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fastq2kmers.py
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fastq2kmers.py
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#!/usr/bin/env python
desc="""Count k-mers occurencies in reads and report freq plot.
Not working for k > 16...
NOT RECOMMENDED! USE JELLYFISH INSTEAD:
#jellyfish
k=31; q=20;
for f in _archives_CANTHE/CAN*read?.fastq.gz; do
s=`echo $f | cut -f2 -d"/" | cut -f1 -d"."`;
if [ ! -s _archives/$s.k$k.q$q.hist ]; then
echo `date` $f $s;
zcat $f | fastq2fasta.py -v -l $k -q $q | jellyfish count -m31 -s1000000000 -o $s.k$k.q$q.jelly /dev/stdin; jellyfish histo -h10000 _archives/$s.k$k.q$q.jelly_0 > _archives/$s.k$k.q$q.hist
fi; done
plot_2d.py -v -i _archives/*.k31.q20.hist -o CANME.k31.q20.png
ver 1.1:
- quality control
- numpy.array for counting
- multiprocessing
ver 1.0:
- Biopython FASTQ parser
-
"""
epilog="""Author:
l.p.pryszcz@gmail.com
Barcelona/Mizerow, 9/05/2013
"""
import argparse, gzip, os, resource, sys
from datetime import datetime
from Bio import SeqIO
from matplotlib import pyplot as plt
from multiprocessing import Pool
import numpy as np
def get_mer(mer):
"""Return forward or reverse sequence"""
merC = mer.complement()
for a, b in zip(mer, merC):
if a<b:
return mer
elif b<a:
return merC
return mer
def init_args(*args):
global k, ns, base2digit
k, ns, base2digit = args
def seq2mers(r):
"""Return list of kmer ids from given read sequence"""
ids = []
for j in range(len(r.seq)-k):
mer = get_mer(r.seq[j:j+k])
if not ns and "N" in mer:
continue
#get id and store it
mid = int("".join(base2digit[base] for base in mer), len(base2digit))
#if mid < len(base2digit)**k/2:
ids.append(mid)
return ids
def get_kmer_counts(input, output, k, ns, nprocs, verbose):
"""Analyse kmers. Multiprocessing enabled"""
#define base2digit dict for 4-char seq
base2digit = {"A": "0", "C": "1", "G": "2", "T": "3"}
if ns:
#change to 5-char seq if Ns in seq
base2digit = {"A": "0", "C": "1", "G": "2", "N": "3", "T": "4"}
#init mer counts
#255 for uint8 #65,535 for uint16 or #4,294,967,295 for uint32
merCounts = np.zeros(len(base2digit)**k/2, dtype='uint16')
#start pool #maxtasksperchild=1000)
p = Pool(nprocs, initializer=init_args, initargs=(k, ns, base2digit))
#process reads
for i, ids in enumerate(p.imap_unordered(seq2mers, SeqIO.parse(input, 'fastq'), \
chunksize=100), 1):
if not i%1e4:
sys.stderr.write(" %s [%s Mb]\r"%(i, resource.getrusage(resource.RUSAGE_SELF).ru_maxrss/1024))
for mid in ids:
merCounts[mid] += 1
sys.stderr.write(" %s [%s Mb]\n"%(i, resource.getrusage(resource.RUSAGE_SELF).ru_maxrss/1024))
#get mer freq
maxCount = merCounts.max()
if maxCount < 100:
maxCount = 100
occurencies = [0]*maxCount
for c in merCounts:
occurencies[c-1] += 1
#write to file
output.write("\n".join("%s\t%s"%xy for xy in enumerate(occurencies,1))+"\n")
return occurencies
'''v1.0
def get_kmer2count(input, kmer, ns, verbose):
"""Count kmer occurencies. Uses 2 threads:
- fastq parsing
- kmers storing
"""
kmer2count = {}
step = 10**3
pI = 0
#parse fastq
for i, r in enumerate(SeqIO.parse(input,'fastq'),1):
#process mers
for j in range(len(r.seq)-kmer):
merF = str(r.seq[j:j+kmer])
if not ns and "N" in merF:
continue
merR = str(r.seq[j:j+kmer].reverse_complement())
#add to dict
if merF in kmer2count:
kmer2count[merF] += 1
elif merR in kmer2count:
kmer2count[merR] += 1
else:
kmer2count[merF] = 1
#print info
if i>pI:
pI += step
sys.stderr.write(" %12i [%s Mb]\r" % (i, resource.getrusage(resource.RUSAGE_SELF).ru_maxrss/1024))
sys.stderr.write(" %12i [%s Mb] kmer2count: %s \n" % (i, resource.getrusage(resource.RUSAGE_SELF).ru_maxrss/1024, len(kmer2count)))
return kmer2count
def get_occurencies(kmer2count, output, verbose):
""" """
#max kmer occurencies
maxCount = max(c for k,c in kmer2count.items())
if maxCount < 100:
maxCount = 100
occurencies = [0]*maxCount
for k,c in kmer2count.items():
occurencies[c-1] += 1
#write to file
output.write("\n".join("%s\t%s"%xy for xy in enumerate(occurencies,1))+"\n")
return occurencies
def seq2int(seq, minseqi, base2digit):
"""Return int representation of seq."""
#convert seq into seq of digits
dseq = "".join(base2digit[base] for base in seq)
#if not Ns in seq, encode as 4-char int
seqi = int("1"+dseq, len(base2digit))
#return iseq minus int for min seq, that is A*kmer
return seqi-minseqi
def get_kmer_counts(input, kmer, ns, verbose):
"""Count kmer occurencies.
sys.getsizeof([0]*4**15) is just 1,073,741,824 elements 10e9
while 4**31=10e18!
Out[35]: 8,589,934,664 -> 8.5Gb for k=15
use numpy
"""
#define base2digit dict for 4-char seq
base2digit = {"A": "0", "C": "1", "G": "2", "T": "3"}
if ns:
#change to 5-char seq if Ns in seq
base2digit = {"A": "0", "C": "1", "G": "2", "N": "3", "T": "4"}
#define lowest & highest possible int representation of seq (AAAAA)
##easier would be int("1"+"0"*kmer,4) and int("3"*kmer,4)
minseqi = seq2int("A"*kmer,0,base2digit)
maxseqi = seq2int("T"*kmer,minseqi,base2digit)
#print minseqi, maxseqi
#define empty occurencies list
counts = np.zeros((maxseqi+1)/2, dtype=int) #[0] * maxseqi
#parse fastq
step = 10**3
pI = 0
for i,r in enumerate(SeqIO.parse(input,'fastq'),1):
#process mers
for j in range(len(r.seq)-kmer):
mer = str(r.seq[j:j+kmer]).upper()
if not ns and "N" in mer:
continue
merR = str(r.seq[j:j+kmer].reverse_complement())
#get smaller seq
if merR < mer:
mer = merR
#update count
meri = seq2int(mer, minseqi, base2digit)
counts[meri] += 1
#print info
if i>pI:
pI += step
sys.stderr.write(" %12i [%s Mb]\r" % (i, resource.getrusage(resource.RUSAGE_SELF).ru_maxrss/1024))
sys.stderr.write(" %12i [%s Mb] kmers: %s \n" % (i, resource.getrusage(resource.RUSAGE_SELF).ru_maxrss/1024, len(kmer2count)))
return counts
'''
def plot(occurencies, kmer, output, title):
"""Plot figure."""
#get figure
plt.figure(figsize=(6,6))
plt.plot(xrange(1,101),occurencies[:100],linewidth=2.0)
#add title and axis labels
plt.title(title+" [k=%s]"%kmer)
plt.xlabel('k-mer frequency')
plt.ylabel('number of k-mers with this frequency')
#show plot if not outfile provided
if output.name=="<stdout>":
plt.show()
else:
format = "png"
fpath = "%s.%s" % (output.name, format)
plt.savefig(fpath, dpi=300, facecolor='w', edgecolor='w',\
orientation='landscape', format=format, transparent=False)
def fastq2kmers(input, output, kmer, ns, nprocs, title, verbose):
"""Process fastq from stdin."""
if verbose:
sys.stdout.write("[fastq2kmers] Parsing fastq...\n")
occurencies = get_kmer_counts(input, output, kmer, ns, nprocs, verbose)
'''
kmer2count = get_kmer2count(input, kmer, ns, verbose)
#get occuriences
if verbose:
sys.stdout.write("[fastq2kmers] Getting frequencies...\n")
occurencies = get_occurencies(kmer2count, output, verbose)'''
#plot
if verbose:
sys.stdout.write("[fastq2kmers] Plotting...\n")
plot(occurencies, kmer, output, title)
def main():
usage = "zcat fastq.gz | %(prog)s -v"
parser = argparse.ArgumentParser(usage=usage, description=desc, epilog=epilog)
parser.add_argument("-v", dest="verbose", default=False, action="store_true", help="verbose")
parser.add_argument('--version', action='version', version='1.0')
parser.add_argument("-i", dest="input", default=sys.stdin, type=file,
help="input stream [stdin]")
parser.add_argument("-o", dest="output", default=sys.stdout, type=argparse.FileType("w"),
help="output stream [stdout]")
parser.add_argument("-k", dest="kmer", default=31, type=int,
help="k-mer [%(default)s]")
parser.add_argument("-t", dest="title", default="",
help="plot title [%(default)s]")
parser.add_argument("-n", "--nprocs", default=4,
help="no. of processes [%(default)s]")
parser.add_argument("--include-Ns", dest="ns", default=False, action="store_true",
help="include k-mers with Ns [%(default)s]")
o = parser.parse_args()
if o.verbose:
sys.stdout.write( "[fastq2kmers] Options: %s\n" % str(o) )
fastq2kmers(o.input, o.output, o.kmer, o.ns, o.nprocs, o.title, o.verbose)
if __name__=='__main__':
t0 = datetime.now()
try:
main()
except KeyboardInterrupt:
sys.stderr.write("\n[fastq2kmers] Ctrl-C pressed! \n")
dt = datetime.now()-t0
sys.stdout.write( "[fastq2kmers] Time elapsed: %s\n" % dt )