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find_telomers.py
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find_telomers.py
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#!/usr/bin/env python
"""
Look for telomeric sequence in genomic reads from Illumina.
USAGE:
out=telomers.txt;
for fn in */q10_1.fastq; do
d=`echo $fn | cut -d'/' -f1`;
echo $d >> $out;
echo "find_telomers.py $d/q10*merFreq.txt";
find_telomers.py $d/q10*merFreq.txt >> $out;
done
"""
import gzip, re, sys
from copy import copy
from Bio.Seq import Seq
from datetime import datetime
def get_kmers( seq,k=5,basesInMerTh=2 ):
"""
"""
mers=set()
for i in range(len(seq)-k):
mer=seq[i:i+k]
#check if mer is homozygous, skip if so
bases=set( base for base in mer )
if seq.count(mer)>1 and len(bases)>basesInMerTh:
mers.add(mer)
return mers
def get_repeats( mer,seqs,minLen=7 ):
"""
"""
#define pattern
pat=re.compile(mer)
repeats=set()
#iterate through sequences
for sid in seqs:
for seq in seqs[sid]:
pSpan=[]
#store info about repeat if at least 2 matches
for m in pat.finditer(seq):
if pSpan:
start,end=pSpan[0],m.span()[0]
if end-start>=minLen:
repeat=seq[ start:end ]
#add repeat info
repeats.add(repeat)
pSpan=m.span()
return repeats
def _unique( repeat,repeats ):
"""Return False if any repositioned repeat or
its reverse complement in repeats.
Otherwise return True.
"""
for i in range( len(repeat) ):
repeat=repeat[1:]+repeat[0]
rcRepeat=str( Seq(repeat).reverse_complement() )
if repeat in repeats or rcRepeat in repeats: return False
return True
def get_unique_repeats( repeats ):
"""Return set of non-redundant repeats.
"""
nrRepeats=set()
for repeat in repeats:
if _unique( repeat,nrRepeats ): nrRepeats.add( repeat )
return nrRepeats
def count_repeats( seqs, repeats ):
"""
"""
#print len(repeats),repeats
#get only non-reduntant repeats
repeats=get_unique_repeats( repeats )
#print len(repeats),repeats
#calculate stats
matches={}
for repeat in repeats:
matches[repeat]=[0,0,0]
for sid in seqs:
#read pattern occurences from sequence id
occurences=int( sid.split('-')[-1] )
for seq in seqs[sid]:
for i in range( 0,len(repeat),1 ):
#create repeat+flanking 5bp
repeat3=3*repeat
_repeat=repeat[i:]+repeat[:i]+repeat3[i:i+len(seq)-len(repeat)]
#print _repeat
if _repeat in seq:
matches[ repeat ][0] += occurences
matches[ repeat ][1] += 1
break
#add scores
for repeat in matches:
o,i,s=matches[repeat]
s=o*len(repeat)
matches[repeat]=o,i,s
return matches
def main():
k=5
seqs={}
for fn in sys.argv[1:]:
if fn.endswith('.gz'):
f=gzip.open(fn)
else:
f=open(fn)
while 1:
#read sequence id (contain occurencies info), sequence and it's reverse complement
sid = f.readline()[1:-1] #>5-1870
seq = f.readline()[:-1] #GTTCAGCAGGAATGCCGAGATCGGAAGAGCGGTTCAGCAGGAA
rSeq = f.readline()[:-1] #TTCCTGCTGAACCGCTCTTCCGATCTCGGCATTCCTGCTGAAC
#stop reading if not sequence id
if not sid: break
#add fn to sequnce id and store
sid = '%s-%s' % (fn,sid)
seqs[sid] = ( seq,rSeq )
f.close()
seqsOrg = copy(seqs)
sids = seqs.keys()
merProcessed= set()
repeats = set()
for sid in sids:
seq,rSeq = seqs.pop(sid)
#print sid,seq,rSeq
mers=get_kmers( seq,k )
for mer in mers:
#check if kmer already processed
if mer in merProcessed: continue
merProcessed.add( mer )
#get repeats flanked by given kmer and add them to repeats
for repeat in get_repeats( mer,seqs ): repeats.add( repeat )
#here it will be cool to collapse overlapping repeats
matches=count_repeats( seqsOrg, repeats )
#print best repeats
i=0
#print '#reads\tunique\tscore\trepeat'
for repeat in sorted( matches.keys(), key=lambda x: matches[x][2], reverse=True ):
o,i,s=matches[repeat]
if not int(i): break
print '%s\t%s\t%s\t%s' % ( o,i,s,repeat, )
if __name__=='__main__':
t0=datetime.now()
main()
dt=datetime.now()-t0
sys.stderr.write( " #Time elapsed: %s\n" % dt )