view trinityrnaseq_protocol/EdgeR_differentialExpression_wrapper.py @ 3:87c03e2aeba3 draft default tip

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−import sys, os, subprocess
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−TRINITY_BASE_DIR = ""
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−if os.environ.has_key('TRINITY_HOME'):
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−    TRINITY_BASE_DIR = os.environ['TRINITY_HOME'];
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−else:
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−    sys.stderr.write("You must set the environmental variable TRINITY_BASE_DIR to the base installation directory of Trinity before running this");
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−    sys.exit(1)
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−
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−usage= "usage: " + " $counts_matrix" + " $dispersion"
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−
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−if len(sys.argv)<2:
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−    print "Require atleast two parameters"
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−else:
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−    print "All good- command going ahead"
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−print " "
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−
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−def run_command(cmd):
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−    print "The command used: " + cmd
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−    pipe=subprocess.Popen(cmd, shell=True, stderr=subprocess.PIPE)
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−    pipe.wait()
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−    ret= pipe.returncode
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−    if ret:
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−        print "command died: " + str(ret)
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−        print pipe.stderr.readlines()
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−        sys.exit(1)
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−    else:
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−        return
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−print " "
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−
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−countmatrix= "counts_matrix"
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−
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−cmd= "cp " + sys.argv[1] + " " + countmatrix 
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−run_command(cmd)
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−
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−cmd= TRINITY_BASE_DIR + "/Analysis/DifferentialExpression/run_DE_analysis.pl "+ " --matrix "+ countmatrix + " --method edgeR " + " --output edgeR_results "+ " --dispersion " + sys.argv[2] + " --tar_gz_outdir"
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−
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−run_command(cmd)
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−
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−sys.exit(0)