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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
def process(ref):
length = ref.getLength()
line = 0
print( ">" + ref.getCanonicalName() )
try:
offset = 0
while offset < length:
chunk = ref.getReferenceChunk ( offset, 5000 )
chunk_len = len (chunk)
chunk_idx = 0
while chunk_idx < chunk_len:
endIndex = chunk_idx + 70 - line
if endIndex > chunk_len:
endIndex = chunk_len
chunk_line = chunk [ chunk_idx : endIndex ]
line = line + len (chunk_line)
chunk_idx = chunk_idx + len (chunk_line)
sys.stdout.write( chunk_line )
if line >= 70:
print("")
line = 0
offset = offset + 5000
except ErrorMsg as x:
pass
def run(acc, refName=None):
# open requested accession using SRA implementation of the API
with NGS.openReadCollection(acc) as run:
if refName:
with run.getReference(refName) as ref:
process(ref)
else:
with run.getReferences() as refs:
while refs.nextReference():
process(refs)
print("")
if len(sys.argv) < 2 or len(sys.argv) > 3:
print ("Usage: DumpReferenceFASTA accession [ reference ]\n")
exit(1)
else:
try:
acc = sys.argv[1]
refName = sys.argv[2] if len(sys.argv) == 3 else None
run ( acc, refName )
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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