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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.Alignment import Alignment
from ngs.AlignmentIterator import AlignmentIterator
def run(acc, splitNum, splitNo): # this function doesn't release NGS objects however it might
# open requested accession using SRA implementation of the API
run = NGS.openReadCollection(acc)
run_name = run.getName()
# compute window to iterate through
MAX_ROW = run.getAlignmentCount()
chunk = MAX_ROW / splitNum
first = int(round(chunk * (splitNo-1)))
next_first = int(round(chunk * (splitNo)))
if next_first > MAX_ROW:
next_first = MAX_ROW
# start iterator on reads
it = run.getAlignmentRange(first+1, next_first-first, Alignment.primaryAlignment)
i = 0
while it.nextAlignment():
print (
it.getReadId() + "\t" +
it.getReferenceSpec() + "\t" +
str(it.getAlignmentPosition()) + "\t" +
it.getShortCigar(False) + "\t" +
it.getFragmentBases() + "\t" +
("aligned" if it.isAligned() else "unaligned")
)
i += 1
print ("Read {} alignments for {}".format(i, run_name))
if len(sys.argv) != 4:
print ("Usage: FragTest accession NumChunks ChunkNo\n")
exit(1)
else:
try:
run(sys.argv[1], int(sys.argv[2]), int(sys.argv[3]))
except ErrorMsg, x:
print (x)
traceback.print_exc()
# x.printStackTrace - not implemented
exit(1)
except BaseException, x:
traceback.print_exc()
exit(1)
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