comparison tabular_to_fastq.py @ 2:b8cdc0507586 draft

planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/tabular_to_fastq commit f2582539542b33240234e8ea6093e25d0aee9b6a

1:92034dcbb40a

#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()

2:b8cdc0507586

# Dan Blankenberg
from __future__ import print_function

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
    skipped_lines = 0
    out = open(output_filename, 'w')
    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()