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obi annotate: fixed annotation at ranks

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This commit is contained in:
Celine Mercier
2020-04-29 14:24:40 +02:00
parent 0bec2631e8
commit 55d4f98d60
1 changed files with 4 additions and 3 deletions
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7
python/obitools3/commands/annotate.pyx
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@ -13,7 +13,8 @@ from obitools3.dms.capi.obiview cimport NUC_SEQUENCE_COLUMN, \
ID_COLUMN, \ ID_COLUMN, \
DEFINITION_COLUMN, \ DEFINITION_COLUMN, \
QUALITY_COLUMN, \ QUALITY_COLUMN, \
COUNT_COLUMN COUNT_COLUMN, \
TAXID_COLUMN
import time import time
import math import math
@ -175,8 +176,8 @@ def sequenceTaggerGenerator(config, taxo=None):
counter[0]+=1 counter[0]+=1
for rank in annoteRank: for rank in annoteRank:
if 'taxid' in seq: if TAXID_COLUMN in seq:
taxid = seq['taxid'] taxid = seq[TAXID_COLUMN]
if taxid is not None: if taxid is not None:
rtaxid = taxo.get_taxon_at_rank(taxid, rank) rtaxid = taxo.get_taxon_at_rank(taxid, rank)
if rtaxid is not None: if rtaxid is not None: