forked from dib-lab/khmer
/
abundance_dist.py
46 lines (34 loc) · 947 Bytes
/
abundance_dist.py
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import sys
sys.path.insert(0, '/u/t/dev/screed')
import screed
from screed.fastq import fastq_iter
from screed.fasta import fasta_iter
K = 15
import khmer
kh = khmer.new_hashtable(K, 1999999973)
filename = '/scratch/gpgc/iowa/850.2.fq'
#filename = 'foo'
for n, record in enumerate(fastq_iter(open(filename))):
if n % 10000 == 0:
print>>sys.stderr, '...', n
if n > 10**6:
break
sequence = record['sequence']
if 'N' in sequence:
continue
kh.consume(sequence)
bins = [0] * 256
for n, record in enumerate(fastq_iter(open(filename))):
if n % 10000 == 0:
print>>sys.stderr, '...', n
if n > 10**5:
break
sequence = record['sequence']
if 'N' in sequence:
continue
for i in range(0, len(sequence) - K + 1):
subseq = sequence[i:i+K]
abundance = kh.get(subseq)
bins[abundance] += 1
for n, count in enumerate(bins):
print n, count