root/galaxy-central/tools/fastq/tabular_to_fastq.py

#Dan Blankenberg
import sys

def main():
    input_filename = sys.argv[1]
    output_filename = sys.argv[2]
    identifier_col = int( sys.argv[3] ) - 1
    sequence_col = int( sys.argv[4] ) - 1
    quality_col = int( sys.argv[5] ) - 1
    
    max_col = max( identifier_col, sequence_col, quality_col )
    num_reads = None
    fastq_read = None
    skipped_lines = 0
    out = open( output_filename, 'wb' )
    for num_reads, line in enumerate( open( input_filename ) ):
        fields = line.rstrip( '\n\r' ).split( '\t' )
        if len( fields ) > max_col:
            out.write( "@%s\n%s\n+\n%s\n" % ( fields[identifier_col], fields[sequence_col], fields[quality_col] ) )
        else:
            skipped_lines += 1
    
    out.close()
    if num_reads is None:
        print "Input was empty."
    else:
        print "%i tabular lines were written as FASTQ reads. Be sure to use the FASTQ Groomer tool on this output before further analysis." % ( num_reads + 1 - skipped_lines )
    
if __name__ == "__main__": main()