def batch_fastqs(fastqs,batch_size,basename="batched",
out_dir=None):
"""
Splits reads from one or more Fastqs into batches
Concatenates input Fastq files and then splits
reads into smaller Fastqs using the external 'batch'
utility.
Arguments:
fastqs (list): list of paths to one or more Fastq
files to take reads from
batch_size (int): number of reads to allocate to
each batch
basename (str): optional basename to use for the
output Fastq files (default: 'batched')
out_dir (str): optional path to a directory where
the batched Fastqs will be written
"""
# Determine number of batches
nreads = get_read_count(fastqs)
nbatches = nreads/batch_size
if nbatches*batch_size < nreads:
nbatches += 1
print "Creating %d batches of %d reads" % (nbatches,
batch_size)
assert(batch_size*nbatches >= nreads)
# Check if fastqs are compressed
gzipped = fastqs[0].endswith('.gz')
if gzipped:
batch_cmd = Command('zcat')
else:
batch_cmd = Command('cat')
# Get the read number
read_number = get_read_number(fastqs[0])
suffix = ".r%s.fastq" % read_number
# Build and run the batching command
batch_cmd.add_args(*fastqs)
batch_cmd.add_args('|',
'split',
'-l',batch_size*4,
'-d',
'-a',3,
'--additional-suffix=%s' % suffix,
'-',
os.path.join(out_dir,"%s.B" % basename))
batch_script = os.path.join(out_dir,"batch.sh")
batch_cmd.make_wrapper_script("/bin/bash",
batch_script)
# Check for successful exit code
retcode = Command("/bin/bash",
batch_script).run_subprocess(
working_dir=out_dir)
if retcode != 0:
raise Exception("Batching failed: exit code %s" % retcode)
print "Batching completed"
# Collect and return the batched Fastq names
batched_fastqs = [os.path.join(out_dir,
"%s.B%03d%s"
% (basename,i,suffix))
for i in xrange(0,nbatches)]
return batched_fastqs
def test_get_read_number_r2(self):
"""get_read_number: check read number for R2 Fastq file
"""
self.assertEqual(get_read_number(self.fastq_r2),2)
