def simple(fastq=None, fp=None):
"""
Return number of reads in a FASTQ file
Uses the FASTQFile.nreads function to do the counting.
Arguments:
fastq: fastq(.gz) file
fp: open file descriptor for fastq file
Returns:
Number of reads
"""
return FASTQFile.nreads(fastq=fastq, fp=fp)
def batch_fastqs(fastqs, nbatches, 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
nbatches (int): number of batches to output reads
into
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
"""
# Count the total number of reads
print "Fetching read counts:"
nreads = 0
for fq in fastqs:
n = FASTQFile.nreads(fq)
print "%s:\t%d" % (os.path.basename(fq), n)
nreads += n
print "Total reads: %d" % nreads
# Determine batch size
batch_size = nreads / nbatches
if nreads % batch_size:
# Round up batch size
batch_size += 1
assert (batch_size * nbatches >= nreads)
print "Creating batches of %d reads" % batch_size
# 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)
# 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
fastqs = sample.fastq_subset(read_number=1) + \
sample.fastq_subset(read_number=2)
for fastq in fastqs:
print "\t\t%s" % fastq
# Report the names of the samples in each project
if options.report:
for project in illumina_data.projects:
print "%s" % IlluminaData.describe_project(project)
# Report statistics for fastq files
if options.stats:
# Print number of reads for each file, and file size
for sample in project.samples:
for fastq in sample.fastq:
fq = os.path.join(sample.dirn, fastq)
nreads = FASTQFile.nreads(fq)
fsize = os.path.getsize(fq)
print "%s\t%s\t%d" % (
fastq, bcf_utils.format_file_size(fsize), nreads)
print ""
# Summary: short report suitable for logging file
if options.summary:
print "%s" % IlluminaData.summarise_projects(illumina_data)
# Print number of undetermined reads
if options.stats and illumina_data.undetermined is not None:
print "Undetermined indices"
for lane in illumina_data.undetermined.samples:
for fastq in lane.fastq:
fq = os.path.join(lane.dirn, fastq)
fastqs = sample.fastq_subset(read_number=1) + \
sample.fastq_subset(read_number=2)
for fastq in fastqs:
print "\t\t%s" % fastq
# Report the names of the samples in each project
if options.report:
for project in illumina_data.projects:
print "%s" % IlluminaData.describe_project(project)
# Report statistics for fastq files
if options.stats:
# Print number of reads for each file, and file size
for sample in project.samples:
for fastq in sample.fastq:
fq = os.path.join(sample.dirn,fastq)
nreads = FASTQFile.nreads(fq)
fsize = os.path.getsize(fq)
print "%s\t%s\t%d" % (fastq,
bcf_utils.format_file_size(fsize),
nreads)
print ""
# Summary: short report suitable for logging file
if options.summary:
print "%s" % IlluminaData.summarise_projects(illumina_data)
# Print number of undetermined reads
if options.stats and illumina_data.undetermined is not None:
print "Undetermined indices"
for lane in illumina_data.undetermined.samples:
for fastq in lane.fastq:
