def inspect_reads(fastq_files, output_prefix, quals):
"""
uncompresses reads, renames reads, and converts quality scores
to 'sanger' format
"""
# setup file iterators
filehandles = [open_compressed(f) for f in fastq_files]
fqiters = [parse_lines(f, numlines=4) for f in filehandles]
output_files = [(output_prefix + "_%d.fq" % (x+1))
for x in xrange(len(fastq_files))]
outfhs = [open(f, "w") for f in output_files]
qual_func = get_qual_conversion_func(quals)
linenum = 0
try:
while True:
pelines = [it.next() for it in fqiters]
for i,lines in enumerate(pelines):
# rename read using line number
lines[0] = "@%d/%d" % (linenum,i+1)
# ignore redundant header
lines[2] = "+"
# convert quality score to sanger
lines[3] = qual_func(lines[3])
print >>outfhs[i], '\n'.join(lines)
linenum += 1
except StopIteration:
pass
except:
logging.error("Unexpected error during FASTQ file processing")
for f in output_files:
if os.path.exists(f):
os.remove(f)
return config.JOB_ERROR
for fh in filehandles:
fh.close()
logging.debug("Inspected %d fragments" % (linenum))
return config.JOB_SUCCESS
def process_input_reads(fastq_files, output_prefix, quals, trim5, trim3):
"""
uncompresses reads, renames reads, and converts quality scores
to 'sanger' format
"""
# setup file iterators for input fastq files
infhs = [open_compressed(f) for f in fastq_files]
fqiters = [parse_lines(f, numlines=4) for f in infhs]
# setup output files
output_files = [(output_prefix + "_%d.fq" % (x + 1))
for x in xrange(len(fastq_files))]
outfhs = [open(f, "w") for f in output_files]
read_name_file = output_prefix + ".txt"
read_name_fh = open(read_name_file, 'w')
# get quality score conversion function
qual_func = get_qual_conversion_func(quals)
linenum = 1
try:
while True:
pelines = [it.next() for it in fqiters]
# get read1 first line of fq record, and remove "@" symbol
read1_name = pelines[0][0][1:]
# remove whitespace and/or read number tags /1 or /2
read1_name = read1_name.split()[0].split("/")[0]
# write to read name database
print >> read_name_fh, read1_name
# convert reads
for i, lines in enumerate(pelines):
# rename read using line number
lines[0] = "@%d/%d" % (linenum, i + 1)
# ignore redundant header
lines[2] = "+"
# trim read
total_length = len(lines[1])
pos3p = max(trim5 + 1, total_length - trim3)
lines[1] = lines[1][trim5:pos3p]
lines[3] = lines[3][trim5:pos3p]
# convert quality score to sanger
lines[3] = qual_func(lines[3])
print >> outfhs[i], '\n'.join(lines)
linenum += 1
except StopIteration:
pass
except:
logging.error("Unexpected error during FASTQ file processing")
for fh in outfhs:
fh.close()
read_name_fh.close()
for f in output_files:
if os.path.exists(f):
os.remove(f)
if os.path.exists(read_name_file):
os.remove(read_name_file)
return config.JOB_ERROR
# cleanup
for fh in infhs:
fh.close()
for fh in outfhs:
fh.close()
read_name_fh.close()
logging.debug("Inspected %d fragments" % (linenum))
return config.JOB_SUCCESS
def process_input_reads(fastq_files, output_prefix, quals, trim5, trim3):
"""
uncompresses reads, renames reads, and converts quality scores
to 'sanger' format
"""
# setup file iterators for input fastq files
infhs = [open_compressed(f) for f in fastq_files]
fqiters = [parse_lines(f, numlines=4) for f in infhs]
# setup output files
output_files = [(output_prefix + "_%d.fq" % (x+1))
for x in xrange(len(fastq_files))]
outfhs = [open(f, "w") for f in output_files]
read_name_file = output_prefix + ".txt"
read_name_fh = open(read_name_file, 'w')
# get quality score conversion function
qual_func = get_qual_conversion_func(quals)
linenum = 1
try:
while True:
pelines = [it.next() for it in fqiters]
# get read1 first line of fq record, and remove "@" symbol
read1_name = pelines[0][0][1:]
# remove whitespace and/or read number tags /1 or /2
read1_name = read1_name.split()[0].split("/")[0]
# write to read name database
print >>read_name_fh, read1_name
# convert reads
for i,lines in enumerate(pelines):
# rename read using line number
lines[0] = "@%d/%d" % (linenum,i+1)
# ignore redundant header
lines[2] = "+"
# trim read
total_length = len(lines[1])
pos3p = max(trim5+1, total_length - trim3)
lines[1] = lines[1][trim5:pos3p]
lines[3] = lines[3][trim5:pos3p]
# convert quality score to sanger
lines[3] = qual_func(lines[3])
print >>outfhs[i], '\n'.join(lines)
linenum += 1
except StopIteration:
pass
except:
logging.error("Unexpected error during FASTQ file processing")
for fh in outfhs:
fh.close()
read_name_fh.close()
for f in output_files:
if os.path.exists(f):
os.remove(f)
if os.path.exists(read_name_file):
os.remove(read_name_file)
return config.JOB_ERROR
# cleanup
for fh in infhs:
fh.close()
for fh in outfhs:
fh.close()
read_name_fh.close()
logging.debug("Inspected %d fragments" % (linenum))
return config.JOB_SUCCESS