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kmer_continue_right.py
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kmer_continue_right.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 trseeker.tools.jellyfish_tools import query_kmers, Kmer2tfAPI
from trseeker.tools.ngrams_tools import print_next_cutoff
try:
from Ariadna.AriadnaPy.tools.aindex import load_aindex, get_left_right_distances
except:
load_aindex = None
get_left_right_distances = lambda x: x
from collections import defaultdict
from trseeker.tools.sequence_patterns import DNA2IUPAC
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
def extend_sequence_right(kmer, kmer2freq, length=23):
sequence = kmer
global_i = 0
while True:
kmer_a = kmer[1:] + 'A'
kmer_c = kmer[1:] + 'C'
kmer_g = kmer[1:] + 'G'
kmer_t = kmer[1:] + 'T'
R, n, nucleotides, max_hits = print_next_cutoff(kmer, kmer2freq, cutoff=c)
if n == 1:
pos = -1
else:
return None
sequence += max_hits[pos][1]
kmer = sequence[-k:]
global_i += 1;
if global_i == length:
return sequence[k-1:]
# def check_snp_bubble(kmer1, kmer2, kmer2freq, length=23):
# print kmer1, extend_sequence_right(kmer1, kmer2freq, length, k=k)
# print kmer2, extend_sequence_right(kmer2, kmer2freq, length, k=k)
def check_pairs(left_kmer, kmer_a, kmer_c, kmer_t, kmer_g, aindex, sequence, key_kmers_solved, nucleotides, key_kmers_unsolved, shift=None, k=23):
count_a = len(get_left_right_distances(left_kmer,kmer_a,aindex))
count_c = len(get_left_right_distances(left_kmer,kmer_c,aindex))
count_t = len(get_left_right_distances(left_kmer,kmer_t,aindex))
count_g = len(get_left_right_distances(left_kmer,kmer_g,aindex))
print "Shift:", shift, max_hits
print "A", count_a, extend_sequence_right(kmer_a, kmer2freq, length=k)
print "C", count_c, extend_sequence_right(kmer_c, kmer2freq, length=k)
print "T", count_t, extend_sequence_right(kmer_t, kmer2freq, length=k)
print "G", count_g, extend_sequence_right(kmer_g, kmer2freq, length=k)
if count_a > min_error and count_c < min_error and count_t < min_error and count_g < min_error:
sequence += 'A'
key_kmers_solved[kmer_a] = len(sequence) - k
for nucl in nucleotides:
if nucl == 'A':
continue
key_kmers_unsolved[kmer_a].append(kmer_a[:-1]+nucl)
return sequence
if count_c > min_error and count_a < min_error and count_t < min_error and count_g < min_error:
sequence += 'C'
key_kmers_solved[kmer_c] = len(sequence) - k
for nucl in nucleotides:
if nucl == 'C':
continue
key_kmers_unsolved[kmer_c].append(kmer_c[:-1]+nucl)
return sequence
if count_t > min_error and count_c < min_error and count_a < min_error and count_g < min_error:
sequence += 'T'
key_kmers_solved[kmer_t] = len(sequence) - k
for nucl in nucleotides:
if nucl == 'T':
continue
key_kmers_unsolved[kmer_t].append(kmer_t[:-1]+nucl)
return sequence
if count_g > min_error and count_c < min_error and count_t < min_error and count_a < min_error:
sequence += 'G'
key_kmers_solved[kmer_g] = len(sequence) - k
for nucl in nucleotides:
if nucl == 'G':
continue
key_kmers_unsolved[kmer_g].append(kmer_g[:-1]+nucl)
return sequence
return None
if __name__ == '__main__':
parser = argparse.ArgumentParser(description='Print cov for fasta')
parser.add_argument('-i','--sequence', help='Start sequence', required=True)
parser.add_argument('--right', help='Stop sequence', required=False, default=None)
parser.add_argument('-j','--jf', help='JF file', required=True)
parser.add_argument('-k','--k', help='k', required=False, default=23)
parser.add_argument('-n','--new', help='Use new', required=False, default=True)
parser.add_argument('-s','--start', help='start', required=False, default=0)
parser.add_argument('--min_error', help='error cutoff', required=False, default=0)
parser.add_argument('-p','--pause', help='pause', required=False, default=False)
parser.add_argument('-x','--xkmer', help='Remove seed kmer', required=False, default=False)
parser.add_argument('-o','--output', help='output', required=False, default=False)
parser.add_argument('--index', help='index', required=False, default=False)
parser.add_argument('--reads', help='reads', required=False, default=False)
parser.add_argument('--aindex', help='aindex', required=False, default=False)
parser.add_argument('-c','--cutoff', help='Minimal coverage to report', required=False, default=0)
args = vars(parser.parse_args())
input_fasta = args["sequence"]
stop_kmer = args["right"]
index_prefix = args["index"]
reads_file = args["reads"]
aindex_prefix = args["aindex"]
xlengths = len(input_fasta)
start = int(args["start"])
jf_path = args["jf"]
k = int(args["k"])
c = int(args["cutoff"])
pause = args["pause"]
min_error = int(args["min_error"])
xkmer = args["xkmer"]
use_new = bool(args["new"])
output_file = args["output"]
sequence = input_fasta.upper()
kmer = sequence[-k:]
ref_kmer = kmer
global_i = 0
if min_error:
settings = {
"index_prefix": index_prefix,
"aindex_prefix": aindex_prefix,
"reads_file": reads_file,
"max_tf": 10000000,
}
aindex = load_aindex(settings)
if output_file:
fh = open(output_file, "w")
if output_file:
fh.write(sequence)
if jf_api and use_new and jf_path.endswith(".jf2"):
jf_api = jellyfish.QueryMerFile(jf_path)
kmer2freq = Kmer2tfAPI(jf_api)
else:
import aindex
settings = {
"index_prefix": jf_path,
}
kmer2freq = aindex.load_aindex(settings, skip_aindex=True, skip_reads=True)
key_kmers_solved = {}
key_kmers_unsolved = defaultdict(list)
while True:
if stop_kmer and sequence.endswith(stop_kmer):
print "Solution found"
print sequence
break
kmer_a = kmer[1:] + 'A'
kmer_c = kmer[1:] + 'C'
kmer_g = kmer[1:] + 'G'
kmer_t = kmer[1:] + 'T'
if global_i and ref_kmer == kmer:
print "Found start kmer"
break
if not use_new:
kmer2freq = query_kmers(jf_path, [kmer_a, kmer_t, kmer_g, kmer_c], both_strands=True, verbose=False)
R, n, nucleotides, max_hits = print_next_cutoff(kmer, kmer2freq, cutoff=c)
# print kmer
# print R, n, nucleotides, max_hits
# raw_input("?")
print n, max_hits, nucleotides
global_i += 1;
if n == 1:
if pause:
raw_input("Next?")
pos = -1
sequence += max_hits[pos][1]
else:
shift = 0
full_stop = False
while True:
if min_error:
left_kmer = sequence[-40-shift:-40+k-shift]
result = check_pairs(left_kmer, kmer_a, kmer_c, kmer_t, kmer_g, aindex, sequence, key_kmers_solved, nucleotides, key_kmers_unsolved, shift=None, k=k)
if result is not None:
sequence = result
break
pos = raw_input("Fork (or STOP)?") or None
# with open("right.temp", "w") as fht:
# fht.write(sequence)
if pos.strip() == "STOP":
full_stop = True
break
if pos != None:
pos = pos.strip()
try:
pos = int(pos)
if pos > 4:
shift = pos
continue
sequence += max_hits[pos][1]
key_kmers_solved[sequence[-k:]] = len(sequence) - k
except:
if len(pos) > 1:
if pos in DNA2IUPAC:
sequence += DNA2IUPAC[pos] + extend_sequence_right(kmer_a[:-1]+pos[0], kmer2freq, length=k)[1:]
break
else:
sequence += pos
key_kmers_solved[sequence[-k:]] = len(sequence) - k
global_i += len(pos)-1
break
if pos and pos.strip() in ["A","C","T","G"]:
sequence += pos
key_kmers_solved[sequence[-k:]] = len(sequence) - k
break
continue
break
# if min_error:
# print "Check solved:"
# keys = key_kmers_solved.keys()
# while keys:
# left_kmer = keys.pop()
# print "Positive:"
# pos_result = check_pairs(left_kmer, kmer_a, kmer_c, kmer_t, kmer_g, aindex, sequence, key_kmers_solved, nucleotides, key_kmers_unsolved, shift=None, k=23)
# print "Negative:"
# for neg_kmer in key_kmers_unsolved[left_kmer]:
# neg_result = check_pairs(left_kmer, kmer_a, kmer_c, kmer_t, kmer_g, aindex, sequence, key_kmers_solved, nucleotides, key_kmers_unsolved, shift=None, k=23)
# if result is not None:
# raw_input("Done?")
# sequence = result
# break
# raw_input("Miss?")
shift += 5
if full_stop:
break
kmer = sequence[-k:]
if output_file:
print start, start+global_i, len(sequence), sequence[-53:], start+global_i+1+k
else:
if xkmer:
print start, start+global_i, len(sequence), sequence[xlengths:]
else:
print start, start+global_i, len(sequence), sequence
if output_file:
fh.write(sequence[-1])
if output_file:
fh.close()