Source

galaxy-central (ngs) / tools / meme / fimo_wrapper.py

#!/usr/bin/env python
#Dan Blankenberg

"""
Read text output from FIMO and create an interval file.
"""
import sys, tempfile, subprocess, shutil, os
from galaxy_utils.sequence.transform import DNA_reverse_complement

buffsize = 1048576

def stop_err( msg ):
    sys.stderr.write( msg )
    sys.exit()

def main():
    assert len( sys.argv ) == 8, "Wrong number of arguments"
    sys.argv.pop(0)
    fimo_cmd = sys.argv.pop(0)
    html_path = sys.argv.pop(0)
    html_out = sys.argv.pop(0)
    interval_out = sys.argv.pop(0)
    txt_out = sys.argv.pop(0)
    xml_out = sys.argv.pop(0)
    gff_out = sys.argv.pop(0)
    
    #run fimo
    try:
        tmp_stderr = tempfile.NamedTemporaryFile()
        #tmp_stderr = open( tmp_filename, 'wb' )
        proc = subprocess.Popen( args=fimo_cmd, shell=True, stderr=tmp_stderr )
        returncode = proc.wait()
        #tmp_stderr.close()
        # get stderr, allowing for case where it's very large
        #tmp_stderr = open( tmp, 'rb' )
        tmp_stderr.seek(0)
        stderr = ''
        try:
            while True:
                stderr += tmp_stderr.read( buffsize )
                if not stderr or len( stderr ) % buffsize != 0:
                    break
        except OverflowError:
            pass
        
        if returncode != 0:
            raise Exception, stderr
    except Exception, e:
        raise Exception, 'Error running FIMO:\n' + str( e )

    shutil.move( os.path.join( html_path, 'fimo.txt' ), txt_out )
    shutil.move( os.path.join( html_path, 'fimo.gff' ), gff_out )
    shutil.move( os.path.join( html_path, 'fimo.xml' ), xml_out )
    shutil.move( os.path.join( html_path, 'fimo.html' ), html_out )
    
    out_file = open( interval_out, 'wb' )
    out_file.write( "#%s\n" % "\t".join( ( "chr", "start", "end", "pattern name", "score", "strand", "matched sequence", "p-value", "q-value" ) ) )
    for line in open( txt_out ):
        if line.startswith( '#' ): continue
        fields = line.rstrip( "\n\r" ).split( "\t" )
        start, end = int( fields[2] ), int( fields[3] )
        sequence = fields[7]
        if start > end:
            start, end = end, start #flip start and end, and set strand
            strand = "-"
            sequence = DNA_reverse_complement( sequence ) #we want sequences relative to strand; FIMO always provides + stranded sequence
        else:
            strand = "+"
        start -= 1 #make 0-based start position
        out_file.write( "%s\n" % "\t".join( [ fields[1], str( start ), str( end ), fields[0], fields[4], strand, sequence, fields[5], fields[6] ] ) )
    out_file.close()

if __name__ == "__main__": main()
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