def main():
parser = argparse.ArgumentParser( description='Create a TBL file for submission to NCBI from GFF3')
## output file to be written
parser.add_argument('-i', '--input_file', type=str, required=True, help='Path to an input file to be read' )
parser.add_argument('-o', '--output_base', type=str, required=True, help='Base name of output files to be created' )
parser.add_argument('-ln', '--lab_name', type=str, required=True, help='Required by NCBI to identify the submitting group' )
parser.add_argument('-nap', '--ncbi_acc_prefix', type=str, required=True, help='Required and assigned by NCBI' )
parser.add_argument('-gf', '--genomic_fasta', type=str, required=False, help='FASTA file of genomic sequence, if not embedded in GFF' )
parser.add_argument('-go', '--go_obo', type=str, required=False, help='GO terms will not be exported unless you pass the path to a GO OBO file')
args = parser.parse_args()
(assemblies, features) = biocodegff.get_gff3_features( args.input_file )
if args.genomic_fasta is not None:
biocodeutils.add_assembly_fasta(assemblies, args.genomic_fasta)
new_assemblies = dict()
## We need to first check the ID format
reformat_IDs = True
## maps old IDs (like tp.assembly.567468735.1) to new ones (like AAGK01000001)
asm_id_map = dict()
asm_num = 1
for asm_id in assemblies:
# pre-formatted IDs are like this: gnl|WGS:XXXX|SeqID|gb|XXXX01xxxxxx
if asm_id.startswith('gnl|WGS:'):
reformat_IDs = False
break
else:
new_id = "gnl|WGS:{0}|SeqID|gb|{0}01{1:06d}".format(args.ncbi_acc_prefix, asm_num)
asm_id_map[asm_id] = new_id
asm_num += 1
new_assemblies[new_id] = assemblies[asm_id]
new_assemblies[new_id].id = new_id
if reformat_IDs == True:
assemblies = new_assemblies
# >gi|68352484|gb|AAGK01000001.1|
# AAGK01000001 NC_007344.1 tp.assembly.567468735.1
ofh = open("{0}.tbl".format(args.output_base), 'wt')
biocodetbl.print_tbl_from_assemblies(assemblies=assemblies, ofh=ofh, go_obo=args.go_obo, lab_name=args.lab_name)
mset = biothings.AssemblySet()
mset.load_from_dict(assemblies)
mset.write_fasta(path="{0}.fna".format(args.output_base))
def main():
parser = argparse.ArgumentParser( description='Put a description of your script here')
## output file to be written
parser.add_argument('-i', '--input_file', type=str, required=True, help='Path to an input file to be read' )
parser.add_argument('-o', '--output_file', type=str, required=True, help='Path to an output file to be created' )
parser.add_argument('-go', '--go_obo', type=str, required=False, help='GO terms will not be exported unless you pass the path to a GO OBO file')
parser.add_argument('-ln', '--lab_name', type=str, required=True, help='Required by NCBI to identify the submitting group' )
args = parser.parse_args()
(assemblies, features) = biocodegff.get_gff3_features( args.input_file )
ofh = open(args.output_file, 'wt')
biocodetbl.print_tbl_from_assemblies(assemblies=assemblies, ofh=ofh, go_obo=args.go_obo, lab_name=args.lab_name)
def main():
parser = argparse.ArgumentParser(
description='Create a TBL file for submission to NCBI from GFF3')
## output file to be written
parser.add_argument('-i',
'--input_file',
type=str,
required=True,
help='Path to an input file to be read')
parser.add_argument('-o',
'--output_base',
type=str,
required=True,
help='Base name of output files to be created')
parser.add_argument(
'-ln',
'--lab_name',
type=str,
required=True,
help='Required by NCBI to identify the submitting group')
parser.add_argument('-nap',
'--ncbi_acc_prefix',
type=str,
required=True,
help='Required and assigned by NCBI')
parser.add_argument(
'-gf',
'--genomic_fasta',
type=str,
required=False,
help='FASTA file of genomic sequence, if not embedded in GFF')
parser.add_argument(
'-go',
'--go_obo',
type=str,
required=False,
help=
'GO terms will not be exported unless you pass the path to a GO OBO file'
)
args = parser.parse_args()
(assemblies, features) = biocodegff.get_gff3_features(args.input_file)
if args.genomic_fasta is not None:
biocodeutils.add_assembly_fasta(assemblies, args.genomic_fasta)
new_assemblies = dict()
## We need to first check the ID format
reformat_IDs = True
## maps old IDs (like tp.assembly.567468735.1) to new ones (like AAGK01000001)
asm_id_map = dict()
asm_num = 1
for asm_id in assemblies:
# pre-formatted IDs are like this: gnl|WGS:XXXX|SeqID|gb|XXXX01xxxxxx
if asm_id.startswith('gnl|WGS:'):
reformat_IDs = False
break
else:
new_id = "gnl|WGS:{0}|SeqID|gb|{0}01{1:06d}".format(
args.ncbi_acc_prefix, asm_num)
asm_id_map[asm_id] = new_id
asm_num += 1
new_assemblies[new_id] = assemblies[asm_id]
new_assemblies[new_id].id = new_id
if reformat_IDs == True:
assemblies = new_assemblies
ofh = open("{0}.tbl".format(args.output_base), 'wt')
biocodetbl.print_tbl_from_assemblies(assemblies=assemblies,
ofh=ofh,
go_obo=args.go_obo,
lab_name=args.lab_name)
mset = biothings.AssemblySet()
mset.load_from_dict(assemblies)
mset.write_fasta(path="{0}.fna".format(args.output_base))