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#!/usr/bin/python3
'''
:py:mod:`obicount`: counts the number of sequence records
=========================================================
.. codeauthor:: Eric Coissac <eric.coissac@metabarcoding.org>
:py:mod:`obicount` counts the number of sequence records and/or the sum of the ``count`` attributes.
*Example:*
.. code-block:: bash
> obicount seq.fasta
Prints the number of sequence records contained in the ``seq.fasta``
file and the sum of their ``count`` attributes.
'''
from obitools.options import getOptionManager
from obitools.format.options import addInputFormatOption
def addCountOptions(optionManager):
group=optionManager.add_option_group('Obicount specific options')
group.add_option('-s','--sequence',
action="store_true", dest="sequence",
default=False,
help="Prints only the number of sequence records."
)
group.add_option('-a','--all',
action="store_true", dest="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)."
)
if __name__ == '__main__':
optionParser = getOptionManager([addCountOptions,addInputFormatOption], progdoc=__doc__)
(options, entries) = optionParser()
count1=0
count2=0
for s in entries:
count1+=1
if 'count' in s:
count2+=s['count']
else:
count2+=1
if options.all==options.sequence:
print(count1,count2)
elif options.all:
print(count2)
else:
print(count1)
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