comparison fasta_extract.py @ 7:4f6eba6beef5 draft

Uploaded

6:d077d91065ea

    if consider_strand:
        attrs += '_s'
    if orphan:
        attrs += '_orphan'
        format = 'gff'
    else:
        format = 'fasta'
    if orphan:
        return os.path.join('output_orphan_dir', '%s_on_data_%d.%s' % (attrs, hid, format))
    return os.path.join('output_dir', '%s_on_data_%d.%s' % (attrs, hid, format))


def stop_err(msg):
    sys.stderr.write(msg)
    sys.exit(1)

args = parser.parse_args()

fasta = Fasta(args.genome_file)

for (input_filename, hid) in args.inputs:
    hid = int(hid)
    extend_existing = args.extend_existing == 'existing'
    consider_strand = args.strand == 'yes'
    reader = csv.reader(open(input_filename, 'rU'), delimiter='\t')
    fasta_output_path = get_output_path(hid,
                                        args.subtract_from_start,

                output.write('%s\n' % bases)
            else:
                orphan_writer.writerow(row)
        except Exception, e:
            stop_err(str(e))

7:4f6eba6beef5

    if consider_strand:
        attrs += '_s'
    if orphan:
        attrs += '_orphan'
        format = 'gff'
        output_dir = 'output_orphan_dir'
    else:
        format = 'fasta'
        output_dir = 'output_dir'
    return os.path.join(output_dir, '%s_on_data_%d.%s' % (attrs, hid, format))


def stop_err(msg):
    sys.stderr.write(msg)
    sys.exit(1)

args = parser.parse_args()

fasta = Fasta(args.genome_file)

for (input_filename, hid) in args.inputs:
    extend_existing = args.extend_existing == 'existing'
    consider_strand = args.strand == 'yes'
    reader = csv.reader(open(input_filename, 'rU'), delimiter='\t')
    fasta_output_path = get_output_path(hid,
                                        args.subtract_from_start,

                output.write('%s\n' % bases)
            else:
                orphan_writer.writerow(row)
        except Exception, e:
            stop_err(str(e))
        finally:
            output.clode()