def split_large_fastq_file(file_name, output_file_pattern, cutoff=1000000): ''' Split large fastq file. For example: output_file_pattern = "/home/akomissarov/data/asian_seabass/raw_reads/500bp_insert_lane1_read1.chunk%s.fastq" ''' def write_data(reads, chunk, output_file_pattern): with open(output_file_pattern % chunk, "w") as fh: for read in reads: fh.write(read.fastq) reads = [] chunk = 1 print "Read data..." for i, read in enumerate(fastq_reader(file_name)): print i, "\r", if reads and i % cutoff == 0: print "\nSave reads", i, "for chunk", chunk write_data(reads, chunk, output_file_pattern) chunk += 1 reads = [] reads.append(read) if reads: print "\nLast one. Save reads", i, "for chunk", chunk write_data(reads, chunk, output_file_pattern)
def clean_single_read_data(fastq1_file, fastq1ok_file, fastq_bad_file, verbose=False, adapters_file=None, cutoff=None, polyG_cutoff=23):
''' Remove reads containing N, # quality, polyG/polyC tracks and adapters.
'''
wh1 = open(fastq1ok_file, "w")
bad = open(fastq_bad_file, "w")
statistics = {
"pe": 0,
"se": 0,
"N": 0,
"zeroQ": 0,
"polyC%s" % polyG_cutoff: 0,
"polyG%s" % polyG_cutoff: 0,
"adapters": 0,
}
if cutoff:
cutoff = int(cutoff)
cutoff_key = "length%s" % cutoff
statistics[cutoff_key] = 0
print "Load adapters file"
adapters = []
if adapters_file:
with open(adapters_file) as fh:
for line in fh:
adap = line.strip().split()[0]
rev_adap = get_revcomp(adap)
if not adap in adapters:
adapters.append(adap)
if not rev_adap in adapters:
adapters.append(rev_adap)
else:
print "Adapter file missing"
print "Number of adapters:", len(adapters)
for i, read1 in enumerate(fastq_reader(fastq1_file)):
error1 = None
if verbose:
print i, round(100 * statistics["se"]/float(i+1), 2), "% of good", statistics, "\r",
if cutoff:
if read1.length < cutoff:
error1 = cutoff_key
if not error1:
error1 = is_bad_read(read1, adapters, polyG_cutoff)
if error1:
bad.write(read1.fastq_with_error(error1))
statistics[error1] += 1
else:
wh1.write(read1.fastq)
statistics["se"] += 1
wh1.close()
bad.close()
if i > 0:
statistics["fraction"] = statistics["pe"]/float(i)
print
print statistics
return statistics
def fastq_to_fasta(fastq_file, fasta_file, verbose=False): ''' Fastq to fasta. ''' print "Fastq to fasta..." with open(fasta_file, "w") as fh: for i, read in enumerate(fastq_reader(fastq_file)): if verbose: print i, "\r", fh.write(read.fasta)
def filter_reads_by_gc(fastq_file, output_file, min_gc, max_gc): ''' Filter reads between min_gc and max_gc. ''' with open(output_file, "w") as fh: for read in fastq_reader(fastq_file): gc = read.gc if gc < max_gc and gc > min_gc: print round(gc, 3), read.seq fh.write(read.fasta)
def iter_pe_data(fastq1_file, fastq2_file):
''' Iterate over PE fastq files.
'''
reader1 = fastq_reader(fastq1_file)
reader2 = fastq_reader(fastq2_file)
while True:
try:
read1 = next(reader1)
except StopIteration:
try:
read2 = next(reader2)
except StopIteration:
break
pass
raise Exception("Not equal number of reads in PE run")
break
try:
read2 = next(reader2)
except StopIteration:
raise Exception("Not equal number of reads in PE run")
yield read1, read2
def main(fastq1_file, fastq2_file, fastq1ok_file, fastq2ok_file, fastq_se_file): """ """ fh1 = fastq_reader(fastq1_file) fh2 = fastq_reader(fastq2_file) wh1 = open(fastq1ok_file, "w") wh2 = open(fastq2ok_file, "w") fse = open(fastq_se_file, "w") i = 0 while True: read1, read2 = get_next_pair(fh1, fh2, fse) if read1 is None: break wh1.write(read1.fastq) wh2.write(read2.fastq) i += 1 print i, "\r", print
def fix_uncorrect_long_quality(fastq_file, corrected_fastq_output): ''' Fix too long quality scores in corrupted HiSeq files. @param fastq_file: fastq_file @param corrected_fastq_output: corrected fastq output ''' bp200 = 0 total = 0. with open(corrected_fastq_output, "w") as fh: for i, read in enumerate(fastq_reader(fastq_file)): print i, "\r", if len(read.seq) != len(read.qual): read.qual = read.qual[:len(read.seq)] print print read.fastq fh.write(read.fastq)
def clean_short_reads(fastq1_file, fastq1ok_file, fastq_short_file, cutoff, verbose=False):
''' Remove short reads from fastq file.
'''
statistics = {
"short": 0,
"ok": 0,
"fraction": 0.0,
}
with open(fastq_short_file, "w") as bad:
with open(fastq1ok_file, "w") as good:
for i, read1 in enumerate(fastq_reader(fastq1_file)):
statistics["fraction"] = statistics["ok"]/float(i+1)
if verbose:
print i, statistics, "\r",
if len(read1.seq) < 100:
bad.write(read1.fastq_with_error("short"))
statistics["short"] += 1
else:
good.write(read1.fastq)
statistics["ok"] += 1
print statistics
return statistics
def separate_reads_witn_n_and_sharps(fastq_file, output_file, reads_with_n_file, reads_with_sharp_file): ''' Separate reads from fastq file witn N and sharp quality scores. ''' reads = [] print "Read data..." k = 0 s = 0 with open(output_file, "w") as good_fh: with open(reads_with_n_file, "w") as bad_fh: with open(reads_with_sharp_file, "w") as sharp_fh: for i, read in enumerate(fastq_reader(fastq_file)): if "n" in read.sequence or "N" in read.sequence: k += 1 print i, k, s, float(k+1)/(i+1), float(s+1)/(i+1), "\r", bad_fh.write(read.fastq) elif "#" in read.qual: s += 1 print i, k, s, float(k+1)/(i+1), float(s+1)/(i+1), "\r", sharp_fh.write(read.fastq) else: good_fh.write(read.fastq) print
#!/usr/bin/env python # -*- coding: utf-8 -*- # #@created: 23.02.2011 #@author: Aleksey Komissarov #@contact: [email protected] from trseeker.seqio.sra_file import fastq_reader fastq_file = "/stripe2/assembly_test/Caenorhabditis_elegans/raw_reads/DRR008443_500bp_1.fastq" output_fastq_file = "/stripe2/assembly_test/Caenorhabditis_elegans/raw_reads/500K_1.fastq" with open(output_fastq_file, "w") as fh: for i, read in enumerate(fastq_reader(fastq_file)): print i, "\r", if i == 500000: break fh.write(read.fastq) fastq_file = "/stripe2/assembly_test/Caenorhabditis_elegans/raw_reads/DRR008443_500bp_2.fastq" output_fastq_file = "/stripe2/assembly_test/Caenorhabditis_elegans/raw_reads/500K_2.fastq" with open(output_fastq_file, "w") as fh: for i, read in enumerate(fastq_reader(fastq_file)): print i, "\r", if i == 500000: break fh.write(read.fastq)
# -*- coding: utf-8 -*- # #@created: 10.10.2013 #@author: Aleksey Komissarov #@contact: [email protected] import sys from trseeker.seqio.sra_file import fastq_reader import argparse if __name__ == '__main__': parser = argparse.ArgumentParser(description='Remove reads with N.') parser.add_argument('-i','--input', help='Fastq file', required=True) parser.add_argument('-o','--output', help='Fastq file', required=True) args = vars(parser.parse_args()) print "Process data" data = [] ok = 0 l = int(args["length"]) with open(args["output"], "w") as fh: for i, read in enumerate(fastq_reader(args["input"])): if i % 10000 == 0: print ok, i, ok/(i+1.), "\r", if 'N' in read.seq: continue fh.write(read.fastq) ok += 1 print print "Final: saved %s (%s) from %s" % (ok, ok/(i+1.), i)
