compare.py

#!/usr/bin/env python

import sys
import screed

if len(sys.argv) != 4:
    print >>sys.stderr, "USAGE: compare.py <mutations.txt> <orig.fasta> <corrected.fasta>"
    sys.exit(1)

fp_out = open('fp.out', 'w')
fn_out = open('fn.out', 'w')

mutations = {}
orig_reads = {}

for line in open(sys.argv[1]):
    lexemes = line.strip().split("\t")
    if len(lexemes) != 4:
        continue

    read_name = lexemes[0]
    pos = int(lexemes[1])
    orig = lexemes[2].upper()
    mut = lexemes[3].upper()

    if read_name not in mutations:
        mutations[read_name] = {}
    if pos not in mutations[read_name]: # only take first mutation for a site
        mutations[read_name][pos] = {"correct" : orig, "mutation" : mut}

for n, record in enumerate(screed.open(sys.argv[2])):
    orig_reads[record["name"]] = record["sequence"].upper()

tps, fps, tns, fns, tot_errors = 0, 0, 0, 0, 0
print >>sys.stderr, "#read\ttp\tfp\ttn\tfn\ttotal_errors"
for n, record in enumerate(screed.open(sys.argv[3])):
    name = record["name"]
    seq = record["sequence"][:100].upper()
    orig = orig_reads[name]

    read_mut = mutations.get(name, {})
    tp, fp, tn, fn = 0, 0, 0, 0

    for pos in range(len(seq)):
        if pos >= len(orig):
            print >>sys.stderr, "{0}\n{1}\n{2}".format(name, seq, orig)
        if pos in read_mut:
            if seq[pos] == read_mut[pos]["correct"]:
                tp += 1
            else:
                fn += 1
                print >>fn_out, seq, orig, pos, name
        else:
            if seq[pos] == orig[pos]:
                tn += 1
            else:
                fp += 1
                print >>fp_out, seq, orig, pos, name

    tps += tp
    fps += fp
    tns += tn
    fns += fn
    tot_errors += len(read_mut)
    print "{0}\t{1}\t{2}\t{3}\t{4}\t{5}".format(name, tp, fp, tn, fn, len(read_mut))

print >>sys.stderr, "Totals\t\t{0}\t{1}\t{2}\t{3}\t{4}".format(tps, fps, tns, fns, tot_errors)

do.sh

  551  export PYTHONPATH=~/dev/khmer:~/dev/screed
  532  python ~/dev/nullgraph/make-reads.py --mutation-details details.out genome.fa > reads.fa
  536  ../scripts/normalize-by-median.py -k 20 -C 20 reads.fa -s reads.ht
  539  python ../sandbox/read_aligner.py reads.ht reads.fa > out 2> errout
  552  python ../sandbox/read_aligner.py reads.ht reads.fa > out 2> errout
  554  ../../2013-read-aligner/compare.py details.out reads.fa out

gistfile1.txt

Foo.

kmer-count-profile.py

#! /usr/bin/env python
import sys
import khmer

kh = khmer.load_counting_hash(sys.argv[1])
print kh.ksize()

for line in open(sys.argv[2]):
    line = line.strip()
    seq_a, seq_b, mutpos, name = line.split()
    mutpos = int(mutpos)
    print name
    for pos in range(len(seq_a) - kh.ksize() + 1):
        signal = ''
        if pos == mutpos:
            signal = '*'
        print '%s%s:%s,%s' % (signal, pos, kh.get(seq_a[pos:pos+kh.ksize()]),
                              kh.get(seq_b[pos:pos+kh.ksize()]),),
    print ''
    print '---'