elif (fea.type == 'gene') or (fea.id in ('p6', 'IN', 'gp41')):
assert prot[-1] == '*'
assert '*' not in prot[:-1]
else:
assert '*' not in prot
print 'Compare to old sequence'
for fea in seqnew.features:
if fea.id not in map(attrgetter('id'), seqold.features):
continue
feaold = seqold.features[map(attrgetter('id'), seqold.features).index(fea.id)]
feaseq = fea.extract(seqnew)
feaoldseq = feaold.extract(seqold)
# NOTE: add an if check here in case of misannotations
assert ''.join(feaseq) == ''.join(feaoldseq)
print 'Importing additional features from old sequence'
for fea in seqold.features:
if fea.id not in map(attrgetter('id'), seqnew.features):
seqnew.features.append(fea)
print 'Added feature:', fea.id
print 'Storing new annotated HXB2 sequence'
save_custom_reference(seqnew, 'HXB2', 'gb')
assert prot[-1] == '*'
assert prot[:-1].count('*') == 1
elif (fea.type == 'gene') or (fea.id in ('p6', 'IN', 'gp41')):
assert prot[-1] == '*'
assert '*' not in prot[:-1]
else:
assert '*' not in prot
print 'Compare to old sequence'
for fea in seqnew.features:
if fea.id not in map(attrgetter('id'), seqold.features):
continue
feaold = seqold.features[map(attrgetter('id'),
seqold.features).index(fea.id)]
feaseq = fea.extract(seqnew)
feaoldseq = feaold.extract(seqold)
# NOTE: add an if check here in case of misannotations
assert ''.join(feaseq) == ''.join(feaoldseq)
print 'Importing additional features from old sequence'
for fea in seqold.features:
if fea.id not in map(attrgetter('id'), seqnew.features):
seqnew.features.append(fea)
print 'Added feature:', fea.id
print 'Storing new annotated HXB2 sequence'
save_custom_reference(seqnew, 'HXB2', 'gb')
elif 1.0 * L2 / L1 > 1.1:
raise ValueError('Feature: '+fea.id+' is too long: '+s)
ref.features.append(feature)
return ref
# Script
if __name__ == '__main__':
parser = argparse.ArgumentParser(description='Annotate like HXB2',
formatter_class=argparse.ArgumentDefaultsHelpFormatter)
parser.add_argument('--refname', required=True,
help='Name of reference to annotate')
parser.add_argument('--verbose', type=int, default=2,
help='Verbosity level [0-3]')
parser.add_argument('--save', action='store_true',
help='Save annotated sequence to file')
args = parser.parse_args()
refname = args.refname
VERBOSE = args.verbose
save = args.save
ref = annotate_like_HXB2(refname, VERBOSE=VERBOSE)
if save:
save_custom_reference(ref, refname, format='gb')
return ref
# Script
if __name__ == '__main__':
parser = argparse.ArgumentParser(
description='Annotate like HXB2',
formatter_class=argparse.ArgumentDefaultsHelpFormatter)
parser.add_argument('--refname',
required=True,
help='Name of reference to annotate')
parser.add_argument('--verbose',
type=int,
default=2,
help='Verbosity level [0-3]')
parser.add_argument('--save',
action='store_true',
help='Save annotated sequence to file')
args = parser.parse_args()
refname = args.refname
VERBOSE = args.verbose
save = args.save
ref = annotate_like_HXB2(refname, VERBOSE=VERBOSE)
if save:
save_custom_reference(ref, refname, format='gb')
