Try to recover illumina dataset with missing .filter files

dotfilter_symlinker.py

#!/bin/env python

import os
import logging
import glob
import random
from collections import *

fters = defaultdict(set)
all = set(["%04d.filter" % x for x in range(1, 70)])

for dotfilter in glob.glob("*.filter"):
    (_, lane, tile) = dotfilter.split("_")
    fters[lane].add(tile)

# symlink all missing filters to previous .filter files
for lane in fters:
    miss_fters = all.difference(fters[lane])
    
    # take an existing .filter from the set...
    src = random.sample(fters[lane],1)
    for dst in miss_fters:
        # ... and symlink the missing ones against it
        print "creating symlink from %s to %s" % ("s_%s_%s" % (lane,src[0]), "s_%s_%s" % (lane,dst))
        os.symlink("s_%s_%s" % (lane,src[0]), "s_%s_%s" % (lane,dst))