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 write_fasta_results(f, polypeptides):
"""
Produces headers like:
>ID PRODUCT_NAME gene::GENE_SYMBOL ec::EC_NUMBERS go::GO_TERMS
Example:
"""
for polypeptide_id in polypeptides:
polypeptide = polypeptides[polypeptide_id]
go_string = ""
ec_string = ""
for go_annot in polypeptide.annotation.go_annotations:
go_string += "GO:{0},".format(go_annot.go_id)
go_string = go_string.rstrip(',')
for ec_annot in polypeptide.annotation.ec_numbers:
ec_string += "{0},".format(ec_annot.number)
ec_string = ec_string.rstrip(',')
header = "{0} {1}".format(polypeptide_id,
polypeptide.annotation.product_name)
if polypeptide.annotation.gene_symbol is not None:
header = "{0} gene::{1}".format(header,
polypeptide.annotation.gene_symbol)
if ec_string != "":
header = "{0} ec::{1}".format(header, ec_string)
if go_string != "":
header = "{0} go::{1}".format(header, go_string)
f.write(">{0}\n".format(header))
f.write("{0}\n".format(utils.wrapped_fasta(polypeptide.residues)))
def write_fasta_results( f, polypeptides ):
"""
Produces headers like:
>ID PRODUCT_NAME gene::GENE_SYMBOL ec::EC_NUMBERS go::GO_TERMS
Example:
"""
for polypeptide_id in polypeptides:
polypeptide = polypeptides[polypeptide_id]
go_string = ""
ec_string = ""
for go_annot in polypeptide.annotation.go_annotations:
go_string += "GO:{0},".format(go_annot.go_id)
go_string = go_string.rstrip(',')
for ec_annot in polypeptide.annotation.ec_numbers:
ec_string += "{0},".format(ec_annot.number)
ec_string = ec_string.rstrip(',')
header = "{0} {1}".format(polypeptide_id, polypeptide.annotation.product_name)
if polypeptide.annotation.gene_symbol is not None:
header = "{0} gene::{1}".format(header, polypeptide.annotation.gene_symbol)
if ec_string != "":
header = "{0} ec::{1}".format(header, ec_string)
if go_string != "":
header = "{0} go::{1}".format(header, go_string)
f.write( ">{0}\n".format( header ) )
f.write( "{0}\n".format(utils.wrapped_fasta(polypeptide.residues)))
