def main():
parser = argparse.ArgumentParser( description='Filters trinity output for longest subcomponents based on naming convention')
## output file to be written
parser.add_argument('-i', '--input', type=str, required=True, help='Path to an input FASTA file' )
parser.add_argument('-o', '--output', type=str, required=False, help='Output file to be created. Default = STDOUT' )
args = parser.parse_args()
## output will either be a file or STDOUT
fout = sys.stdout
if args.output is not None:
fout = open(args.output, 'wt')
seqs = utils.fasta_dict_from_file(args.input)
components = dict()
for seq_id in seqs:
m = re.search("(comp\d+)_", seq_id)
if m:
component_id = m.group(1)
if component_id not in components or len(seqs[seq_id]['s']) > len(components[component_id]['s']):
components[component_id] = seqs[seq_id]
components[component_id]['longest_id'] = seq_id
else:
raise Exception("ERROR: This ID wasn't in the expected format of compN_cN_seqN: {0}".format(seq_id))
for c_id in components:
seq_wrapped = utils.wrapped_fasta(components[c_id]['s'], every=60)
fout.write(">{0} {1}\n{2}\n".format(components[c_id]['longest_id'], components[c_id]['h'], seq_wrapped))
def main():
parser = argparse.ArgumentParser(
description=
'Filters trinity output for longest subcomponents based on naming convention'
)
## output file to be written
parser.add_argument('-i',
'--input',
type=str,
required=True,
help='Path to an input FASTA file')
parser.add_argument('-o',
'--output',
type=str,
required=False,
help='Output file to be created. Default = STDOUT')
args = parser.parse_args()
## output will either be a file or STDOUT
fout = sys.stdout
if args.output is not None:
fout = open(args.output, 'wt')
seqs = utils.fasta_dict_from_file(args.input)
components = dict()
for seq_id in seqs:
m = re.search("(comp\d+)_", seq_id)
if m:
component_id = m.group(1)
if component_id not in components or len(seqs[seq_id]['s']) > len(
components[component_id]['s']):
components[component_id] = seqs[seq_id]
components[component_id]['longest_id'] = seq_id
else:
raise Exception(
"ERROR: This ID wasn't in the expected format of compN_cN_seqN: {0}"
.format(seq_id))
for c_id in components:
seq_wrapped = utils.wrapped_fasta(components[c_id]['s'], every=60)
fout.write(">{0} {1}\n{2}\n".format(components[c_id]['longest_id'],
components[c_id]['h'],
seq_wrapped))
def initialize_polypeptides( log_fh, fasta_file ):
'''
Reads a FASTA file of (presumably) polypeptide sequences and creates a dict of Polypeptide
objects, keyed by ID, with bioannotation.FunctionalAnnotation objects attached.
'''
seqs = utils.fasta_dict_from_file(fasta_file)
polypeptides = dict()
for seq_id in seqs:
polypeptide = things.Polypeptide(id=seq_id, length=len(seqs[seq_id]['s']), residues=seqs[seq_id]['s'])
annotation = annotation.FunctionalAnnotation(product_name=DEFAULT_PRODUCT_NAME)
log_fh.write("INFO: {0}: Set initial product name to '{1}'\n".format(seq_id, DEFAULT_PRODUCT_NAME))
polypeptide.annotation = annotation
polypeptides[seq_id] = polypeptide
return polypeptides
def initialize_polypeptides(log_fh, fasta_file):
'''
Reads a FASTA file of (presumably) polypeptide sequences and creates a dict of Polypeptide
objects, keyed by ID, with bioannotation.FunctionalAnnotation objects attached.
'''
seqs = utils.fasta_dict_from_file(fasta_file)
polypeptides = dict()
for seq_id in seqs:
polypeptide = things.Polypeptide(id=seq_id,
length=len(seqs[seq_id]['s']),
residues=seqs[seq_id]['s'])
annotation = annotation.FunctionalAnnotation(
product_name=DEFAULT_PRODUCT_NAME)
log_fh.write("INFO: {0}: Set initial product name to '{1}'\n".format(
seq_id, DEFAULT_PRODUCT_NAME))
polypeptide.annotation = annotation
polypeptides[seq_id] = polypeptide
return polypeptides
