Module Expr Str Import alias Import alias Import alias Import alias Assign NameStore Str Import alias identifier Import alias identifier Import alias identifier If CompareEq NameLoad Str body Assign NameStore Call AttributeLoad NameLoad attr keyword Str keyword SubscriptLoad Call NameLoad Index 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 Expr Call AttributeLoad NameLoad attr keyword Num keyword NameLoad Assign TupleStore NameStore NameStore Call AttributeLoad NameLoad attr NameLoad keyword NameLoad Assign NameStore TupleLoad TupleLoad Str Str TupleLoad Str Str TupleLoad Str Str TupleLoad Str Str TupleLoad Str Str TupleLoad Str Str TupleLoad Str Str TupleLoad Str Str TupleLoad Str Str TupleLoad Str Str TupleLoad Str Str TupleLoad Str Str TupleLoad Str Str TupleLoad Str Str TupleLoad Str Str Assign NameStore Dict Str Str Str Str Str Str Str Num Num Num Num Num Num Num Assign NameStore Call AttributeLoad NameLoad attr AttributeLoad NameLoad attr keyword AttributeLoad NameLoad attr Assign NameStore Dict Expr Call AttributeLoad AttributeLoad NameLoad attr attr Str For TupleStore NameStore NameStore NameLoad body Expr Call AttributeLoad AttributeLoad NameLoad attr attr BinOpMod Str TupleLoad NameLoad NameLoad NameLoad NameLoad Assign SubscriptStore NameLoad Index TupleLoad NameLoad NameLoad Num Expr Call AttributeLoad AttributeLoad NameLoad attr attr Str Assign TupleStore NameStore NameStore NameStore NameStore NameStore TupleLoad Num Num Num Num Num For NameStore NameLoad body AugAssignAdd NameStore Num If BoolOpOr CompareLtE Call NameLoad SubscriptLoad NameLoad Index Str AttributeLoad NameLoad attr CompareLtE Call NameLoad SubscriptLoad NameLoad Index Str AttributeLoad NameLoad attr body AugAssignAdd NameStore Num Continue Expr Call AttributeLoad AttributeLoad NameLoad attr attr SubscriptLoad NameLoad Index Str For TupleStore NameStore NameStore NameLoad body AugAssignAdd NameStore Num Assign NameStore Call NameLoad SubscriptLoad NameLoad Index BinOpMod Str NameLoad Assign NameStore Call NameLoad SubscriptLoad NameLoad Index BinOpMod Str NameLoad Assign NameStore SubscriptLoad NameLoad Index NameLoad Assign NameStore SubscriptLoad NameLoad Index NameLoad If CompareGtE AttributeLoad NameLoad attr Num body Expr Call AttributeLoad AttributeLoad NameLoad attr attr BinOpMod Str TupleLoad NameLoad NameLoad NameLoad NameLoad NameLoad NameLoad If CompareLt NameLoad NameLoad body AugAssignAdd NameStore Num Expr Call AttributeLoad AttributeLoad NameLoad attr attr Str Continue Assign NameStore Call AttributeLoad NameLoad attr NameLoad NameLoad NameLoad NameLoad If AttributeLoad NameLoad attr body AugAssignAdd SubscriptStore NameLoad Index TupleLoad NameLoad NameLoad Num Expr Call AttributeLoad AttributeLoad NameLoad attr attr BinOpMod Str TupleLoad Call AttributeLoad NameLoad attr AttributeLoad NameLoad attr AttributeLoad NameLoad attr Expr Call AttributeLoad AttributeLoad NameLoad attr attr Str AugAssignAdd NameStore Num Expr Call AttributeLoad AttributeLoad NameLoad attr attr Str For TupleStore NameStore NameStore NameLoad body Expr Call AttributeLoad AttributeLoad NameLoad attr attr BinOpMod Str TupleLoad SubscriptLoad NameLoad Index TupleLoad NameLoad NameLoad BinOpDiv BinOpMult Num SubscriptLoad NameLoad Index TupleLoad NameLoad NameLoad NameLoad Expr Call AttributeLoad AttributeLoad NameLoad attr attr Str If AttributeLoad NameLoad attr body Assign NameStore Call NameLoad AttributeLoad NameLoad attr Str For TupleStore NameStore NameStore NameLoad body Expr Call AttributeLoad NameLoad attr BinOpMod Str TupleLoad NameLoad NameLoad SubscriptLoad NameLoad Index TupleLoad NameLoad NameLoad BinOpDiv BinOpMult Num SubscriptLoad NameLoad Index TupleLoad NameLoad NameLoad NameLoad Expr Call AttributeLoad NameLoad attr Expr Call AttributeLoad AttributeLoad NameLoad attr attr BinOpMod Str TupleLoad NameLoad NameLoad NameLoad NameLoad NameLoad Expr Call AttributeLoad NameLoad attr
N/A N/A 
xrate_tms_lrt.py - 
======================================================

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

Purpose
-------

.. todo::
   
   describe purpose of the script.

Usage
-----

Example::

   python xrate_tms_lrt.py --help

Type::

   python xrate_tms_lrt.py --help

for command line help.

Documentation
-------------

Code
----

 N/A sys N/A string N/A re N/A optparse N/A USAGE filter results from an xrate tms run.

This script filters the output of a series computations with xrate_tms.py.

The output is filtered by length (individual minimum length of N- and 
C-terminus).

For each set of nested models, a log likelihood ratio test is performed.

This program takes as input the file lnl.table Makefile.xrate_tms

 N/A CGAT.Experiment Experiment N/A CGAT.Stats Stats N/A CGAT.CSV CSV N/A N/A __name__ __main__ N/A N/A parser N/A N/A optparse OptionParser version %prog version: $Id: xrate_tms_lrt.py 2781 2009-09-10 11:33:14Z andreas $ usage N/A N/A globals N/A __doc__ N/A N/A N/A parser add_option -l --min-length dest min_length type int help minimum individual length (in nucleotides) of N- and C-terminus [default=%default]. N/A N/A N/A parser add_option -g --filename-graph dest filename_graph type string help output filename with graph information [default=%default]. N/A N/A N/A parser set_defaults min_length 0 filename_graph None N/A N/A options args N/A N/A Experiment Start parser add_csv_options True N/A tests N/A N/A none ds N/A none kappa N/A none omega N/A none omega-ds N/A none kappa-ds N/A omega omega-ds N/A kappa kappa-ds N/A ds omega-ds N/A ds kappa-ds N/A omega-ds all N/A kappa-ds all N/A none all N/A kappa all N/A omega all N/A ds all N/A map_model2params N/A none ds omega kappa omega-ds kappa-ds all 8 7 6 6 5 5 4 N/A reader N/A N/A CSV DictReader N/A sys stdin dialect N/A options csv_dialect N/A stats N/A N/A N/A N/A N/A options stdout write id N/A N/A a b tests N/A N/A N/A N/A N/A options stdout write N/A 	%s:%s	p%s:%s N/A a b a b N/A N/A stats N/A N/A a b 0 N/A N/A N/A N/A options stdout write N/A N/A ninput noutput nskipped nerrors ntests N/A 0 0 0 0 0 N/A row reader N/A N/A ninput 1 N/A N/A N/A N/A int N/A row N/A N:len N/A options min_length N/A N/A int N/A row N/A C:len N/A options min_length N/A N/A nskipped 1 N/A N/A N/A N/A N/A options stdout write N/A row N/A id N/A N/A a b tests N/A N/A ntests 1 N/A lnl_complex N/A float N/A row N/A N/A %s:lnL a N/A lnl_simple N/A float N/A row N/A N/A %s:lnL b N/A df_complex N/A map_model2params N/A a N/A df_simple N/A map_model2params N/A b N/A N/A N/A options loglevel 3 N/A N/A N/A N/A N/A options stdlog write N/A # testing %s: ll=%f,df=%i versus %s:lnl=%f,df=%i
 N/A a lnl_complex df_complex b lnl_simple df_simple N/A N/A lnl_complex lnl_simple N/A N/A nerrors 1 N/A N/A N/A N/A options stdout write 	na	na N/A N/A lrt N/A N/A Stats doLogLikelihoodTest lnl_complex df_complex lnl_simple df_simple N/A N/A lrt mPassed N/A N/A N/A stats N/A N/A a b 1 N/A N/A N/A N/A options stdout write N/A 	%s	%5.2e N/A N/A N/A Stats getSignificance N/A lrt mProbability N/A lrt mProbability N/A N/A N/A N/A options stdout write N/A noutput 1 N/A N/A N/A N/A options stdout write npassed N/A N/A a b tests N/A N/A N/A N/A N/A options stdout write N/A 	%i	%5.2f N/A N/A stats N/A N/A a b N/A N/A 100.0 N/A stats N/A N/A a b noutput N/A N/A N/A N/A options stdout write N/A N/A options filename_graph N/A N/A outfile N/A open N/A options filename_graph w N/A N/A a b tests N/A N/A N/A N/A outfile write N/A %s	%s	%i	%5.2f
 N/A a b N/A stats N/A N/A a b N/A N/A 100.0 N/A stats N/A N/A a b noutput N/A N/A N/A outfile close N/A N/A N/A N/A options stdout write N/A # ninput=%i, noutput=%i, nskipped=%i, ntests=%i, nerrors=%i
 N/A ninput noutput nskipped ntests nerrors N/A N/A N/A Experiment Stop