#!/usr/bin/env python
+from glob import glob
import os
from optparse import OptionParser
import numpy
import sys
+import tarfile
-def make_parser():
- parser = OptionParser()
- parser.add_option('-o', '--output', help='output fastq file', default=None)
- parser.add_option('-s', '--slice',
- help='specify python slice, e.g. 0:75, 0:-1',
- default=None)
- return parser
+class Qseq2Fastq(object):
+ """
+ Convert qseq files to fastq (or fasta) files.
+ """
+ def __init__(self, sources, pass_destination, nopass_destination=None):
+ self.sources = sources
+ self.pass_destination = pass_destination
+ if nopass_destination is not None:
+ self.nopass_destination = nopass_destination
+ else:
+ self.nopass_destination = pass_destination
+
+ self.fastq = True
+ self.flowcell_id = ''
+ self.trim = slice(None)
+ self.reportFilter = False
+
+ def _format_flowcell_id(self):
+ """
+ Return formatted flowcell ID
+ """
+ return self.flowcell_id+"_"
+
+ def _convert_illumina_quality(self, illumina_quality):
+ """
+ Convert an Illumina ASCII encoded quality score to a Phred ASCII quality score.
+ """
+ # Illumina scores are Phred + 64
+ # Fastq scores are Phread + 33
+ # the following code grabs the string, converts to short ints and
+ # subtracts 31 (64-33) to convert between the two score formats.
+ # The numpy solution is twice as fast as some of my other
+ # ideas for the conversion.
+ # sorry about the uglyness in changing from character, to 8-bit int
+ # and back to a character array
+ quality = numpy.asarray(illumina_quality,'c')
+ quality.dtype = numpy.uint8
+ quality -= 31
+ quality.dtype = '|S1' # I'd like to know what the real numpy char type is
+ return quality
+
+ def run(self):
+ if self.fastq:
+ header_template = '@'
+ else:
+ # fasta case
+ header_template = '>'
+ header_template += self._format_flowcell_id() + '%s_%s:%s:%s:%s:%s/%s%s%s'
+
+ for qstream in self.sources:
+ for line in qstream:
+ # parse line
+ record = line.rstrip().split('\t')
+ machine_name = record[0]
+ run_number = record[1]
+ lane_number = record[2]
+ tile = record[3]
+ x = record[4]
+ y = record[5]
+ index = record[6]
+ read = record[7]
+ sequence = record[8].replace('.','N')
+ quality = self._convert_illumina_quality(record[9])
+
+ # add pass qc filter if we want it
+ pass_qc = int(record[10])
+ if self.reportFilter:
+ pass_qc_msg = " pf=%s" % (pass_qc)
+ else:
+ pass_qc_msg = ""
+
+ header = header_template % ( \
+ machine_name,
+ run_number,
+ lane_number,
+ tile,
+ x,
+ y,
+ read,
+ pass_qc_msg,
+ os.linesep)
+
+
+ # if we passed the filter write to the "good" file
+ if pass_qc:
+ destination = self.pass_destination
+ else:
+ destination = self.nopass_destination
+
+ destination.write(header)
+ destination.write(sequence[self.trim])
+ destination.write(os.linesep)
+ if self.fastq:
+ destination.write('+')
+ destination.write(os.linesep)
+ destination.write(quality[self.trim].tostring())
+ destination.write(os.linesep)
+
+def file_generator(pattern_list):
+ for pattern in pattern_list:
+ for filename in glob(pattern):
+ yield open(filename,'r')
+
+def tarfile_generator(tarfilename):
+ archive = tarfile.open(tarfilename,'r|*')
+ for tarinfo in archive:
+ yield archive.extractfile(tarinfo)
+
def parse_slice(slice_text):
if slice_text is None or len(slice_text) == 0:
return slice(*slice_data)
-def qseq2fastq(destination, qseqs, trim=None):
- for q in qseqs:
- for line in open(q):
- # parse line
- record = line.strip().split('\t')
- machine_name = record[0]
- run_number = record[1]
- lane_number = record[2]
- tile = record[3]
- x = record[4]
- y = record[5]
- index = record[6]
- read = record[7]
- sequence = record[8]
- # Illumina scores are Phred + 64
- # Fastq scores are Phread + 33
- # the following code grabs the string, converts to short ints and
- # subtracts 31 (64-33) to convert between the two score formats.
- # The numpy solution is twice as fast as some of my other
- # ideas for the conversion.
- # sorry about the uglyness in changing from character, to 8-bit int
- # and back to a character array
- quality = numpy.asarray(record[9],'c')
- quality.dtype = numpy.uint8
- quality -= 31
- quality.dtype = '|S1' # I'd like to know what the real numpy char type is
-
- pass_qc = record[10]
-
- destination.write('@%s_%s:%s:%s:%s:%s/%s pf=%s%s' % ( \
- machine_name,
- run_number,
- lane_number,
- tile,
- x,
- y,
- read,
- pass_qc,
- os.linesep))
- destination.write(sequence[trim])
- destination.write(os.linesep)
- destination.write('+')
- destination.write(os.linesep)
- destination.write(quality[trim].tostring())
- destination.write(os.linesep)
-
+def make_parser():
+ usage = "%prog: [options] *_qseq.txt"
+ parser = OptionParser(usage)
+ parser.add_option('-a', '--fasta', default=False, action="store_true",
+ help="produce fasta files instead of fastq files")
+ parser.add_option('-f', '--flowcell', default='',
+ help="Set flowcell ID for output file")
+ parser.add_option('-i', '--infile', default=None,
+ help='source tar file (if reading from an archive instead of a directory)')
+ parser.add_option('-o', '--output', default=None,
+ help='output fastq file')
+ parser.add_option('-n', '--nopass-output', default=None,
+ help='if provided send files that failed illumina filter '\
+ 'to a differentfile')
+ parser.add_option('-s', '--slice',
+ help='specify python slice, e.g. 0:75, 0:-1',
+ default=None)
+ parser.add_option('--pf', help="report pass filter flag", default=False,
+ action="store_true")
+ return parser
+
def main(cmdline=None):
parser = make_parser()
opts, args = parser.parse_args(cmdline)
+ if opts.infile is not None:
+ qseq_generator = tarfile_generator(opts.infile)
+ elif len(args) > 0:
+ qseq_generator = file_generator(args)
+ else:
+ qseq_generator = [sys.stdin]
+
+
if opts.output is not None:
- dest = open(opts.output, 'w')
+ output = open(opts.output, 'w')
+ else:
+ output = sys.stdout
+
+ if opts.nopass_output is not None:
+ nopass_output = open(opts.nopass_output, 'w')
else:
- dest = sys.stdout
+ nopass_output = None
- subseq = parse_slice(opts.slice)
+ qseq_parser = Qseq2Fastq(qseq_generator, output, nopass_output)
+ qseq_parser.fastq = not opts.fasta
+ qseq_parser.flowcell_id = opts.flowcell
+ qseq_parser.trim = parse_slice(opts.slice)
+ qseq_parser.reportFilter = opts.pf
- qseq2fastq(dest, args, subseq)
-
- return 0
+ qseq_parser.run()
if __name__ == "__main__":
main()
projects / htsworkflow.git / blobdiff