad orelse Assign NameStore Str Assign NameStore IfExp CompareIn Str AttributeLoad NameLoad attr Call AttributeLoad Str attr AttributeLoad NameLoad attr AttributeLoad NameLoad attr Assign NameStore Call AttributeLoad Str attr GeneratorExp Call NameLoad NameLoad comprehension NameStore ListLoad BinOpAdd BinOpAdd NameLoad Str NameLoad BinOpAdd Str AttributeLoad NameLoad attr BinOpAdd Str NameLoad Assign NameStore Call AttributeLoad Str attr GeneratorExp Call NameLoad NameLoad comprehension NameStore ListLoad AttributeLoad NameLoad attr NameLoad NameLoad AttributeLoad NameLoad attr AttributeLoad NameLoad attr NameLoad AttributeLoad NameLoad attr Str NameLoad Return NameLoad decorator_list decorator_list ClassDef bases NameLoad body FunctionDef arguments args NameParam NameParam NameParam defaults NameLoad body Expr Call AttributeLoad Call NameLoad NameLoad NameLoad attr NameLoad For NameStore Call NameLoad NameLoad body If CompareEq SubscriptLoad NameLoad Index Num Str body Continue Expr Call AttributeLoad NameLoad attr Call NameLoad NameLoad keyword NameLoad decorator_list decorator_list FunctionDef arguments args defaults body Assign NameStore TupleLoad 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 Call NameLoad NameLoad For NameStore NameLoad body Print AttributeLoad NameLoad attr 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 NameLoad Assign NameStore Call NameLoad NameLoad For NameStore NameLoad body Assign NameStore Call NameLoad AttributeLoad NameLoad attr Print AttributeLoad NameLoad attr decorator_list FunctionDef arguments args NameParam defaults body Expr Str ImportFrom alias ImportFrom alias alias Assign NameStore Call NameLoad AttributeLoad NameLoad attr Expr Call AttributeLoad NameLoad attr Str keyword NameLoad keyword BinOpAdd BinOpAdd Str Str Str Expr Call AttributeLoad NameLoad attr Str keyword Str keyword NameLoad 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 Dict Assign NameStore Call NameLoad NameLoad keyword NameLoad Assign NameStore BoolOpOr AttributeLoad NameLoad attr Str Assign NameStore AttributeLoad NameLoad attr Assign NameStore SubscriptLoad NameLoad Index NameLoad For NameStore NameLoad body Assign NameStore AttributeLoad NameLoad attr Assign NameStore BinOpAdd BinOpAdd BinOpAdd AttributeLoad NameLoad attr Str NameLoad Call AttributeLoad Str attr AttributeLoad NameLoad attr Assign NameStore AttributeLoad NameLoad attr If CompareNotIn NameLoad NameLoad body Assign SubscriptStore NameLoad Index NameLoad Dict Str Str Str Str Str Str Str Str NameLoad AttributeLoad NameLoad attr AttributeLoad NameLoad attr AttributeLoad NameLoad attr AttributeLoad NameLoad attr AttributeLoad NameLoad attr ListLoad ListLoad Expr Call AttributeLoad SubscriptLoad SubscriptLoad NameLoad Index NameLoad Index Str attr TupleLoad AttributeLoad NameLoad attr AttributeLoad NameLoad attr Expr Call AttributeLoad SubscriptLoad SubscriptLoad NameLoad Index NameLoad Index Str attr Call AttributeLoad NameLoad attr keyword NameLoad keyword NameLoad keyword NameLoad For NameStore Call AttributeLoad NameLoad attr body Assign NameStore Call NameLoad Call AttributeLoad Str attr GeneratorExp Call NameLoad NameLoad comprehension NameStore BinOpMult ListLoad Num NameLoad keyword NameLoad Assign NameStore SubscriptLoad NameLoad Index Str Assign AttributeStore NameLoad attr SubscriptLoad NameLoad Index Str Assign AttributeStore NameLoad attr SubscriptLoad NameLoad Index Str Assign AttributeStore NameLoad attr SubscriptLoad NameLoad Index Str Assign AttributeStore NameLoad attr SubscriptLoad NameLoad Index Str Assign AttributeStore NameLoad attr SubscriptLoad NameLoad Index Str Assign TupleStore AttributeStore NameLoad attr AttributeStore NameLoad attr Call NameLoad SubscriptLoad NameLoad Index Str Print Call AttributeLoad NameLoad attr keyword NameLoad keyword NameLoad keyword Str keyword NameLoad Print Call AttributeLoad Str attr SubscriptLoad NameLoad Index Str decorator_list If CompareEq NameLoad Str body Expr Call NameLoad
N/A N/A 
btab format, used by BLAST and NUCMER, found spec here:
<http://www.agcol.arizona.edu/~matthew/formats.html>

btab format used by aat, found spec here:
<http://ergatis.diagcomputing.org/cgi/documentation.cgi?article=components&page=aat_aa>
 N/A sys jcvi.formats.base LineFile must_open jcvi.formats.gff valid_gff_type jcvi.apps.base OptionParser ActionDispatcher BtabLine N/A object N/A __init__ N/A N/A self row aat_dialect N/A False N/A N/A args N/A N/A N/A N/A row strip split N/A N/A self nargs N/A len args N/A N/A self query N/A N/A N/A N/A args N/A 0 split N/A 0 N/A N/A self qLen N/A int N/A args N/A 2 N/A N/A self qStart N/A int N/A args N/A 6 N/A N/A self qStop N/A int N/A args N/A 7 N/A N/A self qFrame N/A int N/A args N/A 16 N/A N/A self qStrand N/A N/A N/A args N/A 17 Minus - + N/A N/A self subject N/A args N/A 5 N/A N/A self sStart N/A int N/A args N/A 8 N/A N/A self sStop N/A int N/A args N/A 9 N/A N/A self sDesc N/A args N/A 15 N/A N/A self sLen N/A int N/A args N/A 18 N/A N/A N/A self qStrand - N/A N/A N/A N/A self sStart N/A self sStop N/A N/A self sStop N/A self sStart N/A N/A self pctid N/A float N/A args N/A 10 N/A N/A self pctsim N/A float N/A args N/A 11 N/A N/A self date N/A args N/A 1 N/A N/A self method N/A args N/A 3 N/A N/A self database N/A args N/A 4 N/A aat_dialect N/A N/A N/A self score N/A float N/A args N/A 12 N/A N/A self chainNum N/A int N/A args N/A 13 N/A N/A self segmentNum N/A int N/A args N/A 14 N/A N/A self key N/A N/A - join N/A N/A str x N/A x N/A N/A self query N/A self subject N/A self chainNum N/A N/A N/A self score N/A float N/A args N/A 13 N/A N/A self evalue N/A float N/A args N/A 19 N/A N/A self pvalue N/A N/A N/A len args 20 N/A float N/A args N/A 20 None N/A __getitem__ N/A N/A self key N/A N/A N/A N/A getattr self key N/A blastline N/A N/A self N/A N/A N/A N/A N/A join N/A N/A self query N/A N/A N/A self subject N/A self sDesc N/A %.2f N/A self pctid 0 0 0 N/A %d N/A self qStart N/A %d N/A self qStop N/A %d N/A self sStart N/A %d N/A self sStop N/A %.1g N/A self evalue N/A %.1f N/A self score N/A property gffline N/A N/A self source type primary_tag id N/A None match_part Parent None N/A N/A source N/A N/A source N/A self method source N/A N/A type valid_gff_type N/A N/A score N/A N/A {0:.2f} format N/A self pctid N/A target N/A N/A join N/A N/A str x N/A x N/A N/A self subject N/A self sStart N/A self sStop N/A attributes N/A N/A ; join N/A N/A str x N/A x N/A N/A N/A primary_tag = id N/A Target= target N/A N/A score . N/A note N/A N/A N/A self sDesc N/A N/A "{0}" format N/A self sDesc N/A self sDesc N/A attributes N/A N/A ; join N/A N/A str x N/A x N/A N/A N/A primary_tag = id N/A Name= N/A self subject N/A Note= note N/A line N/A N/A join N/A N/A str x N/A x N/A N/A self query source type N/A self qStart N/A self qStop score N/A self qStrand . attributes N/A line N/A N/A Btab N/A LineFile N/A __init__ N/A N/A self filename aat_dialect N/A False N/A N/A N/A N/A N/A super Btab self __init__ filename N/A line N/A must_open filename N/A N/A N/A N/A line N/A 0 # N/A N/A N/A N/A N/A self append N/A BtabLine line aat_dialect aat_dialect N/A N/A main N/A N/A N/A N/A N/A actions N/A N/A blast convert btab to BLAST -m8 format N/A bed convert btab to bed format N/A gff convert from btab (generated by AAT) to gff3 format N/A p N/A ActionDispatcher actions N/A N/A N/A p dispatch N/A globals N/A blast N/A N/A args N/A N/A N/A 
    %prog blast btabfile

    Convert to BLAST -m8 format.
     N/A p N/A OptionParser N/A blast __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 btabfile args N/A btab N/A Btab btabfile N/A b btab N/A N/A N/A b blastline N/A bed N/A N/A args N/A N/A N/A 
    %prog bed btabfile

    Convert btab to bed format.
     jcvi.formats.blast BlastLine N/A p N/A OptionParser N/A bed __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 btabfile args N/A btab N/A Btab btabfile N/A b btab N/A N/A Bline N/A BlastLine N/A b blastline N/A N/A Bline bedline N/A gff N/A N/A args N/A N/A N/A 
    %prog gff btabfile

    Convert btab file generated by AAT to gff3 format.
     jcvi.utils.range range_minmax jcvi.formats.gff valid_gff_parent_child valid_gff_type N/A p N/A OptionParser N/A gff __doc__ N/A N/A N/A p add_option --source default None help N/A N/A Specify GFF source.  By default, it picks algorithm used to generate btab file.  [default: %default] N/A N/A N/A p add_option --type default protein_match choices valid_gff_type help GFF feature type [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 btabfile args N/A btabdict N/A N/A btab N/A Btab btabfile aat_dialect True N/A osource N/A N/A opts source aat N/A otype N/A opts type N/A octype N/A valid_gff_parent_child N/A otype N/A b btab N/A N/A nargs N/A b nargs N/A id N/A N/A N/A N/A b query - otype N/A N/A {0:05d} format N/A b chainNum N/A key N/A b key N/A N/A key btabdict N/A N/A N/A btabdict N/A key N/A id method query subject strand sDesc coords children id N/A b method N/A b query N/A b subject N/A b qStrand N/A b sDesc N/A N/A N/A N/A N/A N/A N/A btabdict N/A key N/A coords append N/A N/A b qStart N/A b qStop N/A N/A N/A N/A N/A btabdict N/A key N/A children append N/A N/A b gffline source osource type octype id id N/A v N/A N/A btabdict itervalues N/A N/A b N/A BtabLine N/A N/A join N/A N/A str x N/A x N/A N/A 0 nargs aat_dialect True N/A id N/A v N/A id N/A N/A b query N/A v N/A query N/A N/A b method N/A v N/A method N/A N/A b subject N/A v N/A subject N/A N/A b qStrand N/A v N/A strand N/A N/A b sDesc N/A v N/A sDesc N/A N/A N/A b qStart N/A b qStop N/A range_minmax N/A v N/A coords N/A N/A N/A b gffline source osource type otype primary_tag ID id id N/A N/A N/A join N/A v N/A children N/A N/A N/A __name__ __main__ N/A N/A N/A main