Module Expr Str Import alias Import alias identifier Import alias identifier Expr Str FunctionDef arguments args NameParam NameParam defaults body Assign NameStore Call AttributeLoad NameLoad attr AttributeLoad NameLoad attr If CompareEq Call NameLoad NameLoad Num body Assign TupleStore NameStore NameStore NameStore SubscriptLoad NameLoad Slice Num orelse If CompareEq Call NameLoad NameLoad Num body Assign TupleStore NameStore NameStore NameLoad Assign NameStore NameLoad orelse Expr Call AttributeLoad AttributeLoad NameLoad attr attr BinOpMod Str NameLoad Raise NameLoad Return TupleLoad NameLoad NameLoad NameLoad decorator_list FunctionDef arguments args NameParam NameParam defaults body Expr Str Assign NameStore Dict Assign NameStore Dict For NameStore NameLoad body TryExcept body Assign TupleStore NameStore NameStore NameStore Call NameLoad NameLoad NameLoad handlers ExceptHandler type NameLoad body Continue If CompareNotIn NameLoad NameLoad body Assign SubscriptStore NameLoad Index NameLoad Call NameLoad Assign SubscriptStore NameLoad Index NameLoad Call NameLoad Expr Call AttributeLoad SubscriptLoad NameLoad Index NameLoad attr NameLoad Expr Call AttributeLoad SubscriptLoad NameLoad Index NameLoad attr NameLoad Return TupleLoad NameLoad NameLoad decorator_list FunctionDef arguments args NameParam NameParam NameParam defaults body Expr Str Assign NameStore ListLoad For NameStore NameLoad body TryExcept body Assign TupleStore NameStore NameStore NameStore Call NameLoad NameLoad NameLoad handlers ExceptHandler type NameLoad body Continue If CompareIn NameLoad NameLoad body Expr Call AttributeLoad NameLoad attr NameLoad Return NameLoad decorator_list FunctionDef arguments args NameParam defaults NameLoad body Expr Str If CompareIs NameLoad NameLoad body Assign NameStore AttributeLoad NameLoad attr Assign NameStore Call AttributeLoad NameLoad attr keyword Str Expr Call AttributeLoad NameLoad attr Str Str keyword Str keyword Str keyword Str Expr Call AttributeLoad NameLoad attr Str Str keyword Str keyword Str keyword Str keyword TupleLoad Str Str Str Str keyword Str Expr Call AttributeLoad NameLoad attr Str Str keyword Str keyword Str keyword Str Expr Call AttributeLoad NameLoad attr keyword Str keyword Str keyword ListLoad keyword Str Assign TupleStore NameStore NameStore Call AttributeLoad NameLoad attr NameLoad Assign TupleStore AttributeStore NameLoad attr AttributeStore NameLoad attr NameLoad Assign TupleStore NameStore NameStore Call AttributeLoad NameLoad attr Call NameLoad AttributeLoad NameLoad attr Str Assign TupleStore NameStore NameStore Call AttributeLoad NameLoad attr Call NameLoad AttributeLoad NameLoad attr Str Assign TupleStore NameStore NameStore Call NameLoad NameLoad NameLoad Assign TupleStore NameStore NameStore Call NameLoad NameLoad NameLoad Expr Call AttributeLoad AttributeLoad NameLoad attr attr Str Expr Call AttributeLoad AttributeLoad NameLoad attr attr Str Expr Call AttributeLoad AttributeLoad NameLoad attr attr Str For NameStore Call AttributeLoad Call NameLoad Call AttributeLoad NameLoad attr attr Call NameLoad Call AttributeLoad NameLoad attr body Assign TupleStore NameStore NameStore NameStore NameStore TupleLoad Str Str Str Str If CompareIn NameLoad NameLoad body Assign NameStore SubscriptLoad NameLoad Index NameLoad Assign NameStore SubscriptLoad NameLoad Index NameLoad Assign NameStore BinOpMod Str Call NameLoad SubscriptLoad NameLoad Index NameLoad Assign NameStore BinOpMod Str Call NameLoad SubscriptLoad NameLoad Index NameLoad orelse Assign TupleStore NameStore NameStore TupleLoad NameLoad NameLoad If CompareIn NameLoad NameLoad body Assign NameStore SubscriptLoad NameLoad Index NameLoad Assign NameStore SubscriptLoad NameLoad Index NameLoad Assign NameStore BinOpMod Str Call NameLoad SubscriptLoad NameLoad Index NameLoad Assign NameStore BinOpMod Str Call NameLoad SubscriptLoad NameLoad Index NameLoad orelse Assign TupleStore NameStore NameStore TupleLoad NameLoad NameLoad If BoolOpAnd CompareIn NameLoad NameLoad NameLoad body Assign NameStore BinOpMod Str Call NameLoad Call AttributeLoad NameLoad attr NameLoad Assign NameStore BinOpMod Str Call NameLoad Call AttributeLoad NameLoad attr NameLoad Assign NameStore BinOpMod Str Call NameLoad Call AttributeLoad NameLoad attr NameLoad Assign NameStore BinOpMod Str Call NameLoad Call AttributeLoad NameLoad attr NameLoad orelse Assign TupleStore NameStore NameStore NameStore NameStore BinOpMult ListLoad Str Num If BoolOpAnd CompareIn NameLoad NameLoad NameLoad body Assign NameStore BinOpMod Str Call NameLoad Call AttributeLoad NameLoad attr NameLoad Assign NameStore BinOpMod Str Call NameLoad Call AttributeLoad NameLoad attr NameLoad Assign NameStore BinOpMod Str Call NameLoad Call AttributeLoad NameLoad attr NameLoad Assign NameStore BinOpMod Str Call NameLoad Call AttributeLoad NameLoad attr NameLoad orelse Assign TupleStore NameStore NameStore NameStore NameStore BinOpMult ListLoad Str Num Expr Call AttributeLoad AttributeLoad NameLoad attr attr Call AttributeLoad Str attr TupleLoad NameLoad NameLoad NameLoad NameLoad NameLoad Expr Call AttributeLoad AttributeLoad NameLoad attr attr Str Expr Call AttributeLoad AttributeLoad NameLoad attr attr Call AttributeLoad Str attr TupleLoad NameLoad NameLoad NameLoad NameLoad Expr Call AttributeLoad AttributeLoad NameLoad attr attr Str Expr Call AttributeLoad AttributeLoad NameLoad attr attr Call AttributeLoad Str attr TupleLoad NameLoad NameLoad NameLoad NameLoad If AttributeLoad NameLoad attr body If BoolOpAnd CompareIn NameLoad NameLoad NameLoad body Assign NameStore BinOpMod Str BinOpDiv BinOpMult Num Call NameLoad Call AttributeLoad NameLoad attr NameLoad Call NameLoad NameLoad Assign NameStore BinOpMod Str BinOpDiv BinOpMult Num Call NameLoad Call AttributeLoad NameLoad attr NameLoad Call NameLoad NameLoad If BoolOpAnd CompareIn NameLoad NameLoad NameLoad body Assign NameStore BinOpMod Str BinOpDiv BinOpMult Num Call NameLoad Call AttributeLoad NameLoad attr NameLoad Call NameLoad NameLoad Assign NameStore BinOpMod Str BinOpDiv BinOpMult Num Call NameLoad Call AttributeLoad NameLoad attr NameLoad Call NameLoad NameLoad Expr Call AttributeLoad AttributeLoad NameLoad attr attr Str Expr Call AttributeLoad AttributeLoad NameLoad attr attr Call AttributeLoad Str attr TupleLoad NameLoad NameLoad NameLoad NameLoad Expr Call AttributeLoad AttributeLoad NameLoad attr attr Str For NameStore AttributeLoad NameLoad attr body Assign NameStore NameLoad If BoolOpAnd CompareEq NameLoad Str NameLoad NameLoad body Assign NameStore Call NameLoad Call AttributeLoad NameLoad attr NameLoad NameLoad NameLoad orelse If BoolOpAnd CompareEq NameLoad Str NameLoad NameLoad body Assign NameStore Call NameLoad Call AttributeLoad NameLoad attr NameLoad NameLoad NameLoad If NameLoad body Assign NameStore Call NameLoad BinOpMod AttributeLoad NameLoad attr NameLoad Str For NameStore NameLoad body Expr Call AttributeLoad NameLoad attr BinOpMod Str TupleLoad NameLoad Expr Call AttributeLoad NameLoad attr Expr Call AttributeLoad NameLoad attr decorator_list If CompareEq NameLoad Str body Expr Call AttributeLoad NameLoad attr Call NameLoad AttributeLoad NameLoad attr
N/A N/A 
diff_transcript_sets.py - 
======================================================

:Author: Andreas Heger
:Release: $Id$
:Date: |today|
:Tags: Python

Purpose
-------

.. todo::
   
   describe purpose of the script.

Usage
-----

Example::

   python diff_transcript_sets.py --help

Type::

   python diff_transcript_sets.py --help

for command line help.

Command line options
--------------------

 N/A sys N/A CGAT.Experiment E N/A CGAT.IOTools IOTools N/A  program $Id: diff_transcript_sets.py 2781 2009-09-10 11:33:14Z andreas $

show differences between two transcript sets.
 parseIdentifier N/A N/A id options N/A N/A N/A data N/A N/A id split N/A options separator N/A N/A N/A len data 4 N/A N/A N/A species transcript gene N/A data N/A 3 N/A N/A N/A N/A len data 2 N/A N/A N/A species gene data N/A transcript gene N/A N/A N/A N/A N/A options stderr write N/A # parsing error for '%s'
 id N/A ValueError N/A N/A species transcript gene N/A countGenesTranscripts N/A N/A inlist options N/A N/A N/A count number of genes/transcripts in list. N/A genes N/A N/A transcripts N/A N/A x inlist N/A N/A N/A N/A N/A species transcript gene N/A parseIdentifier x options N/A N/A N/A ValueError N/A N/A N/A N/A species genes N/A N/A N/A genes N/A species N/A set N/A N/A transcripts N/A species N/A set N/A N/A N/A N/A transcripts N/A species add transcript N/A N/A N/A N/A genes N/A species add gene N/A N/A genes transcripts N/A getTranscriptsForGenes N/A N/A genes transcripts options N/A N/A N/A get transcripts for list of genes. N/A result N/A N/A x transcripts N/A N/A N/A N/A N/A species transcript gene N/A parseIdentifier x options N/A N/A N/A ValueError N/A N/A N/A N/A gene genes N/A N/A N/A N/A result append x N/A result N/A main N/A N/A argv N/A None N/A N/A script main.

    parses command line options in sys.argv, unless *argv* is given.
     N/A N/A argv None N/A N/A argv N/A sys argv N/A parser N/A N/A E OptionParser version %prog version: $Id: diff_transcript_sets.py 2781 2009-09-10 11:33:14Z andreas $ N/A N/A N/A parser add_option -p --add-percent dest add_percent action store_true help add percent columns N/A N/A N/A parser add_option -d --dump-sets dest dump_sets action append type choice choices N/A rest_genes1 rest_genes2 intersection union help dump sets of transcripts/genes N/A N/A N/A parser add_option -o --output-filename-pattern dest output_pattern type string help output pattern to use for dumped sets. Should contain one %s. N/A N/A N/A parser set_defaults separator | add_percent False dump_sets N/A output_pattern %s N/A N/A options args N/A N/A E Start parser N/A N/A N/A options filename1 N/A options filename2 args N/A N/A ids1 nerrors1 N/A N/A IOTools ReadList N/A open N/A options filename1 r N/A N/A ids2 nerrors2 N/A N/A IOTools ReadList N/A open N/A options filename2 r N/A N/A genes1 transcripts1 N/A countGenesTranscripts ids1 options N/A N/A genes2 transcripts2 N/A countGenesTranscripts ids2 options N/A N/A N/A N/A options stdout write species	ngenes1	ntranscripts1	ngenes2	ntranscripts2	tr_inter	tr_union	tr_rest1	tr_rest2	tr_inter	g_union	g_rest1	g_rest2 N/A N/A N/A N/A options stdout write 	tr_rest1	tr_rest2	g_rest1	g_rest2 N/A N/A N/A N/A options stdout write N/A species N/A N/A N/A set N/A N/A genes1 keys union N/A set N/A N/A genes2 keys N/A N/A N/A nt1 nt2 ng1 ng2 N/A na na na na N/A N/A species genes1 N/A N/A g1 N/A genes1 N/A species N/A t1 N/A transcripts1 N/A species N/A nt1 N/A %i N/A len N/A transcripts1 N/A species N/A ng1 N/A %i N/A len N/A genes1 N/A species N/A N/A N/A t1 g1 N/A None None N/A N/A species genes2 N/A N/A g2 N/A genes2 N/A species N/A t2 N/A transcripts2 N/A species N/A nt2 N/A %i N/A len N/A transcripts2 N/A species N/A ng2 N/A %i N/A len N/A genes2 N/A species N/A N/A N/A t2 g2 N/A None None N/A N/A N/A species transcripts1 transcripts2 N/A N/A ct N/A %i N/A len N/A N/A t1 intersection t2 N/A ut N/A %i N/A len N/A N/A t2 union t1 N/A rt1 N/A %i N/A len N/A N/A t1 difference t2 N/A rt2 N/A %i N/A len N/A N/A t2 difference t1 N/A N/A N/A ct ut rt1 rt2 N/A N/A na 4 N/A N/A N/A species genes1 genes2 N/A N/A cg N/A %i N/A len N/A N/A g1 intersection g2 N/A ug N/A %i N/A len N/A N/A g2 union g1 N/A rg1 N/A %i N/A len N/A N/A g1 difference g2 N/A rg2 N/A %i N/A len N/A N/A g2 difference g1 N/A N/A N/A cg ug rg1 rg2 N/A N/A na 4 N/A N/A N/A N/A options stdout write N/A N/A join N/A species nt1 ng1 nt2 ng2 N/A N/A N/A N/A options stdout write N/A N/A N/A N/A options stdout write N/A N/A join N/A ct ut rt1 rt2 N/A N/A N/A N/A options stdout write N/A N/A N/A N/A options stdout write N/A N/A join N/A cg ug rg1 rg2 N/A N/A options add_percent N/A N/A N/A N/A species genes1 genes2 N/A N/A rg1 N/A %5.2f N/A N/A 100.0 N/A len N/A N/A g1 difference g2 N/A len g1 N/A rg2 N/A %5.2f N/A N/A 100.0 N/A len N/A N/A g2 difference g1 N/A len g2 N/A N/A N/A species transcripts1 transcripts2 N/A N/A rt1 N/A %5.2f N/A N/A 100.0 N/A len N/A N/A t1 difference t2 N/A len t1 N/A rt2 N/A %5.2f N/A N/A 100.0 N/A len N/A N/A t2 difference t1 N/A len t2 N/A N/A N/A N/A options stdout write N/A N/A N/A N/A options stdout write N/A N/A join N/A rt1 rt2 rg1 rg2 N/A N/A N/A N/A options stdout write N/A choice N/A options dump_sets N/A N/A output_set None N/A N/A N/A choice rest_genes1 g1 g2 N/A N/A output_set N/A getTranscriptsForGenes N/A N/A g1 difference g2 ids1 options N/A N/A N/A N/A choice rest_genes2 g1 g2 N/A N/A output_set N/A getTranscriptsForGenes N/A N/A g2 difference g1 ids2 options N/A output_set N/A N/A outfile N/A open N/A N/A options output_pattern choice w N/A x output_set N/A N/A N/A N/A outfile write N/A %s
 N/A x N/A N/A N/A outfile close N/A N/A N/A E Stop N/A N/A N/A __name__ __main__ N/A N/A N/A N/A sys exit N/A main N/A sys argv