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#===========================================================================
#
# PUBLIC DOMAIN NOTICE
# National Center for Biotechnology Information
#
# This software/database is a "United States Government Work" under the
# terms of the United States Copyright Act. It was written as part of
# the author's official duties as a United States Government employee and
# thus cannot be copyrighted. This software/database is freely available
# to the public for use. The National Library of Medicine and the U.S.
# Government have not placed any restriction on its use or reproduction.
#
# Although all reasonable efforts have been taken to ensure the accuracy
# and reliability of the software and data, the NLM and the U.S.
# Government do not and cannot warrant the performance or results that
# may be obtained by using this software or data. The NLM and the U.S.
# Government disclaim all warranties, express or implied, including
# warranties of performance, merchantability or fitness for any particular
# purpose.
#
# Please cite the author in any work or product based on this material.
#
#===========================================================================
#
import sys
import traceback
from ngs import NGS
from ngs.ErrorMsg import ErrorMsg
from ngs.ReadCollection import ReadCollection
from ngs.Reference import Reference
from ngs.ReferenceIterator import ReferenceIterator
def run(acc):
# open requested accession using SRA implementation of the API
with NGS.openReadCollection(acc) as run:
run_name = run.getName()
# get requested reference
with run.getReferences() as it:
i = 0
while it.nextReference():
print ("{}\t{}\t{}\t{}".format(it.getCommonName(),
it.getCanonicalName(),
it.getLength(),
"circular" if it.getIsCircular() else "linear",
))
print ("Read {} references for {}".format(i, run_name))
if len(sys.argv) != 2:
print ("Usage: RefTest accession\n")
exit(1)
else:
try:
run(sys.argv[1])
except ErrorMsg as x:
print (x)
traceback.print_exc()
# x.printStackTrace - not implemented
exit(1)
except BaseException as x:
traceback.print_exc()
exit(1)
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