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obi import: added an option to specify the NA value in the input file

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(default is 'NA', same as in R's read.table function)
This commit is contained in:
Celine Mercier
2017-07-11 12:10:33 +02:00
parent df2ad41150
commit ced9a268a1
1 changed files with 13 additions and 3 deletions
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14
python/obitools3/commands/import.pyx
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@ -104,9 +104,15 @@ def addOptions(parser):
const='pep', const='pep',
help="Input file contains protein sequences") help="Input file contains protein sequences")
group.add_argument('--NA',
action="store", dest="import:NA",
metavar='<NA_value>',
default='NA',
type=str,
help="Character string for Not Available values in the input file "
"(default: 'NA'")
# TODO: Handling of NA values. Check None. Specify in doc? None or NA? Possiblity to specify in option?
# look in R read.table option to specify NA value
def run(config): def run(config):
cdef int i cdef int i
@ -192,6 +198,10 @@ def run(config):
value = seq['tags'][tag] value = seq['tags'][tag]
# Check NA value
if value == config['import']['NA'] :
value = None
if tag not in dcols : if tag not in dcols :
value_type = type(value) value_type = type(value)