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galaxy-central / tools / fastq / fastq_to_tabular.py

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#Dan Blankenberg
import sys
from galaxy_utils.sequence.fastq import fastqReader

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

def main():
    if len(sys.argv) != 5:
        stop_err("Wrong number of arguments. Expect: fasta tabular desrc_split [type]")
    input_filename = sys.argv[1]
    output_filename = sys.argv[2]
    descr_split = int( sys.argv[3] ) - 1
    if descr_split < 0:
        stop_err("Bad description split value (should be 1 or more)")
    input_type = sys.argv[4] or 'sanger' #input type should ordinarily be unnecessary
    
    num_reads = None
    fastq_read = None
    out = open( output_filename, 'wb' )
    if descr_split == 0:
        #Don't divide the description into multiple columns
        for num_reads, fastq_read in enumerate( fastqReader( open( input_filename ), format = input_type ) ):
            out.write( "%s\t%s\t%s\n" % ( fastq_read.identifier[1:].replace( '\t', ' ' ), fastq_read.sequence.replace( '\t', ' ' ), fastq_read.quality.replace( '\t', ' ' ) ) )
    else:
        for num_reads, fastq_read in enumerate( fastqReader( open( input_filename ), format = input_type ) ):
            words = fastq_read.identifier[1:].replace( '\t', ' ' ).split(None, descr_split)
            #pad with empty columns if required
            words += [""]*(descr_split-len(words))
            out.write( "%s\t%s\t%s\n" % ("\t".join(words), fastq_read.sequence.replace( '\t', ' ' ), fastq_read.quality.replace( '\t', ' ' ) ) )
    out.close()
    if num_reads is None:
        print "No valid FASTQ reads could be processed."
    else:
        print "%i FASTQ reads were converted to Tabular." % ( num_reads + 1 )
    
if __name__ == "__main__": main()