Module Expr Str ImportFrom alias identifier Import alias ClassDef bases AttributeLoad NameLoad attr body Expr Str FunctionDef arguments args NameParam NameParam NameParam defaults NameLoad body Expr Str Assign NameStore SubscriptLoad Call AttributeLoad NameLoad attr Str Index Num Assign NameStore Call NameLoad Lambda arguments args NameParam defaults Call AttributeLoad NameLoad attr Call AttributeLoad NameLoad attr Str Assign AttributeStore NameLoad attr Dict For NameStore NameLoad body Assign NameStore Call NameLoad Lambda arguments args NameParam defaults Call AttributeLoad NameLoad attr Call AttributeLoad NameLoad attr Str Assign TupleStore NameStore NameStore TupleLoad SubscriptLoad NameLoad Index Num SubscriptLoad NameLoad Index Num If CompareGt Call NameLoad NameLoad Num body Assign NameStore SubscriptLoad NameLoad Slice Num If BoolOpAnd CompareEq SubscriptLoad NameLoad Index Num Str CompareEq SubscriptLoad NameLoad Index Num Str body Assign NameStore SubscriptLoad NameLoad Slice Num Num orelse TryExcept body Assign NameStore Call NameLoad NameLoad Assign NameStore Call NameLoad NameLoad handlers ExceptHandler type NameLoad body Pass ExceptHandler type NameLoad body Pass If CompareEq NameLoad Str body Assign NameStore Call AttributeLoad NameLoad attr Str Assign SubscriptStore AttributeLoad NameLoad attr Index NameLoad NameLoad decorator_list FunctionDef arguments args NameParam defaults body Expr Str Assign NameStore ListLoad For TupleStore NameStore NameStore Call AttributeLoad AttributeLoad NameLoad attr attr body If CompareEq NameLoad Str body Assign NameStore Call AttributeLoad Str attr NameLoad Expr Call AttributeLoad NameLoad attr BinOpMod Str TupleLoad NameLoad Call NameLoad NameLoad Return Call AttributeLoad Str attr NameLoad decorator_list decorator_list FunctionDef arguments args NameParam defaults body Expr Str For NameStore NameLoad body If Call AttributeLoad NameLoad attr Str body Raise NameLoad If Call AttributeLoad NameLoad attr Str body Continue If CompareEq Call NameLoad Call AttributeLoad NameLoad attr Num body Continue Assign NameStore Call NameLoad Expr Call AttributeLoad NameLoad attr NameLoad Expr Yield NameLoad decorator_list FunctionDef arguments args NameParam defaults body Expr Str For NameStore NameLoad body Assign NameStore Call NameLoad Expr Call AttributeLoad NameLoad attr Call NameLoad NameLoad Expr Yield NameLoad decorator_list FunctionDef arguments args NameParam defaults body Expr Str Assign NameStore Call NameLoad For NameStore Call AttributeLoad NameLoad attr NameLoad Lambda arguments args NameParam defaults AttributeLoad NameLoad attr body If CompareIn SubscriptLoad NameLoad Index Num NameLoad body Raise Call NameLoad Str Expr Call AttributeLoad NameLoad attr SubscriptLoad NameLoad Index Num Expr Yield SubscriptLoad NameLoad Index Num decorator_list
N/A N/A 
GFF3 - Classes, functions and iterators for working with GFF3 files
-------------------------------------------------------------------

This module mostly inherits from the :mod:`GTF` and replaces selected
functionality to allow working with :term:`GFF3` formatted files.

 CGAT GTF GTF N/A itertools Entry N/A N/A GTF Entry N/A N/A representation of a :term:`GFF3` formatted entry.

    This class inherits from :class:`GTF.Entry`, but changes
    the parsing to reflect GFF3.
     parseInfo N/A N/A self attributes line N/A None N/A N/A  Parse the attributes line of an entry,
        line parameter provided purely for backwards compatability N/A attributes N/A N/A N/A attributes split # N/A 0 N/A fields N/A map N/A N/A N/A x N/A N/A N/A x strip N/A N/A attributes split ; N/A N/A self attributes N/A N/A f fields N/A N/A d N/A map N/A N/A N/A x N/A N/A N/A x strip N/A N/A f split = N/A N/A n v N/A N/A d N/A 0 N/A d N/A 1 N/A N/A N/A len d 2 N/A N/A v N/A d N/A 1 N/A N/A N/A N/A v N/A 0 " N/A N/A v N/A -1 " N/A N/A v N/A v N/A 1 -1 N/A N/A N/A N/A v N/A float v N/A v N/A int v N/A N/A N/A ValueError N/A N/A N/A N/A TypeError N/A N/A N/A N/A n Parent N/A N/A v N/A N/A v split , N/A N/A N/A self attributes N/A n v N/A getAttributeField N/A N/A self N/A N/A N/A  return the attributes field as a ; delimied field  N/A aa N/A N/A N/A k v N/A N/A N/A self attributes items N/A N/A N/A k Parent N/A N/A v N/A N/A , join v N/A N/A N/A aa append N/A %s=%s N/A k N/A str v N/A N/A N/A ; join aa N/A N/A flat_file_iterator N/A N/A infile N/A N/A N/A  simple iterator that iterators over lines in a field
    and yeilds GFF3 Entry objects  N/A line infile N/A N/A N/A N/A line startswith ##FASTA N/A N/A StopIteration N/A N/A N/A line startswith # N/A N/A N/A N/A N/A len N/A N/A line strip 0 N/A N/A N/A gff_entry N/A Entry N/A N/A N/A gff_entry read line N/A N/A gff_entry N/A iterator_from_gff N/A N/A gff_iterator N/A N/A N/A  to make this slot in with other gtf using scripts,
    allow copying of an entry into gff3 format. Acts via str,
    probably not the most efficient way to do things N/A gff gff_iterator N/A N/A result N/A Entry N/A N/A N/A result read N/A str gff N/A N/A result N/A chrom_iterator N/A N/A gff3_iterator N/A N/A N/A  takes a an iterator and returns an iterator over iterators,
    with a new instance every time a new chromosome is found  N/A seen N/A set N/A chrom_set N/A N/A itertools groupby gff3_iterator N/A N/A N/A x N/A N/A x contig N/A N/A N/A N/A chrom_set N/A 0 seen N/A N/A N/A ValueError File doesn't appear to be chromosome sorted N/A N/A N/A seen add N/A chrom_set N/A 0 N/A N/A N/A chrom_set N/A 1 N/A