blob: 25b4a083e980e0b2df8c302f0dd7f6f439efa280 (
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import os
import json
import sys
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")
blacklist = set()
if len(sys.argv) > 1:
with open(sys.argv[1]) as bl:
for l in bl:
blacklist.add(l.strip())
for i, r in enumerate(reads):
with open(r["path"], "rt") as fa:
label = fa.readline().strip()
original_labels.write("<%s> <http://biohackathon.org/bh20-seq-schema/original_fasta_label> \"%s\" .\n" % (subjects[i], label[1:].replace('"', '\\"')))
skip = (subjects[i] in blacklist or label[1:] in blacklist)
if skip:
original_labels.write("<%s> <http://biohackathon.org/bh20-seq-schema/excluded_from_graph> \"true\"^^<http://www.w3.org/2001/XMLSchema#boolean> .\n" % (subjects[i]))
if not skip:
relabeled_fasta.write(">"+subjects[i]+"\n")
data = fa.read(8096)
while data:
if not skip:
relabeled_fasta.write(data)
endswithnewline = data.endswith("\n")
data = fa.read(8096)
if not skip and not endswithnewline:
relabeled_fasta.write("\n")
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