Sequence utils

removeCopies

#!/usr/bin/python
'''
Reads a FASTA files and rewrites it keeping only the unique IDs

Important: we assume that if two proteins have the same ID, they have the same sequence
'''
import sys
from Bio import SeqIO

if len(sys.argv) < 3:
    print 'Usage: removeCopies INPUT OUTPUT'
    sys.exit(1)

fname, out = sys.argv[1:3]

def unique(records):
    count = 0
    already = set()
    for r in records:
        count += 1
        if r.id not in already:
            already.add(r.id)
            yield r
    print "%i saved sequences, %i inputs" % (len(already), count)

SeqIO.write(unique(SeqIO.parse(fname, "fasta")), out, "fasta")

A print statement inside the function is just perfect, thanks!

I've noticed that pypy 1.9 takes twice the time to run as compared to python 2.7: I expected it to be faster...