Fixed the ultimate bug with embl (and genbank) parsers: raising any

exception in a python generator makes it unable to resume. So now,
exceptions are not raised but printed, then functions return None and
that's handled at higher level.
This commit is contained in:
Celine Mercier
2019-03-15 16:06:06 +01:00
parent 832f582802
commit e8090a44c9
2 changed files with 14 additions and 6 deletions

View File

@ -45,7 +45,7 @@ def emblParser(bytes text):
s = _seqMatcher.search(text).group()
s = _cleanSeq.sub(b'', s).upper()
acs = _acMatcher.search(text).group()
acs = acs.replace(b';', b' ')
acs = acs.split()
@ -55,11 +55,11 @@ def emblParser(bytes text):
de = _deMatcher.search(header).group()
de = _cleanDe.sub(b' ', de).strip().strip(b'.')
except AttributeError,e:
print('=======================================================')
print(text)
print('=======================================================')
raise e
except Exception as e:
print("\nCould not import sequence id:", text.split()[1], "(error raised:", e, ")")
# Do not raise any Exception if you need the possibility to resume the generator
# (Python generators can't resume after any exception is raised)
return None
tags = {}
extractTaxon(ft, tags)