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Ask screed to parse descriptions #11

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f6e573d
Ask screed to parse descriptions
humberto-ortiz Dec 11, 2016
3208b1e
Record names in screed changed format
humberto-ortiz Dec 11, 2016
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7 changes: 4 additions & 3 deletions annotate-seqs.py
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Original file line number Diff line number Diff line change
Expand Up @@ -26,11 +26,12 @@ def main():
print 'Scanning sequences -- first pass to gather info'
for n, record in enumerate(screed.open(transcript_file)):
tr = record.name.split('.')[2]
tr = tr.split()[0]
assert tr.startswith('tr')

if n % 25000 == 0:
print '...', n
name = record.name
name = record.name.split()[0]
annot = None

o = ortho.get(name)
Expand Down Expand Up @@ -83,6 +84,7 @@ def main():
for n, record in enumerate(screed.open(transcript_file)):
seqid = record.name.split('.')[1]
tr = record.name.split('.')[2]
tr = tr.split()[0]

ortho_col = ""
homol_score = ""
Expand All @@ -92,7 +94,7 @@ def main():

if n % 25000 == 0:
print '... x2', n
name = record.name
name = record.name.split()[0]
annot = None

o = ortho.get(name)
Expand All @@ -103,7 +105,6 @@ def main():
annot_ortho_count += 1
else:
h = homol.get(name)

if h and transform_name(h[0][0]) in namedb.mouse_names:
h, score = h[0]
score = round(float(score) / float(len(record.sequence)) * 100)
Expand Down
2 changes: 1 addition & 1 deletion make-namedb.py
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Original file line number Diff line number Diff line change
Expand Up @@ -9,7 +9,7 @@
d = {}
e = {}
is_ncbi = False
for record in screed.open(sys.argv[1]):
for record in screed.open(sys.argv[1], parse_description=True):
if record.name.startswith('gi|'):
is_ncbi = True
ident = record.name.split('|')[3]
Expand Down