56 lines
1.6 KiB
Cython
56 lines
1.6 KiB
Cython
#cython: language_level=3
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from obitools3.uri.decode import open_uri
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from obitools3.apps.config import logger
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from obitools3.dms import DMS
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from obitools3.apps.optiongroups import addSequenceInputOption
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from obitools3.dms.capi.obiview cimport COUNT_COLUMN
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__title__="Counts sequence records"
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def addOptions(parser):
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addSequenceInputOption(parser)
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group = parser.add_argument_group('obi count specific options')
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group.add_argument('-s','--sequence',
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action="store_true", dest="count:sequence",
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default=False,
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help="Prints only the number of sequence records.")
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group.add_argument('-a','--all',
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action="store_true", dest="count:all",
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default=False,
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help="Prints only the total count of sequence records (if a sequence has no `count` attribute, its default count is 1) (default: False).")
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def run(config):
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DMS.obi_atexit()
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logger("info", "obi count")
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# Open the input
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input = open_uri(config['obi']['inputURI'])
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if input is None:
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raise Exception("Could not read input")
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entries = input[1]
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count1 = len(entries)
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count2 = 0
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if COUNT_COLUMN in entries and ((config['count']['sequence'] == config['count']['all']) or (config['count']['all'])) :
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for e in entries:
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count2+=e[COUNT_COLUMN]
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if COUNT_COLUMN in entries and (config['count']['sequence'] == config['count']['all']):
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print(count1,count2)
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elif COUNT_COLUMN in entries and config['count']['all']:
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print(count2)
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else:
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print(count1)
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