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obi import: small efficiency improvement when dealing with NA values

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Celine Mercier
2017-10-04 15:44:48 +02:00
parent b4088a7928
commit 532d8e9cd7
1 changed files with 5 additions and 2 deletions
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7
python/obitools3/commands/import.pyx
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@ -79,6 +79,7 @@ def run(config):
cdef list old_elements_names cdef list old_elements_names
cdef list new_elements_names cdef list new_elements_names
cdef ProgressBar pb cdef ProgressBar pb
cdef bytes NA_value
global obi_errno global obi_errno
@ -102,6 +103,8 @@ def run(config):
iseq = input[1] iseq = input[1]
NA_value = config['obi']['nastring']
get_quality = False get_quality = False
NUC_SEQS_view = False NUC_SEQS_view = False
if isinstance(output[1], View) : if isinstance(output[1], View) :
@ -141,9 +144,9 @@ def run(config):
if tag != b"ID" and tag != b"DEFINITION" and tag != b"NUC_SEQ" and tag != b"QUALITY" : # TODO hmmm... if tag != b"ID" and tag != b"DEFINITION" and tag != b"NUC_SEQ" and tag != b"QUALITY" : # TODO hmmm...
value = seq[tag] value = seq[tag]
# Check NA value # Check NA value
if value == config['obi']['nastring'] : if value == NA_value :
value = None value = None
if tag not in dcols : if tag not in dcols :