-
Notifications
You must be signed in to change notification settings - Fork 0
/
Reciprocal.py
64 lines (55 loc) · 2.19 KB
/
Reciprocal.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
import os
import random
from Bio.Blast import NCBIXML
import FetchUtil
from helpers import commands
if not os.path.exists('XML'):
os.mkdir('XML')
if not os.path.exists('dicts'):
os.mkdir('dicts')
def bestrecipblast(org, seed, thresh=5, queue=None):
"""Returns the best pairwise reciprocal BLAST using seed accession no. from against org organism"""
seedorg = FetchUtil.fetch_organism(seed)[0]
acclist = {}
ac = []
FetchUtil.fetch_fasta(seed)
dum = str(int(int(seed.split('.')[0][-5:]) * random.random()))
commands.run_blast(seed, thresh, dum, org)
with open('XML' + os.sep + dum + '.xml') as qoutput:
parser = NCBIXML.parse(qoutput)
for lin in parser:
for align in lin.alignments:
for hsp in align.hsps:
if (hsp.positives / float(hsp.align_length)) >= .4 and (
float(hsp.align_length) / len(hsp.query)) >= .25:
ac.append(align.title.split('|')[1])
print("Done. Number of sequences found: " + repr(len(ac)))
for o in ac:
print(o)
FetchUtil.fetch_fasta(o)
commands.run_blast(o, thresh, dum, seedorg[0])
with open('XML' + os.sep + dum + '.xml') as q1output:
parse = NCBIXML.parse(q1output)
acc = []
print('blasted')
for lin in parse:
for align in lin.alignments:
for hsp in align.hsps:
if (hsp.positives / float(hsp.align_length)) >= .4 and (
float(hsp.align_length) / len(hsp.query)) > .25:
acc.append(align.title.split('|')[1])
else:
continue
print("Done. Number of sequences found: " + repr(len(acc)))
if seed in acc:
print('it\'s twue!')
name = FetchUtil.fetch_organism(o)[0]
acclist[name] = [o, str(ac.index(o) + 1) + '/' + str(len(ac)),
str(acc.index(seed) + 1) + '/' + str(len(acc))]
with open('dicts' + os.sep + seed, 'a') as dicts:
dicts.write(str(acclist) + '\n')
break
if queue is not None:
queue.put(acclist)
else:
return acclist