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BUG obiconvert: could add sequences without/with bad taxid

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This commit is contained in:
Frédéric Boyer
2015-02-06 13:46:31 +00:00
parent 733707a849
commit 673ea5bd64
1 changed files with 3 additions and 2 deletions
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5
src/obitools/ecopcr/sequence.py
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@ -69,7 +69,7 @@ class EcoPCRDBSequenceWriter(object):
ecoTaxonomyWriter(dbname,self._taxonomy) ecoTaxonomyWriter(dbname,self._taxonomy)
print >> sys.stderr,"Ok" print >> sys.stderr,"Ok"
# Identifiy the next sequence file numbre # Identifiy the next sequence file number
if fileidx is None: if fileidx is None:
p = re.compile(r'([0-9]{3})\.sdx') p = re.compile(r'([0-9]{3})\.sdx')
fileidx = max(list(int(p.search(i).group(1)) fileidx = max(list(int(p.search(i).group(1))
@ -107,7 +107,8 @@ class EcoPCRDBSequenceWriter(object):
totalSize = 4 + 20 + 4 + 4 + 4 + cptseqlength + delength totalSize = 4 + 20 + 4 + 4 + 4 + cptseqlength + delength
if self._taxonomy is None or 'taxid' not in seq: if self._taxonomy is None or 'taxid' not in seq :
raise Exception("Taxonomy error: "+seq.id)
taxon=-1 taxon=-1
else: else:
taxon=self._taxonomy.findIndex(seq['taxid']) taxon=self._taxonomy.findIndex(seq['taxid'])