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count: added option to specify the count column

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This commit is contained in:
mercierc
2021-06-01 09:05:14 +12:00
parent b908b581c8
commit 47691a8f58
1 changed files with 13 additions and 5 deletions
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16
python/obitools3/commands/count.pyx
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@ -29,6 +29,12 @@ def addOptions(parser):
default=False,
help="Prints only the total count of sequence records (if a sequence has no `count` attribute, its default count is 1) (default: False).")
group.add_argument('-c','--count-tag',
action="store", dest="count:countcol",
default='COUNT',
type=str,
help="Name of the tag/column associated with the count information (default: COUNT).")
def run(config):
@ -42,17 +48,19 @@ def run(config):
raise Exception("Could not read input")
entries = input[1]
countcol = config['count']['countcol']
count1 = len(entries)
count2 = 0
if COUNT_COLUMN in entries and ((config['count']['sequence'] == config['count']['all']) or (config['count']['all'])) :
if countcol in entries and ((config['count']['sequence'] == config['count']['all']) or (config['count']['all'])) :
for e in entries:
PyErr_CheckSignals()
count2+=e[COUNT_COLUMN]
count2+=e[countcol]
if COUNT_COLUMN in entries and (config['count']['sequence'] == config['count']['all']):
if countcol in entries and (config['count']['sequence'] == config['count']['all']):
print(count1,count2)
elif COUNT_COLUMN in entries and config['count']['all']:
elif countcol in entries and config['count']['all']:
print(count2)
else:
print(count1)