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kmer_cov_for_fasta.py
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kmer_cov_for_fasta.py
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#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
#@created: 10.10.2013
#@author: Aleksey Komissarov
#@contact: [email protected]
import sys
from trseeker.seqio.fasta_file import sc_iter_fasta
import argparse
from intervaltree import IntervalTree
from collections import defaultdict
from trseeker.tools.jellyfish_tools import query_kmers, Kmer2tfAPI
jf_api = True
try:
from jellyfish import jellyfish
except:
print("Failed: from jellyfish import jellyfish")
try:
import jellyfish
except:
print("Failed: import jellyfish")
jf_api = False
if __name__ == '__main__':
parser = argparse.ArgumentParser(description='Print cov for fasta')
parser.add_argument('-i','--fasta', help='Fasta file', required=True)
parser.add_argument('-j','--jf', help='JF file', required=True)
parser.add_argument('-o','--output', help='Ouput file', required=True)
parser.add_argument('-k','--k', help='k', required=True)
parser.add_argument('-a','--annotation', help='Annotation file', required=False, default=False)
parser.add_argument('-m','--multu', help='Save as multifasta', required=False, default=False)
parser.add_argument('-n','--new', help='New jf', required=False, default=True)
parser.add_argument('-c','--cutoff', help='Minimal coverage to report', required=True)
parser.add_argument('-s','--onlyhits', help='Save only hits', required=False, default=False)
args = vars(parser.parse_args())
annotation_file = args["annotation"]
multi = args["multu"]
if annotation_file:
tree = IntervalTree()
with open(annotation_file) as fh:
data = fh.readlines()
for line in data:
line = line.strip().split()
s,e = int(line[0]), int(line[1])
if s > e:
s,e = e,s
tree.addi(s-1,e-1, " ".join(line[2:]))
input_fasta = args["fasta"]
only_hits = bool(args["onlyhits"])
jf_path = args["jf"]
use_new = bool(args["new"])
k = int(args["k"])
c = int(args["cutoff"])
fh = open(args["output"], "w")
if jf_api and use_new:
jf_api = jellyfish.QueryMerFile(jf_path)
kmer2freq = Kmer2tfAPI(jf_api)
for sid, seq_obj in enumerate(sc_iter_fasta(input_fasta)):
print seq_obj.header, "Length:", seq_obj.length
sequence = seq_obj.sequence.upper()
n = len(sequence)
kmers = set()
for i in xrange(n-k+1):
kmer= sequence[i:i+k]
tf = kmer2freq[kmer]
if tf > 0:
print i, tf
raw_input("Next item?")
# kmers.add()
# kmers.add('A' + sequence[i:i+k-1])
# kmers.add('C' + sequence[i:i+k-1])
# kmers.add('G' + sequence[i:i+k-1])
# kmers.add('T' + sequence[i:i+k-1])
# kmers.add(sequence[i+1:i+k] + 'A')
# kmers.add(sequence[i+1:i+k] + 'C')
# kmers.add(sequence[i+1:i+k] + 'T')
# kmers.add(sequence[i+1:i+k] + 'G')
# print "Kmers:", len(kmers)
# print "Load kmers"
# kmers = list(kmers)
# # step = 1000
# # for i in xrange(0, len(kmers), step):
# # kmer2freq.update(query_kmers(jf_path, kmers[i:i+step], both_strands=True, verbose=False))
# # print "Loaded", i, i+step, "total size:", len(kmer2freq)
# if not (jf_api and use_new):
# kmer2freq = defaultdict(int)
# kmer2freq = query_kmers(jf_path, kmers, both_strands=True, verbose=30, new=use_new, batch_size=2000)
# print "Results:"
# for i in xrange(n-k+1):
# kmer = sequence[i:i+k].upper()
# a_kmer = kmer2freq['A' + kmer[:-1]]
# c_kmer = kmer2freq['C' + kmer[:-1]]
# g_kmer = kmer2freq['G' + kmer[:-1]]
# t_kmer = kmer2freq['T' + kmer[:-1]]
# kmer_a = kmer2freq[kmer[1:] + 'A']
# kmer_c = kmer2freq[kmer[1:] + 'C']
# kmer_g = kmer2freq[kmer[1:] + 'G']
# kmer_t = kmer2freq[kmer[1:] + 'T']
# if kmer_a < c: kmer_a = 0
# if kmer_c < c: kmer_c = 0
# if kmer_g < c: kmer_g = 0
# if kmer_t < c: kmer_t = 0
# if a_kmer < c: a_kmer = 0
# if c_kmer < c: c_kmer = 0
# if g_kmer < c: g_kmer = 0
# if t_kmer < c: t_kmer = 0
# prev_hits = len([x for x in [a_kmer, c_kmer, g_kmer, t_kmer] if x >= c])
# next_hits = len([x for x in [kmer_a, kmer_c, kmer_g, kmer_t] if x >= c])
# prefix = " "
# if prev_hits > 1 and next_hits > 1:
# prefix = "FF"
# elif prev_hits > 1:
# prefix = "F-"
# elif next_hits > 1:
# prefix = "-F"
# if int(kmer2freq[kmer]) == 0:
# if only_hits:
# continue
# prefix = "--"
# s = prefix, i, "-", kmer, "Prev:", a_kmer, c_kmer, g_kmer, t_kmer, "Next:", kmer_a, kmer_c, kmer_g, kmer_t, "*"*prev_hits, "*"*next_hits, " ".join([x.data for x in tree[i]])
# else:
# s = prefix, i, kmer2freq[kmer], kmer, "Prev:", a_kmer, c_kmer, g_kmer, t_kmer, "Next:", kmer_a, kmer_c, kmer_g, kmer_t, "*"*prev_hits, "*"*next_hits, " ".join([x.data for x in tree[i]])
# print s
# fh.write("%s\n" % "\t".join(map(str, s)))
# if not multi:
# break
#
# fh.close()