blob: 6b022a057e0eb4019bcc2371da5b77de4dce68bc (
plain)
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
|
import os
import json
def readitems(stem):
items = []
b = 1
while os.path.exists("%s%i" % (stem, b)):
with open("%s%i" % (stem, b)) as f:
items.extend(json.load(f))
b += 1
return items
reads = readitems("block")
subjects = readitems("subs")
relabeled_fasta = open("relabeledSeqs.fasta", "wt")
original_labels = open("originalLabels.ttl", "wt")
for i, r in enumerate(reads):
with open(r["path"], "rt") as fa:
label = fa.readline()
original_labels.write("<%s> <http://biohackathon.org/bh20-seq-schema/original_fasta_label> \"%s\" .\n" % (subjects[i], label[1:].strip().replace('"', '\\"')))
relabeled_fasta.write(">"+subjects[i]+"\n")
data = fa.read(8096)
while data:
relabeled_fasta.write(data)
endswithnewline = data.endswith("\n")
data = fa.read(8096)
if not endswithnewline:
relabeled_fasta.write("\n")
|
