def main():
parser = argparse.ArgumentParser( description='Script for reporting of possible polycistronic genes transcripts based on a reference annotation and RNA-seq transcript assemblies')
## output file to be written
parser.add_argument('-r', '--reference_file', type=str, required=True, help='GFF3 file of a reference annotation' )
parser.add_argument('-q', '--query_file', type=str, required=True, help='GFF3 file with alternative annotation (such as an RNA-seq assemby)' )
parser.add_argument('-o', '--output_file', type=str, required=True, help='Path to an output file to be created' )
args = parser.parse_args()
(ref_assemblies, ref_feats) = gff.get_gff3_features(args.reference_file)
(qry_assemblies, qry_genes) = gff.get_gff3_features(args.query_file)
for assembly_id in ref_assemblies:
# we expect to find this assembly ID in the qry set too
if assembly_id not in qry_assemblies:
print("WARN: expected to find assembly_id {0} in both reference and query sets".format(assembly_id))
continue
for ref_gene in ref_assemblies[assembly_id].genes():
overlaps = list()
polypeptides = ref_gene.polypeptides()
if len(polypeptides) == 0:
print("WARN: skipped gene {0} because it has no polypeptides".format(ref_gene.id))
continue
ref_annot = ref_gene.polypeptides()[0].annotation
for qry_gene in qry_assemblies[assembly_id].genes():
overlap = ref_gene.overlaps_with(qry_gene)
if overlap:
#print("DEBUG: {0} and {1} appear to overlap".format(ref_gene.id, qry_gene.id) )
overlaps.append(overlap)
# add a dbxref to the gene
ref_annot.add_dbxref("overlaps_old_locusTagID:{0}".format(qry_gene.id))
if len(overlaps) > 0:
print("INFO: ref_gene {0} had {1} overlaps".format(ref_gene.id, len(overlaps)))
gff.print_gff3_from_assemblies(assemblies=ref_assemblies, ofh=open(args.output_file, 'w'))
def main():
parser = argparse.ArgumentParser( description='Creates a single GFF from the output of a few different model prediction tools (coding and non-coding)')
## output file to be written
parser.add_argument('-m', '--model_gff', type=str, required=True, help='Input (pass-through) GFF file' )
parser.add_argument('-o', '--output_gff', type=str, required=False, help='Output file to be written. Default=STDOUT' )
parser.add_argument('-b', '--barrnap_gff', type=str, required=False, help='GFF file from Barrnap prediction' )
parser.add_argument('-g', '--genomic_fasta', type=str, required=True, help='Source genomic FASTA file' )
parser.add_argument('-a', '--aragorn_out', type=str, required=False, help='Raw output file (with -w) from ARAGORN prediction' )
args = parser.parse_args()
(assemblies, features) = gff.get_gff3_features(args.model_gff)
utils.add_assembly_fasta(assemblies, args.genomic_fasta)
if args.barrnap_gff:
add_barrnap_features(assemblies, features, args.barrnap_gff)
if args.aragorn_out:
add_aragorn_features(assemblies, features, args.aragorn_out)
with open(args.output_gff, 'wt') as f:
gff.print_gff3_from_assemblies(ofh=f, assemblies=assemblies)
def main():
parser = argparse.ArgumentParser( description='Extends GFF gene models to the first in-frame stop')
## 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')
parser.add_argument('-el', '--extension_limit', type=int, required=False, default=100, help='Optional. Limits how far an extension will happen looking for an in-frame stop codon')
args = parser.parse_args()
(assemblies, features) = gff.get_gff3_features(args.input_file)
# deal with the FASTA file if the user passed one
if args.genome_fasta is not None:
utils.add_assembly_fasta(assemblies, args.genome_fasta)
total_mRNAs = 0
mRNAs_with_terminal_stops = 0
stop_codons = ['TAG', 'TAA', 'TGA']
mRNAs_corrected = 0
for assembly_id in sorted(assemblies):
print("Assembly {0} has length {1}".format(assembly_id, assemblies[assembly_id].length))
for gene in sorted(assemblies[assembly_id].genes()):
for mRNA in gene.mRNAs():
coding_seq = mRNA.get_CDS_residues()
total_mRNAs += 1
translation = utils.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))
print("\tCDS: {0}".format(coding_seq))
print("\tcoding sequence ends with {0}, last three a.a.: {1}".format(coding_seq[-3:], translation[-3:]))
mRNA_loc = mRNA.location_on(assemblies[assembly_id])
CDSs = sorted(mRNA.CDSs())
CDS_frame_overhang = len(coding_seq) % 3
print("\tCDS frame overhang: {0}".format(CDS_frame_overhang))
codon_step_size = 3
if mRNA_loc.strand == 1:
# get the in-frame end coordinate of the last CDS position
CDS_pos = CDSs[-1].location_on(assemblies[assembly_id]).fmax - CDS_frame_overhang
mRNA_limit = mRNA_loc.fmax + args.extension_limit
else:
# get the in-frame end coordinate of the last CDS position
CDS_pos = CDSs[0].location_on(assemblies[assembly_id]).fmin + CDS_frame_overhang
mRNA_limit = mRNA_loc.fmin - args.extension_limit
codon_step_size = -3
print("\tmRNA:{0}-{1} ({3}), CDS end: {2}. Extending ... \n\t".format(mRNA_loc.fmin, mRNA_loc.fmax, CDS_pos, mRNA_loc.strand), end='')
new_stop_found = False
# We have to step backwards to start if on the reverse strand
CDS_pos += codon_step_size
while True:
if (mRNA_loc.strand == 1 and CDS_pos > mRNA_limit) or (mRNA_loc.strand == -1 and CDS_pos < mRNA_limit):
print(" Reached the mRNA limit")
break
elif CDS_pos < 1:
print(" Reached beginning of the molecule")
break
else:
next_codon = assemblies[assembly_id].residues[CDS_pos:CDS_pos + 3]
if mRNA_loc.strand == -1:
next_codon = utils.reverse_complement(next_codon)
print(".{0}({1}-{2})".format(next_codon, CDS_pos, CDS_pos - 3), end='')
else:
print(".{0}({1}-{2})".format(next_codon, CDS_pos - 3, CDS_pos), end='')
if next_codon in stop_codons:
if mRNA_loc.strand == 1:
mRNA.extend_stop(on=assemblies[assembly_id], to=(CDS_pos + 3))
print(" Found a stop, extending to: {0} ({1})".format(CDS_pos + 3, mRNA_loc.strand))
else:
mRNA.extend_stop(on=assemblies[assembly_id], to=CDS_pos)
print(" Found a stop, extending to: {0} ({1})".format(CDS_pos, mRNA_loc.strand))
new_stop_found = True
break
CDS_pos += codon_step_size
if new_stop_found == True:
print("\tCDS_pos: UPDATE: {0}".format(CDS_pos))
mRNAs_corrected += 1
else:
print("\tCDS_pos: SAME: {0}".format(CDS_pos))
print("\nTotal mRNAs found:{0}".format(total_mRNAs))
print("mRNAs initially with terminal stops: {0}".format(mRNAs_with_terminal_stops))
print("mRNAs successfully extended: {0}".format(mRNAs_corrected))
ofh = open(args.output_gff, 'wt')
gff.print_gff3_from_assemblies(assemblies=assemblies, ofh=ofh)
def main():
parser = argparse.ArgumentParser(
description=
'Script for reporting of possible polycistronic genes transcripts based on a reference annotation and RNA-seq transcript assemblies'
)
## output file to be written
parser.add_argument('-r',
'--reference_file',
type=str,
required=True,
help='GFF3 file of a reference annotation')
parser.add_argument(
'-q',
'--query_file',
type=str,
required=True,
help=
'GFF3 file with alternative annotation (such as an RNA-seq assemby)')
parser.add_argument('-o',
'--output_file',
type=str,
required=True,
help='Path to an output file to be created')
args = parser.parse_args()
(ref_assemblies, ref_feats) = gff.get_gff3_features(args.reference_file)
(qry_assemblies, qry_genes) = gff.get_gff3_features(args.query_file)
for assembly_id in ref_assemblies:
# we expect to find this assembly ID in the qry set too
if assembly_id not in qry_assemblies:
print(
"WARN: expected to find assembly_id {0} in both reference and query sets"
.format(assembly_id))
continue
for ref_gene in ref_assemblies[assembly_id].genes():
overlaps = list()
polypeptides = ref_gene.polypeptides()
if len(polypeptides) == 0:
print("WARN: skipped gene {0} because it has no polypeptides".
format(ref_gene.id))
continue
ref_annot = ref_gene.polypeptides()[0].annotation
for qry_gene in qry_assemblies[assembly_id].genes():
overlap = ref_gene.overlaps_with(qry_gene)
if overlap:
#print("DEBUG: {0} and {1} appear to overlap".format(ref_gene.id, qry_gene.id) )
overlaps.append(overlap)
# add a dbxref to the gene
ref_annot.add_dbxref("overlaps_old_locusTagID:{0}".format(
qry_gene.id))
if len(overlaps) > 0:
print("INFO: ref_gene {0} had {1} overlaps".format(
ref_gene.id, len(overlaps)))
gff.print_gff3_from_assemblies(assemblies=ref_assemblies,
ofh=open(args.output_file, 'w'))
def main():
parser = argparse.ArgumentParser(
description='Extends GFF gene models to the first in-frame stop')
## 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'
)
parser.add_argument(
'-el',
'--extension_limit',
type=int,
required=False,
default=100,
help=
'Optional. Limits how far an extension will happen looking for an in-frame stop codon'
)
args = parser.parse_args()
(assemblies, features) = gff.get_gff3_features(args.input_file)
# deal with the FASTA file if the user passed one
if args.genome_fasta is not None:
utils.add_assembly_fasta(assemblies, args.genome_fasta)
total_mRNAs = 0
mRNAs_with_terminal_stops = 0
stop_codons = ['TAG', 'TAA', 'TGA']
mRNAs_corrected = 0
for assembly_id in sorted(assemblies):
print("Assembly {0} has length {1}".format(
assembly_id, assemblies[assembly_id].length))
for gene in sorted(assemblies[assembly_id].genes()):
for mRNA in gene.mRNAs():
coding_seq = mRNA.get_CDS_residues()
total_mRNAs += 1
translation = utils.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))
print("\tCDS: {0}".format(coding_seq))
print(
"\tcoding sequence ends with {0}, last three a.a.: {1}"
.format(coding_seq[-3:], translation[-3:]))
mRNA_loc = mRNA.location_on(assemblies[assembly_id])
CDSs = sorted(mRNA.CDSs())
CDS_frame_overhang = len(coding_seq) % 3
print(
"\tCDS frame overhang: {0}".format(CDS_frame_overhang))
codon_step_size = 3
if mRNA_loc.strand == 1:
# get the in-frame end coordinate of the last CDS position
CDS_pos = CDSs[-1].location_on(
assemblies[assembly_id]).fmax - CDS_frame_overhang
mRNA_limit = mRNA_loc.fmax + args.extension_limit
else:
# get the in-frame end coordinate of the last CDS position
CDS_pos = CDSs[0].location_on(
assemblies[assembly_id]).fmin + CDS_frame_overhang
mRNA_limit = mRNA_loc.fmin - args.extension_limit
codon_step_size = -3
print(
"\tmRNA:{0}-{1} ({3}), CDS end: {2}. Extending ... \n\t"
.format(mRNA_loc.fmin, mRNA_loc.fmax, CDS_pos,
mRNA_loc.strand),
end='')
new_stop_found = False
# We have to step backwards to start if on the reverse strand
CDS_pos += codon_step_size
while True:
if (mRNA_loc.strand == 1 and CDS_pos > mRNA_limit) or (
mRNA_loc.strand == -1
and CDS_pos < mRNA_limit):
print(" Reached the mRNA limit")
break
elif CDS_pos < 1:
print(" Reached beginning of the molecule")
break
else:
next_codon = assemblies[assembly_id].residues[
CDS_pos:CDS_pos + 3]
if mRNA_loc.strand == -1:
next_codon = utils.reverse_complement(
next_codon)
print(".{0}({1}-{2})".format(
next_codon, CDS_pos, CDS_pos - 3),
end='')
else:
print(".{0}({1}-{2})".format(
next_codon, CDS_pos - 3, CDS_pos),
end='')
if next_codon in stop_codons:
if mRNA_loc.strand == 1:
mRNA.extend_stop(
on=assemblies[assembly_id],
to=(CDS_pos + 3))
print(
" Found a stop, extending to: {0} ({1})"
.format(CDS_pos + 3, mRNA_loc.strand))
else:
mRNA.extend_stop(
on=assemblies[assembly_id], to=CDS_pos)
print(
" Found a stop, extending to: {0} ({1})"
.format(CDS_pos, mRNA_loc.strand))
new_stop_found = True
break
CDS_pos += codon_step_size
if new_stop_found == True:
print("\tCDS_pos: UPDATE: {0}".format(CDS_pos))
mRNAs_corrected += 1
else:
print("\tCDS_pos: SAME: {0}".format(CDS_pos))
print("\nTotal mRNAs found:{0}".format(total_mRNAs))
print("mRNAs initially with terminal stops: {0}".format(
mRNAs_with_terminal_stops))
print("mRNAs successfully extended: {0}".format(mRNAs_corrected))
ofh = open(args.output_gff, 'wt')
gff.print_gff3_from_assemblies(assemblies=assemblies, ofh=ofh)
def main():
parser = argparse.ArgumentParser(
description='Extends GFF gene models to the first in-frame stop')
## 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) = gff.get_gff3_features(args.input_file)
# deal with the FASTA file if the user passed one
if args.genome_fasta is not None:
utils.add_assembly_fasta(assemblies, args.genome_fasta)
start_codons = ['ATG', 'GTG', 'TTG']
stop_codons = ['TAG', 'TAA', 'TGA']
newly_marked_5prime_partial = 0
newly_marked_3prime_partial = 0
for assembly_id in sorted(assemblies):
for gene in sorted(assemblies[assembly_id].genes()):
gene_loc = gene.location_on(assemblies[assembly_id])
for mRNA in gene.mRNAs():
mRNA_loc = mRNA.location_on(assemblies[assembly_id])
coding_seq = mRNA.get_CDS_residues()
translation = utils.translate(coding_seq)
if not translation.endswith('*'):
newly_marked_3prime_partial += 1
CDSs = sorted(mRNA.CDSs())
if mRNA_loc.strand == 1:
mRNA_loc.fmax_partial = True
CDSs[-1].location_on(
assemblies[assembly_id]).fmax_partial = True
gene_loc.fmax_partial = True
# The exon is tricky, as there's no direct link between the CDS fragment
# and the corresponding exon. The assumption here is that there won't
# be terminal non-coding exons if the CDS is partial.
mRNA.exons()[-1].location_on(
assemblies[assembly_id]).fmax_partial = True
else:
mRNA_loc.fmin_partial = True
gene_loc.fmin_partial = True
CDSs[0].location_on(
assemblies[assembly_id]).fmin_partial = True
mRNA.exons()[0].location_on(
assemblies[assembly_id]).fmin_partial = True
start_codon = coding_seq[0:3].upper().replace('U', 'T')
if start_codon not in start_codons:
newly_marked_5prime_partial += 1
CDSs = sorted(mRNA.CDSs())
if mRNA_loc.strand == 1:
mRNA_loc.fmin_partial = True
CDSs[0].location_on(
assemblies[assembly_id]).fmin_partial = True
gene_loc.fmin_partial = True
# The exon is tricky, as there's no direct link between the CDS fragment
# and the corresponding exon. The assumption here is that there won't
# be terminal non-coding exons if the CDS is partial.
mRNA.exons()[0].location_on(
assemblies[assembly_id]).fmin_partial = True
else:
mRNA_loc.fmax_partial = True
gene_loc.fmax_partial = True
CDSs[-1].location_on(
assemblies[assembly_id]).fmax_partial = True
mRNA.exons()[-1].location_on(
assemblies[assembly_id]).fmax_partial = True
print(
"Genes marked as 5' partial: {0}".format(newly_marked_5prime_partial))
print(
"Genes marked as 3' partial: {0}".format(newly_marked_3prime_partial))
ofh = open(args.output_gff, 'wt')
gff.print_gff3_from_assemblies(assemblies=assemblies, ofh=ofh)
def main():
parser = argparse.ArgumentParser( description='Extends GFF gene models to the first in-frame stop')
## 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) = gff.get_gff3_features(args.input_file)
# deal with the FASTA file if the user passed one
if args.genome_fasta is not None:
utils.add_assembly_fasta(assemblies, args.genome_fasta)
start_codons = ['ATG', 'GTG', 'TTG']
stop_codons = ['TAG', 'TAA', 'TGA']
newly_marked_5prime_partial = 0
newly_marked_3prime_partial = 0
for assembly_id in sorted(assemblies):
for gene in sorted(assemblies[assembly_id].genes()):
gene_loc = gene.location_on(assemblies[assembly_id])
for mRNA in gene.mRNAs():
mRNA_loc = mRNA.location_on(assemblies[assembly_id])
coding_seq = mRNA.get_CDS_residues()
translation = utils.translate(coding_seq)
if not translation.endswith('*'):
newly_marked_3prime_partial += 1
CDSs = sorted(mRNA.CDSs())
if mRNA_loc.strand == 1:
mRNA_loc.fmax_partial = True
CDSs[-1].location_on(assemblies[assembly_id]).fmax_partial = True
gene_loc.fmax_partial = True
# The exon is tricky, as there's no direct link between the CDS fragment
# and the corresponding exon. The assumption here is that there won't
# be terminal non-coding exons if the CDS is partial.
mRNA.exons()[-1].location_on(assemblies[assembly_id]).fmax_partial = True
else:
mRNA_loc.fmin_partial = True
gene_loc.fmin_partial = True
CDSs[0].location_on(assemblies[assembly_id]).fmin_partial = True
mRNA.exons()[0].location_on(assemblies[assembly_id]).fmin_partial = True
start_codon = coding_seq[0:3].upper().replace('U', 'T')
if start_codon not in start_codons:
newly_marked_5prime_partial += 1
CDSs = sorted(mRNA.CDSs())
if mRNA_loc.strand == 1:
mRNA_loc.fmin_partial = True
CDSs[0].location_on(assemblies[assembly_id]).fmin_partial = True
gene_loc.fmin_partial = True
# The exon is tricky, as there's no direct link between the CDS fragment
# and the corresponding exon. The assumption here is that there won't
# be terminal non-coding exons if the CDS is partial.
mRNA.exons()[0].location_on(assemblies[assembly_id]).fmin_partial = True
else:
mRNA_loc.fmax_partial = True
gene_loc.fmax_partial = True
CDSs[-1].location_on(assemblies[assembly_id]).fmax_partial = True
mRNA.exons()[-1].location_on(assemblies[assembly_id]).fmax_partial = True
print ("Genes marked as 5' partial: {0}".format(newly_marked_5prime_partial))
print ("Genes marked as 3' partial: {0}".format(newly_marked_3prime_partial))
ofh = open(args.output_gff, 'wt')
gff.print_gff3_from_assemblies(assemblies=assemblies, ofh=ofh)