-
Notifications
You must be signed in to change notification settings - Fork 1
/
kmer_continue_left.py
138 lines (103 loc) · 3.88 KB
/
kmer_continue_left.py
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
#!/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 trseeker.tools.jellyfish_tools import query_kmers, Kmer2tfAPI
from trseeker.tools.ngrams_tools import print_prev_cutoff
from trseeker.tools.sequence_tools import get_revcomp
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','--sequence', help='Start sequence', required=True)
parser.add_argument('-j','--jf', help='JF file', required=True)
parser.add_argument('-n','--new', help='Use new', required=False, default=True)
parser.add_argument('-k','--k', help='k', required=False, default=23)
parser.add_argument('-s','--start', help='start', required=False, default=0)
parser.add_argument('-c','--cutoff', help='Minimal coverage to report', required=False, default=0)
parser.add_argument('--upper', help='Maximal coverage to report', required=False, default=0)
parser.add_argument('-o','--output', help='output', required=False, default=False)
args = vars(parser.parse_args())
input_fasta = args["sequence"]
start = int(args["start"])
jf_path = args["jf"]
k = int(args["k"])
c = int(args["cutoff"])
use_new = bool(args["new"])
sequence = input_fasta.upper()
kmer = sequence[:k]
output_file = args["output"]
print sequence
print "Kmer:", kmer
if jf_api and use_new:
jf_api = jellyfish.QueryMerFile(jf_path)
kmer2freq = Kmer2tfAPI(jf_api)
global_i = 0
ref_kmer = kmer
final_sequence = [kmer]
while True:
a_kmer = 'A' + kmer[:-1]
c_kmer = 'C' + kmer[:-1]
g_kmer = 'G' + kmer[:-1]
t_kmer = 'T' + kmer[:-1]
if not use_new:
kmer2freq = query_kmers(jf_path, [a_kmer, c_kmer, t_kmer, g_kmer], both_strands=True, verbose=False)
R, n, nucleotides, max_hits = print_prev_cutoff(kmer, kmer2freq, cutoff=c)
if global_i and ref_kmer == kmer:
print "Found start kmer"
break
print n, max_hits
global_i -= 1;
skip = False
if n == 1:
# raw_input("Next?")
pos = -1
else:
while True:
pos = raw_input("Fork (number, save, dec, inc)?") or None
# with open("left.temp", "w") as fh:
# fh.write(sequence)
if pos.strip() in ["dec", "inc"]:
pos = raw_input("Set c:") or 0
c = 0
if pos != 0:
c = int(pos.strip())
skip = True
break
if pos.strip() in ["save"]:
with open(output_file, "w") as fh:
fh.write("".join(final_sequence))
print "Saved."
if pos != None:
try:
pos = int(pos.strip())
except:
continue
break
if skip:
continue
sequence = max_hits[pos][1] + sequence
kmer = sequence[:k]
if output_file:
print start, start+global_i, len(sequence), sequence[:53]
else:
print start, start+global_i, len(sequence), sequence
if output_file:
final_sequence.insert(0, max_hits[pos][1])
if output_file:
with open(output_file, "w") as fh:
fh.write("".join(final_sequence))