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#cython: language_level=3
from obitools3.uri.decode import open_uri
from obitools3.apps.config import logger
from obitools3.dms import DMS
from obitools3.apps.optiongroups import addMinimalInputOption
from obitools3.dms.capi.obiview cimport COUNT_COLUMN
from cpython.exc cimport PyErr_CheckSignals
__title__="Count sequence records"
def addOptions(parser):
addMinimalInputOption(parser)
group = parser.add_argument_group('obi count specific options')
group.add_argument('-s','--sequence',
action="store_true", dest="count:sequence",
default=False,
help="Prints only the number of sequence records (much faster, default: False).")
group.add_argument('-a','--all',
action="store_true", dest="count:all",
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):
DMS.obi_atexit()
logger("info", "obi count")
# Open the input
input = open_uri(config['obi']['inputURI'])
if input is None:
raise Exception("Could not read input")
entries = input[1]
countcol = config['count']['countcol']
count1 = len(entries)
count2 = 0
if countcol in entries and ((config['count']['sequence'] == config['count']['all']) or (config['count']['all'])) :
for e in entries:
PyErr_CheckSignals()
count2+=e[countcol]
if countcol in entries and (config['count']['sequence'] == config['count']['all']):
print(count1,count2)
elif countcol in entries and config['count']['all']:
print(count2)
else:
print(count1)
input[0].close(force=True)
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