def main():
parser = argparse.ArgumentParser( description='Checks the CDS features against a genome sequence to report/correct phase columns.')
## output file to be written
parser.add_argument('-i', '--input_file', type=str, required=True, help='Path to the input GFF3' )
parser.add_argument('-g', '--genome_fasta', type=str, required=False, help='Optional. You must specify this unless the FASTA sequences for the molecules are embedded in the GFF')
parser.add_argument('-p', '--print_n_with_stops', type=int, required=False, default=0, help='Optional. Pass the number of sequences with internal stops you want printed (usually for debugging purposes)' )
parser.add_argument('-o', '--output_fasta', type=str, required=False, help='Optional. Writes an output (translated) FASTA file for all those features which had internal stops')
args = parser.parse_args()
(assemblies, features) = biocodegff.get_gff3_features( args.input_file )
# deal with the FASTA file if the user passed one
if args.genome_fasta is not None:
biocodeutils.add_assembly_fasta(assemblies, args.genome_fasta)
total_mRNAs = 0
mRNAs_with_stops = 0
# If this is set to the ID of any particular mRNA feature, the CDS and translation will be printed for it.
debug_mRNA = None
fasta_out_fh = None
if args.output_fasta is not None:
fasta_out_fh = open(args.output_fasta, 'wt')
for assembly_id in assemblies:
for gene in assemblies[assembly_id].genes():
for mRNA in gene.mRNAs():
coding_seq = mRNA.get_CDS_residues()
total_mRNAs += 1
if debug_mRNA is not None and mRNA.id == debug_mRNA:
print("CDS:{0}".format(coding_seq))
if biocodeutils.translate(coding_seq).rstrip('*').count('*') > 0:
mRNAs_with_stops += 1
translated_seq = biocodeutils.translate(coding_seq)
if fasta_out_fh is not None:
loc = mRNA.location_on(assemblies[assembly_id])
fasta_out_fh.write(">{0} {1} {2}-{3} ({4})\n".format(mRNA.id, assembly_id, loc.fmin + 1, loc.fmax, loc.strand) )
fasta_out_fh.write("{0}\n".format(biocodeutils.wrapped_fasta(translated_seq)))
if debug_mRNA is not None and mRNA.id == debug_mRNA:
print("TRANSLATION WITH STOP ({1}): {0}".format(translated_seq, mRNA.id) )
if mRNAs_with_stops <= args.print_n_with_stops:
print("\nmRNA id: {0}".format(mRNA.id) )
print("\tCDS:{0}".format(coding_seq))
print("\tTRANSLATION WITH STOP ({1}): {0}".format(translated_seq, mRNA.id) )
print("\nTotal mRNAs found:{0}".format(total_mRNAs))
print("mRNAs with embedded stops: {0}".format(mRNAs_with_stops))
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='Removes gene models whose sequence has been masked.')
## output file to be written
parser.add_argument('-i', '--input_gff3', type=str, required=True, help='Path to the input GFF3' )
parser.add_argument('-m', '--masked_fasta', type=str, required=True, help='FASTA with sequence masked with N characters')
parser.add_argument('-p', '--percent_repeat_coverage_cutoff', type=int, required=True, help='Genes with an mRNA covered by this percentage of repeats will be excluded' )
parser.add_argument('-o', '--output_gff3', type=str, required=False, help='Path to GFF3 output file to be created')
parser.add_argument('-r', '--removed_gff3', type=str, required=False, help='If passed, writes the deleted genes to this file')
args = parser.parse_args()
(assemblies, features) = biocodegff.get_gff3_features( args.input_gff3 )
biocodeutils.add_assembly_fasta(assemblies, args.masked_fasta)
gff_out = open(args.output_gff3, 'wt')
gff_out.write("##gff-version 3\n")
rem_out = None
gene_count = 0
kept_count = 0
if args.removed_gff3 is not None:
rem_out = open(args.removed_gff3, 'wt')
rem_out.write("##gff-version 3\n")
for assembly_id in assemblies:
for gene in assemblies[assembly_id].genes():
keep = True
gene_count += 1
for mRNA in gene.mRNAs():
coding_seq = mRNA.get_CDS_residues()
n_count = coding_seq.count('N')
perc_repeat = (n_count / len(coding_seq)) * 100
if perc_repeat >= args.percent_repeat_coverage_cutoff:
keep = False
if keep == True:
kept_count += 1
gene.print_as(fh=gff_out, source='IGS', format='gff3')
else:
if rem_out is not None:
gene.print_as(fh=rem_out, source='IGS', format='gff3')
print("INFO: {0} genes kept out of {1} ({2:.1f}%)".format(kept_count, gene_count, ((kept_count/gene_count) * 100)))
def main():
parser = argparse.ArgumentParser(
description='Extracts the protein or CDS seqeunces from a GFF3 file')
## output file to be written
parser.add_argument('-i',
'--input_file',
type=str,
required=True,
help='Path to an input GFF3 file to be read')
parser.add_argument('-o',
'--output_file',
type=str,
required=False,
help='Path to an output FASTA file to be created')
parser.add_argument('-t',
'--type',
type=str,
required=False,
default='protein',
choices=['protein', 'cds'],
help='Type of features to export')
parser.add_argument(
'-f',
'--fasta',
type=str,
required=False,
help=
'If the FASTA entries for the underlying assemblies is absent from the GFF3 document passed, you will need to specify this option'
)
parser.add_argument('--check_ends', dest='check_ends', action='store_true')
parser.set_defaults(check_ends=False)
args = parser.parse_args()
## output will either be a file or STDOUT
fout = sys.stdout
if args.output_file is not None:
fout = open(args.output_file, 'wt')
(assemblies, features) = biocodegff.get_gff3_features(args.input_file)
# only doing the standard codon table for now
start_codons = ['ATG', 'GTG', 'TTG']
stop_codons = ['TAG', 'TAA', 'TGA']
## add sequence residues from external FASTA file if the user passed one
if args.fasta is not None:
biocodeutils.add_assembly_fasta(assemblies, args.fasta)
for assembly_id in assemblies:
for gene in assemblies[assembly_id].genes():
for mRNA in gene.mRNAs():
## initial values of id and header to export (can be overridden by available annotation)
export_id = mRNA.id
export_header = None
if mRNA.locus_tag is not None:
export_id = mRNA.locus_tag
## Add the gene product name if there is one
for polypeptide in mRNA.polypeptides():
if polypeptide.annotation is not None:
if polypeptide.annotation.product_name is not None:
export_header = polypeptide.annotation.product_name
break
fout.write(">{0}".format(export_id))
if export_header is not None:
fout.write(" {0}\n".format(export_header))
else:
fout.write("\n")
coding_seq = mRNA.get_CDS_residues()
if args.check_ends == True:
# check the starting codon
start_codon = coding_seq[0:3].upper()
if start_codon not in start_codons:
sys.stderr.write(
"WARN: Non-canonical start codon ({0}) in mRNA {1}\n"
.format(start_codon, mRNA.id))
stop_codon = coding_seq[-3:].upper()
if stop_codon not in stop_codons:
sys.stderr.write(
"WARN: Non-canonical stop codon ({0}) in mRNA {1}\n"
.format(stop_codon, mRNA.id))
if args.type == 'cds':
fout.write("{0}\n".format(
biocodeutils.wrapped_fasta(coding_seq)))
else:
translated_seq = biocodeutils.translate(coding_seq)
fout.write("{0}\n".format(
biocodeutils.wrapped_fasta(translated_seq)))
def main():
parser = argparse.ArgumentParser( description='Extracts the protein or CDS seqeunces from a GFF3 file')
## output file to be written
parser.add_argument('-i', '--input_file', type=str, required=True, help='Path to an input GFF3 file to be read' )
parser.add_argument('-o', '--output_file', type=str, required=False, help='Path to an output FASTA file to be created' )
parser.add_argument('-t', '--type', type=str, required=False, default='protein', choices=['protein', 'cds'], help='Type of features to export')
parser.add_argument('-f', '--fasta', type=str, required=False, help='If the FASTA entries for the underlying assemblies is absent from the GFF3 document passed, you will need to specify this option' )
parser.add_argument('--check_ends', dest='check_ends', action='store_true')
parser.set_defaults(check_ends=False)
args = parser.parse_args()
## output will either be a file or STDOUT
fout = sys.stdout
if args.output_file is not None:
fout = open(args.output_file, 'wt')
(assemblies, features) = biocodegff.get_gff3_features(args.input_file)
# only doing the standard codon table for now
start_codons = ['ATG', 'GTG', 'TTG']
stop_codons = ['TAG', 'TAA', 'TGA']
## add sequence residues from external FASTA file if the user passed one
if args.fasta is not None:
biocodeutils.add_assembly_fasta(assemblies, args.fasta)
for assembly_id in assemblies:
for gene in assemblies[assembly_id].genes():
for mRNA in gene.mRNAs():
## initial values of id and header to export (can be overridden by available annotation)
export_id = mRNA.id
export_header = None
if mRNA.locus_tag is not None:
export_id = mRNA.locus_tag
## Add the gene product name if there is one
for polypeptide in mRNA.polypeptides():
if polypeptide.annotation is not None:
if polypeptide.annotation.product_name is not None:
export_header = polypeptide.annotation.product_name
break
fout.write(">{0}".format(export_id))
if export_header is not None:
fout.write(" {0}\n".format(export_header))
else:
fout.write("\n")
coding_seq = mRNA.get_CDS_residues(for_translation=True)
if args.check_ends == True:
# check the starting codon
start_codon = coding_seq[0:3].upper()
if start_codon not in start_codons:
sys.stderr.write("WARN: Non-canonical start codon ({0}) in mRNA {1}\n".format(start_codon, mRNA.id))
stop_codon = coding_seq[-3:].upper()
if stop_codon not in stop_codons:
sys.stderr.write("WARN: Non-canonical stop codon ({0}) in mRNA {1}\n".format(stop_codon, mRNA.id))
if args.type == 'cds':
fout.write("{0}\n".format(biocodeutils.wrapped_fasta(coding_seq)))
else:
translated_seq = biocodeutils.translate(coding_seq)
fout.write("{0}\n".format(biocodeutils.wrapped_fasta(translated_seq)))
def main():
parser = argparse.ArgumentParser(
description=
'Checks the CDS features against a genome sequence to report/correct phase columns.'
)
## output file to be written
parser.add_argument('-i',
'--input_file',
type=str,
required=True,
help='Path to the input GFF3')
parser.add_argument(
'-g',
'--genome_fasta',
type=str,
required=False,
help=
'Optional. You must specify this unless the FASTA sequences for the molecules are embedded in the GFF'
)
parser.add_argument(
'-o',
'--output_gff',
type=str,
required=False,
help=
'Optional. Writes an output GFF3 file with CDS (and containing features) extended to nearest stop'
)
args = parser.parse_args()
(assemblies, features) = biocodegff.get_gff3_features(args.input_file)
# deal with the FASTA file if the user passed one
if args.genome_fasta is not None:
biocodeutils.add_assembly_fasta(assemblies, args.genome_fasta)
total_mRNAs = 0
mRNAs_with_terminal_stops = 0
stop_codons = ['TAG', 'TAA', 'TGA']
for assembly_id in assemblies:
print("Assembly {0} has length {1}".format(
assembly_id, assemblies[assembly_id].length))
for gene in assemblies[assembly_id].genes():
for mRNA in gene.mRNAs():
coding_seq = mRNA.get_CDS_residues()
total_mRNAs += 1
translation = biocodeutils.translate(coding_seq)
if translation.endswith('*'):
mRNAs_with_terminal_stops += 1
else:
print("gene:{1}, mRNA: {0} is missing a stop".format(
mRNA.id, gene.id))
mRNA_loc = mRNA.location_on(assemblies[assembly_id])
CDSs = sorted(mRNA.CDSs())
codon_step_size = 3
if mRNA_loc.strand == 1:
CDS_pos = CDSs[-1].location_on(
assemblies[assembly_id]).fmax
mRNA_limit = mRNA_loc.fmax
else:
CDS_pos = CDSs[0].location_on(
assemblies[assembly_id]).fmin
mRNA_limit = mRNA_loc.fmin
codon_step_size = -3
print("\tmRNA:{0}-{1}, CDS end: {2}\n\tExtending".format(
mRNA_loc.fmin, mRNA_loc.fmax, CDS_pos),
end='')
new_stop_found = False
# We have to step backwards to start if on the reverse strand
if codon_step_size < 0:
CDS_pos += codon_step_size
while True:
if (codon_step_size < 0 and CDS_pos < mRNA_limit) or (
codon_step_size > 0 and CDS_pos > mRNA_limit):
print(" Reached the mRNA limit")
break
else:
next_codon = assemblies[assembly_id].residues[
CDS_pos:CDS_pos + 3]
print(".{0}({1})".format(next_codon, CDS_pos),
end='')
if next_codon in stop_codons:
new_stop_found = True
print(" Found a stop")
break
CDS_pos += codon_step_size
if new_stop_found == True:
print("\tCDS_pos: UPDATE: {0}".format(CDS_pos))
else:
print("\tCDS_pos: SAME: {0}".format(CDS_pos))
print("\nTotal mRNAs found:{0}".format(total_mRNAs))
print("mRNAs with terminal stops: {0}".format(mRNAs_with_terminal_stops))
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))
def main():
parser = argparse.ArgumentParser(
description=
'Checks the CDS features against a genome sequence report non-terminal internal stops.'
)
## output file to be written
parser.add_argument('-i',
'--input_file',
type=str,
required=True,
help='Path to the input GFF3')
parser.add_argument(
'-g',
'--genome_fasta',
type=str,
required=False,
help=
'Optional. You must specify this unless the FASTA sequences for the molecules are embedded in the GFF'
)
parser.add_argument(
'-p',
'--print_n_with_stops',
type=int,
required=False,
default=0,
help=
'Optional. Pass the number of sequences with internal stops you want printed (usually for debugging purposes)'
)
parser.add_argument(
'-o',
'--output_fasta',
type=str,
required=False,
help=
'Optional. Writes an output (translated) FASTA file for all those features which had internal stops'
)
args = parser.parse_args()
(assemblies, features) = biocodegff.get_gff3_features(args.input_file)
# deal with the FASTA file if the user passed one
if args.genome_fasta is not None:
biocodeutils.add_assembly_fasta(assemblies, args.genome_fasta)
total_mRNAs = 0
mRNAs_with_stops = 0
# If this is set to the ID of any particular mRNA feature, the CDS and translation will be printed for it.
debug_mRNA = None
fasta_out_fh = None
if args.output_fasta is not None:
fasta_out_fh = open(args.output_fasta, 'wt')
for assembly_id in assemblies:
for gene in assemblies[assembly_id].genes():
for mRNA in gene.mRNAs():
coding_seq = mRNA.get_CDS_residues()
total_mRNAs += 1
if debug_mRNA is not None and mRNA.id == debug_mRNA:
print("CDS:{0}".format(coding_seq))
if biocodeutils.translate(coding_seq).rstrip('*').count(
'*') > 0:
mRNAs_with_stops += 1
translated_seq = biocodeutils.translate(coding_seq)
if fasta_out_fh is not None:
loc = mRNA.location_on(assemblies[assembly_id])
fasta_out_fh.write(">{0} {1} {2}-{3} ({4})\n".format(
mRNA.id, assembly_id, loc.fmin + 1, loc.fmax,
loc.strand))
fasta_out_fh.write("{0}\n".format(
biocodeutils.wrapped_fasta(translated_seq)))
if debug_mRNA is not None and mRNA.id == debug_mRNA:
print("TRANSLATION WITH STOP ({1}): {0}".format(
translated_seq, mRNA.id))
if mRNAs_with_stops <= args.print_n_with_stops:
print("\nmRNA id: {0}".format(mRNA.id))
print("\tCDS:{0}".format(coding_seq))
print("\tTRANSLATION WITH STOP ({1}): {0}".format(
translated_seq, mRNA.id))
print("\nTotal mRNAs found:{0}".format(total_mRNAs))
print("mRNAs with embedded stops: {0}".format(mRNAs_with_stops))
def main():
parser = argparse.ArgumentParser(
description='Removes gene models whose sequence has been masked.')
## output file to be written
parser.add_argument('-i',
'--input_gff3',
type=str,
required=True,
help='Path to the input GFF3')
parser.add_argument('-m',
'--masked_fasta',
type=str,
required=True,
help='FASTA with sequence masked with N characters')
parser.add_argument(
'-p',
'--percent_repeat_coverage_cutoff',
type=int,
required=True,
help=
'Genes with an mRNA covered by this percentage of repeats will be excluded'
)
parser.add_argument('-o',
'--output_gff3',
type=str,
required=False,
help='Path to GFF3 output file to be created')
parser.add_argument(
'-r',
'--removed_gff3',
type=str,
required=False,
help='If passed, writes the deleted genes to this file')
args = parser.parse_args()
(assemblies, features) = biocodegff.get_gff3_features(args.input_gff3)
biocodeutils.add_assembly_fasta(assemblies, args.masked_fasta)
gff_out = open(args.output_gff3, 'wt')
gff_out.write("##gff-version 3\n")
rem_out = None
gene_count = 0
kept_count = 0
if args.removed_gff3 is not None:
rem_out = open(args.removed_gff3, 'wt')
rem_out.write("##gff-version 3\n")
for assembly_id in assemblies:
for gene in assemblies[assembly_id].genes():
keep = True
gene_count += 1
for mRNA in gene.mRNAs():
coding_seq = mRNA.get_CDS_residues()
n_count = coding_seq.count('N')
perc_repeat = (n_count / len(coding_seq)) * 100
if perc_repeat >= args.percent_repeat_coverage_cutoff:
keep = False
if keep == True:
kept_count += 1
gene.print_as(fh=gff_out, source='IGS', format='gff3')
else:
if rem_out is not None:
gene.print_as(fh=rem_out, source='IGS', format='gff3')
print("INFO: {0} genes kept out of {1} ({2:.1f}%)".format(
kept_count, gene_count, ((kept_count / gene_count) * 100)))
