view extract_bcs.py @ 55:4bedd35bcdff draft

Move deps from macros to individual tools

#!/usr/bin/env python

import argparse
import logging
import re
from sys import stdout
from Bio.SeqIO.QualityIO import FastqGeneralIterator
# avoid ugly python IOError when stdout output is piped into another program
# and then truncated (such as piping to head)
from signal import signal, SIGPIPE, SIG_DFL
signal(SIGPIPE, SIG_DFL)

tool_description = """
Exract barcodes from a FASTQ file according to a user-specified pattern.

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
License: Apache
Email: [e-mail]
Status: Testing
"""

# parse command line arguments
parser = argparse.ArgumentParser(description=tool_description,
                                 epilog=epilog,
                                 formatter_class=argparse.RawDescriptionHelpFormatter)
# positional arguments
parser.add_argument(
    "infile",
    help="Path to fastq file.")
parser.add_argument(
    "pattern",
    help="Pattern of barcode nucleotides starting at 5'-end. X positions will be moved to the header, N positions will be kept.")
# optional arguments
parser.add_argument(
    "-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(
    "-d", "--debug",
    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.basicConfig(level=logging.INFO, format="%(filename)s - %(levelname)s - %(message)s")
else:
    logging.basicConfig(format="%(filename)s - %(levelname)s - %(message)s")
logging.info("Parsed arguments:")
logging.info("  infile: '{}'".format(args.infile))
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)
if pattern_match is None:
    raise ValueError("Error: supplied pattern '{}' is not valid.".format(args.pattern))

# check if at least one barcode position is included in the pattern
has_bcpos_pattern = re.compile("X")
pattern_match = has_bcpos_pattern.search(args.pattern)
if pattern_match is None:
    raise ValueError("Error: supplied pattern '{}' does not contain a barcode position 'X'.".format(args.pattern))

logging.info("Barcode pattern analysis:")
# get X positions of pattern string
barcode_nt_pattern = re.compile("X+")
barcode_positions = []
for m in re.finditer(barcode_nt_pattern, args.pattern):
    logging.info('  found barcode positions in pattern: %02d-%02d: %s' % (m.start(), m.end(), m.group(0)))
    barcode_positions.append((m.start(), m.end()))
logging.info("  barcode positions: {}".format(barcode_positions))
# get last position of a barcode nt in the pattern
# reads must be long enough for all
min_readlen = barcode_positions[-1][-1]
logging.info("  last position of a barcode nt in pattern: {}".format(min_readlen))
logging.info("")

# get coordinates of nucleotides to keep
# the tail after the last barcode nt is handled separately
seq_positions = []
last_seq_start = 0
for bcstart, bcstop in barcode_positions:
    seq_positions.append((last_seq_start, bcstart))
    last_seq_start = bcstop
logging.info("  sequence positions: {}".format(seq_positions))
logging.info("  start of sequence tail: {}".format(last_seq_start))

samout = (open(args.outfile, "w") if args.outfile is not None else stdout)
if args.out_bc_fasta is not None:
    faout = open(args.out_bc_fasta, "w")
for header, seq, qual in FastqGeneralIterator(open(args.infile)):

    # skip reads that are too short to extract the full requested barcode
    if len(seq) < min_readlen:
        logging.warning("skipping read '{}', is too short to extract the full requested barcode".format(header))
        logging.debug("seq: {}".format(seq))
        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 = []
    for seqstart, seqstop in seq_positions:
        new_seq_list.append(seq[seqstart:seqstop])
        new_qual_list.append(qual[seqstart:seqstop])
    new_seq_list.append(seq[last_seq_start:])
    new_qual_list.append(qual[last_seq_start:])
    new_seq = "".join(new_seq_list)
    new_qual = "".join(new_qual_list)
    # check if at least one nucleotide is left. having none would break fastq
    if len(new_seq) == 0:
        logging.warning("skipping read '{}', no sequence remains after barcode extraction".format(header))
        logging.debug("seq: {}".format(seq))
        logging.debug("len(seq): {}".format(len(seq)))
        continue

    # write barcode nucleotides into header
    if args.add_to_head:
        annotated_header = " ".join([header, barcode])
    else:
        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()