def demultiplex_fastq(index, fastq1, fastq2):
filter = {'index': index}
fp1 = FastQParser(fastq1,filter)
if fastq2 is not None:
fp2 = FastQParser(fastq2,filter)
for r1 in fp1:
if fastq2 is not None:
r2 = fp2.next()
assert is_read_pair(r1,r2), "Mismatching headers for expected read pair"
sys.stderr.write("{}\n".format("\n".join(r2)))
sys.stdout.write("{}\n".format("\n".join(r1)))
def demultiplex_fastq(index, fastq1, fastq2):
filter = {"index": index}
fp1 = FastQParser(fastq1, filter)
if fastq2 is not None:
fp2 = FastQParser(fastq2, filter)
for r1 in fp1:
if fastq2 is not None:
r2 = fp2.next()
assert is_read_pair(r1, r2), "Mismatching headers for expected read pair"
sys.stderr.write("{}\n".format("\n".join(r2)))
sys.stdout.write("{}\n".format("\n".join(r1)))
def _split_fastq(fastq_input, outdir, outprefix, outsuffix, samples):
if not os.path.exists(outdir):
os.mkdir(outdir)
out_handles = {}
for file in fastq_input:
iter = FastQParser(file)
for record in iter:
index = record[0].rfind(":")
i = record[0][index + 1:].strip()
# open a file handle to the index file if it's not already available
if i not in out_handles:
out_file = os.path.join(
outdir,
"%s_%s%s" % (outprefix, samples.get(i, i), outsuffix))
out_handles[i] = FastQWriter(out_file)
out_handles[i].write(record)
# summarize the written records and close the file handles
counts = {}
for i, oh in out_handles.items():
counts[i] = oh.rwritten()
oh.close()
return counts
def count_top_indexes(count_num, index_file, index_length, progress_interval):
"""
Determine the most common indexes, sampling at most 200,000 reads.
"""
assert (type(count_num) == int
and count_num > 0), "Number passed must be a positive integer."
fqp_ind = FastQParser(index_file)
# This should perhaps be added to the FastQParser class
print("Counting total number of lines in fastq file...",
file=sys.stderr,
end="")
total_lines = int(
subprocess.check_output(shlex.split(
"wc -l {}".format(index_file))).split()[0])
total_reads = total_lines / 4
print(" complete.", file=sys.stderr)
index_tally = collections.defaultdict(int)
reads_processed = 0
# Subsample if file is large
if (total_reads) > 200000:
print("Subsampling 200,000 reads from index file...", file=sys.stderr)
fqp_ind = iter_sample_fast(fqp_ind, 200000, total_reads)
print("Complete.", file=sys.stderr)
total_reads = 200000
print("Tallying indexes in {} records...".format(total_reads),
file=sys.stderr)
start_time = datetime.datetime.now()
for index in fqp_ind:
index_read_seq = index[1]
index_seq = index_read_seq[:index_length]
index_tally[index_seq] += 1
reads_processeds += 1
if reads_processed % progress_interval == 0:
print_progress(reads_processed, total_reads, start_time)
print("\n", file=sys.stderr)
if count_num > len(index_tally.keys()):
print(
"Number of indexes found ({}) is fewer than those requested ({}). Printing all indexes found."
.format(len(index_tally.keys()), count_num),
file=sys.stderr)
print("Printing indexes...", file=sys.stderr)
count_num = len(index_tally.keys())
print("{:<20} {:>20} {:>11}".format("Index", "Occurences", "Percentage"))
for index, _ in sorted(index_tally.items(),
key=(lambda x: x[1]),
reverse=True)[:count_num]:
percentage = (100.0 * index_tally[index]) / total_reads
print("{:<20} {:>20,} {:>10.2f}%".format(index, index_tally[index],
percentage))
from bloomfaster import Elf
import collections
import sys
# Slight modification to read from input file instead of stdin
from scilifelab.utils.fastq_utils import (FastQParser, FastQWriter)
__doc__ %= sys.argv[0]
if len(sys.argv) > 2:
print sys.argv
print __doc__
sys.exit()
print >> sys.stderr, "Command: ", " ".join(sys.argv)
infile = sys.argv[1]
fp = FastQParser(infile)
for _ in fp:
pass
records = fp.rread()
print >> sys.stderr, records, "records in file ", infile
# say 1 out of 1000 is false positive.
bloom = Elf(records, error_rate=1e-3)
fp.seek(0)
checks = []
for _, seq, _, _ in fp:
if seq in bloom:
checks.append(seq)
bloom.add(seq)
# now checks contains anything that could be a duplicate according to
from bloomfaster import Elf
import collections
import sys
# Slight modification to read from input file instead of stdin
from scilifelab.utils.fastq_utils import (FastQParser, FastQWriter)
__doc__ %= sys.argv[0]
if len(sys.argv) > 2:
print sys.argv
print __doc__
sys.exit()
print >>sys.stderr, "Command: ", " ".join(sys.argv)
infile = sys.argv[1]
fp = FastQParser(infile)
for _ in fp:
pass
records = fp.rread()
print >>sys.stderr, records, "records in file ", infile
# say 1 out of 1000 is false positive.
bloom = Elf(records, error_rate=1e-3)
fp.seek(0)
checks = []
for _,seq,_,_ in fp:
if seq in bloom:
checks.append(seq)
bloom.add(seq)
# now checks contains anything that could be a duplicate according to