Module Expr Str Import alias Import alias Import alias Import alias ImportFrom alias ImportFrom alias identifier ImportFrom alias identifier ClassDef bases NameLoad body Expr Str Pass FunctionDef arguments args NameParam defaults body Return Call NameLoad AttributeLoad NameLoad attr decorator_list decorator_list ClassDef bases NameLoad body Expr Str FunctionDef arguments args NameParam NameParam NameParam defaults body Assign AttributeStore NameLoad attr BinOpAdd BinOpAdd NameLoad Str NameLoad decorator_list decorator_list ClassDef bases NameLoad body Expr Str FunctionDef arguments args NameParam NameParam defaults body Assign AttributeStore NameLoad attr NameLoad decorator_list decorator_list ClassDef bases body Assign NameStore Str FunctionDef arguments args NameParam defaults body Assign AttributeStore NameLoad attr NameLoad decorator_list FunctionDef arguments args NameParam defaults body If BoolOpAnd AttributeLoad NameLoad attr CompareNotEq AttributeLoad NameLoad attr Str body Expr Call AttributeLoad NameLoad attr BinOpMod Str AttributeLoad NameLoad attr decorator_list FunctionDef arguments args NameParam NameParam NameParam NameParam NameParam NameParam defaults NameLoad Num NameLoad Dict body Assign AttributeStore NameLoad attr Call AttributeLoad NameLoad attr Assign AttributeStore NameLoad attr Str Assign AttributeStore NameLoad attr Str If NameLoad body Print BinOpMod Str AttributeLoad NameLoad attr Expr Call AttributeLoad NameLoad attr Call NameLoad BinOpAdd BinOpAdd AttributeLoad NameLoad attr Str AttributeLoad NameLoad attr Str keyword Str Assign NameStore Call AttributeLoad Str attr TupleLoad AttributeLoad NameLoad attr BinOpMod Str AttributeLoad NameLoad attr BinOpMod Str AttributeLoad NameLoad attr Assign NameStore Call AttributeLoad NameLoad attr NameLoad keyword NameLoad keyword AttributeLoad NameLoad attr keyword AttributeLoad NameLoad attr keyword AttributeLoad NameLoad attr keyword NameLoad Assign TupleStore NameStore NameStore Call AttributeLoad NameLoad attr If CompareNotEq AttributeLoad NameLoad attr Num body Raise NameLoad BinOpMod Str TupleLoad AttributeLoad NameLoad attr NameLoad NameLoad AttributeLoad NameLoad attr If NameLoad body Print BinOpMod Str TupleLoad AttributeLoad NameLoad attr NameLoad Assign NameStore Call AttributeLoad NameLoad attr Expr Call AttributeLoad NameLoad attr Call NameLoad BinOpMod Str TupleLoad AttributeLoad NameLoad attr AttributeLoad NameLoad attr Str keyword Str If UnaryOpNot NameLoad body Expr Call AttributeLoad NameLoad attr AttributeLoad NameLoad attr Return NameLoad decorator_list decorator_list If CompareEq NameLoad Str body 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 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 NameLoad keyword NameLoad keyword NameLoad keyword Str Assign TupleStore NameStore NameStore Call AttributeLoad NameLoad attr NameLoad Expr Call AttributeLoad NameLoad attr
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WrapperMuscle.py - 
======================================================

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

Code
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 N/A os N/A tempfile N/A subprocess N/A shutil types * CGAT Experiment Experiment CGAT Mali Mali Error N/A Exception N/A N/A Base class for exceptions in this module. N/A __str__ N/A N/A self N/A N/A N/A N/A str N/A self message N/A N/A ParsingError N/A Error N/A N/A Exception raised for errors while parsing

    Attributes:
        message -- explanation of the error
     __init__ N/A N/A self message line N/A N/A N/A N/A self message N/A N/A message  at line  line N/A N/A UsageError N/A Error N/A N/A Exception raised for errors while starting

    Attributes:
        message -- explanation of the error
     __init__ N/A N/A self message N/A N/A N/A N/A self message message N/A N/A Muscle N/A N/A N/A mExecutable muscle -maxmb 10000 __init__ N/A N/A self N/A N/A N/A N/A self mTempdir None N/A __del__ N/A N/A self N/A N/A N/A N/A N/A self mTempdir N/A N/A self mTempdir tmp N/A N/A N/A N/A os system N/A rm -rf %s N/A self mTempdir N/A Run N/A N/A self mali tree dump test options N/A None 0 False N/A N/A N/A N/A self mTempdir N/A N/A tempfile mkdtemp N/A N/A self mFilenameInput input N/A N/A self mFilenameOutput output N/A test N/A N/A N/A # temporary directory is %s N/A self mTempdir N/A N/A N/A mali writeToFile N/A open N/A N/A N/A self mTempdir / N/A self mFilenameInput w format fasta N/A statement N/A N/A join N/A N/A self mExecutable N/A -in %s N/A self mFilenameInput N/A -out %s N/A self mFilenameOutput N/A s N/A N/A subprocess Popen statement shell True stdout N/A subprocess PIPE stderr N/A subprocess PIPE cwd N/A self mTempdir close_fds True N/A N/A out err N/A N/A s communicate N/A N/A N/A s returncode 0 N/A N/A UsageError N/A Error in running %s 
%s
%s
Temporary directory in %s N/A N/A self mExecutable err out N/A self mTempdir N/A dump N/A N/A N/A # stdout output of %s:
%s
###################################### N/A N/A self mExecutable out N/A result N/A N/A Mali Mali N/A N/A N/A result readFromFile N/A open N/A %s/%s N/A N/A self mTempdir N/A self mFilenameOutput r format fasta N/A N/A test N/A N/A N/A N/A shutil rmtree N/A self mTempdir N/A result N/A N/A N/A N/A __name__ __main__ N/A N/A parser N/A N/A E OptionParser version %prog version: $Id: WrapperMuscle.py 2784 2009-09-10 11:41:14Z andreas $ N/A N/A N/A parser add_option -t --filename-input-tree dest filename_input_tree type string help filename with tree information. N/A N/A N/A parser add_option -T --filename-output-tree dest filename_output_tree type string help output filename with tree information. N/A N/A N/A parser add_option -p --program dest program type string help program to use. N/A N/A N/A parser add_option -o --options dest options type string help input options. N/A N/A N/A parser set_defaults filename_input_tree None filename_output_tree None program None options N/A N/A options args N/A N/A Experiment Start parser N/A N/A N/A Experiment Stop