comparison extract_bcs.py @ 7:bb59215dfd8f draft

Uploaded

6:1bfc5a5de843

By default output is written to stdout.

Example usage:
- remove barcode nucleotides at positions 1-3 and 6-7 from FASTQ; write modified
  FASTQ entries to output.fastq and barcode nucleotides to barcodes.fa:
fastq_extract_barcodes.py barcoded_input.fastq XXXNNXX --out output.fastq --bcs barcodes.fa
"""

epilog = """
Author: Daniel Maticzka
Copyright: 2015

    "-o", "--outfile",
    help="Write results to this file.")
parser.add_argument(
    "-b", "--bcs",
    dest="out_bc_fasta",
    help="If set, barcodes are written to this file in FASTA format.")
parser.add_argument(
    "-a", "--add-bc-to-fastq",
    dest="add_to_head",
    help="If set, append extracted barcodes to the FASTQ headers.",
    action="store_true"
)
parser.add_argument(
    "-v", "--verbose",
    help="Be verbose.",
    action="store_true")
parser.add_argument(

    help="Print lots of debugging information",
    action="store_true")
parser.add_argument(
    '--version',
    action='version',
    version='1.0.0')

args = parser.parse_args()
if args.debug:
    logging.basicConfig(level=logging.DEBUG, format="%(asctime)s - %(filename)s - %(levelname)s - %(message)s")
elif args.verbose:

logging.info("  pattern: '{}'".format(args.pattern))
if args.outfile:
    logging.info("  outfile: enabled writing to file")
    logging.info("  outfile: '{}'".format(args.outfile))
if args.out_bc_fasta:
    logging.info("  bcs: enabled writing barcodes to fasta file")
    logging.info("  bcs: {}".format(args.out_bc_fasta))
logging.info("")

# check if supplied pattern is valid
valid_pattern = re.compile("^[XN]+$")
pattern_match = valid_pattern.match(args.pattern)

        logging.debug("len(seq): {}".format(len(seq)))
        continue

    # extract barcode nucleotides
    barcode_list = []
    for bcstart, bcstop in barcode_positions:
        barcode_list.append(seq[bcstart:bcstop])
    barcode = "".join(barcode_list)
    logging.debug("extracted barcode: {}".format(barcode))

    # create new sequence and quality string without barcode nucleotides
    new_seq_list = []
    new_qual_list = []

        annotated_header = header
    samout.write("@%s\n%s\n+\n%s\n" % (annotated_header, new_seq, new_qual))

    # write barcode to fasta if requested
    if args.out_bc_fasta is not None:
        faout.write(">{}\n{}\n".format(header, barcode))

# close files
samout.close()
if args.out_bc_fasta is not None:
    faout.close()

7:bb59215dfd8f

By default output is written to stdout.

Example usage:
- remove barcode nucleotides at positions 1-3 and 6-7 from FASTQ; write modified
  FASTQ entries to output.fastq and barcode nucleotides to barcodes.fa:
fastq_extract_barcodes.py barcoded_input.fastq XXXNNXX --out output.fastq --bcs barcodes.fastq
"""

epilog = """
Author: Daniel Maticzka
Copyright: 2015

    "-o", "--outfile",
    help="Write results to this file.")
parser.add_argument(
    "-b", "--bcs",
    dest="out_bc_fasta",
    help="Write barcodes to this file in FASTQ format.")
parser.add_argument(
    "--fasta-barcodes",
    dest="save_bcs_as_fa",
    action="store_true",
    help="Save extracted barcodes in FASTA format.")
parser.add_argument(
    "-a", "--add-bc-to-fastq",
    dest="add_to_head",
    help="Append extracted barcodes to the FASTQ headers.",
    action="store_true")
parser.add_argument(
    "-v", "--verbose",
    help="Be verbose.",
    action="store_true")
parser.add_argument(

    help="Print lots of debugging information",
    action="store_true")
parser.add_argument(
    '--version',
    action='version',
    version='0.1.0')

args = parser.parse_args()
if args.debug:
    logging.basicConfig(level=logging.DEBUG, format="%(asctime)s - %(filename)s - %(levelname)s - %(message)s")
elif args.verbose:

logging.info("  pattern: '{}'".format(args.pattern))
if args.outfile:
    logging.info("  outfile: enabled writing to file")
    logging.info("  outfile: '{}'".format(args.outfile))
if args.out_bc_fasta:
    logging.info("  bcs: enabled writing barcodes to fastq file")
    logging.info("  bcs: {}".format(args.out_bc_fasta))
if args.save_bcs_as_fa:
    logging.info("  fasta-barcodes: write barcodes in fasta format instead of fastq")
logging.info("")

# check if supplied pattern is valid
valid_pattern = re.compile("^[XN]+$")
pattern_match = valid_pattern.match(args.pattern)

        logging.debug("len(seq): {}".format(len(seq)))
        continue

    # extract barcode nucleotides
    barcode_list = []
    barcode_qual_list = []
    for bcstart, bcstop in barcode_positions:
        barcode_list.append(seq[bcstart:bcstop])
        barcode_qual_list.append(qual[bcstart:bcstop])
    barcode = "".join(barcode_list)
    barcode_quals = "".join(barcode_qual_list)
    logging.debug("extracted barcode: {}".format(barcode))

    # create new sequence and quality string without barcode nucleotides
    new_seq_list = []
    new_qual_list = []

        annotated_header = header
    samout.write("@%s\n%s\n+\n%s\n" % (annotated_header, new_seq, new_qual))

    # write barcode to fasta if requested
    if args.out_bc_fasta is not None:
        if args.save_bcs_as_fa:
            faout.write(">{}\n{}\n".format(header, barcode))
        else:
            faout.write("@{}\n{}\n+\n{}\n".format(header, barcode, barcode_quals))

# close files
samout.close()
if args.out_bc_fasta is not None:
    faout.close()