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Convert to Python3 #55

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28 changes: 14 additions & 14 deletions BioCompass/BioCompass.py
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Original file line number Diff line number Diff line change
Expand Up @@ -102,9 +102,9 @@ def parse_antiSMASH(content):


QueryCluster = OrderedDict()
for k in re.search(
for k in list(re.search(
rule_query_cluster, parsed['QueryCluster'],
re.VERBOSE).groupdict().keys():
re.VERBOSE).groupdict().keys()):
QueryCluster[k] = []
for row in re.finditer(
rule_query_cluster, parsed['QueryCluster'], re.VERBOSE):
Expand Down Expand Up @@ -186,7 +186,7 @@ def __getitem__(self, item):
return self.data[item]

def keys(self):
return self.data.keys()
return list(self.data.keys())

def load(self, filename):
self.data = {}
Expand Down Expand Up @@ -221,8 +221,8 @@ def efetch_hit(term, seq_start, seq_stop):
downloaded = True
except:
nap = ntry*3
print "Fail to download (term). I'll take a nap of %s seconds ", \
" and try again."
print("Fail to download (term). I'll take a nap of %s seconds ", \
" and try again.")
time.sleep(ntry*3)

return content
Expand All @@ -233,7 +233,7 @@ def download_hits(filename, output_path):
"""
c = antiSMASH_file(filename)

for cs in c['SignificantHits'].keys():
for cs in list(c['SignificantHits'].keys()):
locus = c['SignificantHits'][cs]['locus']
table_genes = c['SignificantHits'][cs]['TableGenes']

Expand All @@ -244,25 +244,25 @@ def download_hits(filename, output_path):
max(table_genes['location_end'])))

if os.path.isfile(filename_out):
print "Already downloaded %s" % filename_out
print("Already downloaded %s" % filename_out)
else:
print "Requesting cluster_subject: %s, start: %s, end: %s" % (
print("Requesting cluster_subject: %s, start: %s, end: %s" % (
locus,
min(table_genes['location_start']),
max(table_genes['location_end']))
max(table_genes['location_end'])))

content = efetch_hit(
term=locus,
seq_start=min(table_genes['location_start']),
seq_stop=max(table_genes['location_end']))

print "Saving %s" % filename_out
print("Saving %s" % filename_out)
with open(filename_out, 'w') as f:
f.write(content)


import urlparse
import urllib2
import urllib.parse
import urllib.request, urllib.error, urllib.parse
import tempfile
import tarfile
import os
Expand All @@ -274,10 +274,10 @@ def download_mibig(outputdir, version='1.3'):

server = 'http://mibig.secondarymetabolites.org'
filename = "mibig_gbk_%s.tar.gz" % version
url = urlparse.urljoin(server, filename)
url = urllib.parse.urljoin(server, filename)

with tempfile.NamedTemporaryFile(delete=True) as f:
u = urllib2.urlopen(url)
u = urllib.request.urlopen(url)
f.write(u.read())
f.file.flush()
tar = tarfile.open(f.name)
Expand Down
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