def main():
parser = argparse.ArgumentParser(
description=
'Reverse or reverse-complement selected sequences within a multi-FASTA'
)
## output file to be written
parser.add_argument('-f',
'--fasta_file',
type=str,
required=True,
help='Path to an input FASTA file')
parser.add_argument('-i',
'--id_file',
type=str,
required=True,
help='Path to file with IDs to process')
parser.add_argument(
'-a',
'--action',
type=str,
required=True,
choices=['reverse', 'revcomp'],
help='What should be done to the sequences in the ID file')
parser.add_argument('-o',
'--output_file',
type=str,
required=False,
default=None,
help='Optional Path to an output file to be created')
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')
seqs = utils.fasta_dict_from_file(args.fasta_file)
ids = list()
for line in open(args.id_file):
line = line.rstrip()
ids.append(line)
for seq_id in seqs:
seq = seqs[seq_id]
if seq_id in ids:
if args.action == 'reverse':
seq['s'] = seq['s'][::-1]
elif args.action == 'revcomp':
seq['s'] = utils.reverse_complement(seq['s'])
## write this sequence, 60bp per line
fout.write(">{0}\n".format(seq_id))
for i in range(0, len(seq['s']), 60):
fout.write(seq['s'][i:i + 60] + "\n")
def main():
parser = argparse.ArgumentParser( description='Extract regions from a multi-FASTA file')
## output file to be written
parser.add_argument('-f', '--fasta_file', type=str, required=True, help='Path to an input FASTA file' )
parser.add_argument('-c', '--coords_file', type=str, required=True, help='Path to a tab-delimited file with coordinates' )
parser.add_argument('-m', '--mol_col', type=int, required=True, help='Tabdel file column with molecule identifiers' )
parser.add_argument('-x', '--start_coord_col', type=int, required=True, help='Tabdel file column with coordinate start positions' )
parser.add_argument('-y', '--stop_coord_col', type=int, required=True, help='Tabdel file column with coordinate stop positions' )
parser.add_argument('-n', '--name_col', type=int, required=False, default=None, help='Optional tabdel file column with name for exported fragment' )
parser.add_argument('-o', '--output_file', type=str, required=False, default=None, help='Optional Path to an output file to be created' )
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')
seqs = utils.fasta_dict_from_file(args.fasta_file)
start_col = args.start_coord_col - 1
stop_col = args.stop_coord_col - 1
mol_col = args.mol_col - 1
for line in open(args.coords_file):
line = line.rstrip()
cols = line.split('\t')
if len(cols) < 3:
continue
(fmin, fmax, strand) = utils.humancoords_to_0interbase(int(cols[start_col]), int(cols[stop_col]))
mol_id = cols[mol_col]
if mol_id not in seqs:
raise Exception("ERROR: molecule ID ({0}) not found in FASTA file".format(mol_id))
seq = seqs[mol_id]['s'][fmin:fmax]
seq_id = None
if args.name_col is None:
seq_id = "{0}___{1}.{2}.{3}".format( mol_id, fmin, fmax, strand )
else:
seq_id = cols[int(args.name_col) - 1]
if strand == -1:
seq = utils.reverse_complement(seq)
## write this sequence, 60bp per line
fout.write(">{0}\n".format(seq_id))
for i in range(0, len(seq), 60):
fout.write(seq[i : i + 60] + "\n")
def main():
parser = argparse.ArgumentParser(
description="Reverse or reverse-complement selected sequences within a multi-FASTA"
)
## output file to be written
parser.add_argument("-f", "--fasta_file", type=str, required=True, help="Path to an input FASTA file")
parser.add_argument("-i", "--id_file", type=str, required=True, help="Path to file with IDs to process")
parser.add_argument(
"-a",
"--action",
type=str,
required=True,
choices=["reverse", "revcomp"],
help="What should be done to the sequences in the ID file",
)
parser.add_argument(
"-o",
"--output_file",
type=str,
required=False,
default=None,
help="Optional Path to an output file to be created",
)
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")
seqs = utils.fasta_dict_from_file(args.fasta_file)
ids = list()
for line in open(args.id_file):
line = line.rstrip()
ids.append(line)
for seq_id in seqs:
seq = seqs[seq_id]
if seq_id in ids:
if args.action == "reverse":
seq["s"] = seq["s"][::-1]
elif args.action == "revcomp":
seq["s"] = utils.reverse_complement(seq["s"])
## write this sequence, 60bp per line
fout.write(">{0}\n".format(seq_id))
for i in range(0, len(seq["s"]), 60):
fout.write(seq["s"][i : i + 60] + "\n")
def get_residues(self):
if len(self.locations) == 0:
raise Exception("ERROR: gene.get_residues() requested but gene {0} isn't located on anything.".format(self.id))
elif len(self.locations) > 1:
raise Exception("ERROR: gene {0} is located on multiple molecules. Can't automatically extract the residues.".format(self.id))
loc = self.location()
mol = loc.on
# make sure this thing has its residues populated
if len(mol.residues) <= 0:
raise Exception("ERROR: gene.get_residues() requested but its molecule {0} has no stored residues".format(mol.id))
self.residues = mol.residues[loc.fmin:loc.fmax]
self.length = len(self.residues)
if loc.strand == -1:
self.residues = utils.reverse_complement(self.residues)
return self.residues
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='Put a description of your script here')
## output file to be written
parser.add_argument('-s', '--sam_file', type=str, required=True, help='Input SAM file with reads aligned to reference' )
parser.add_argument('-fi', '--fasta_in', type=str, required=False, help='Path to a FASTA file representing sequences that were aligned against. If this is passed, you should also pass the -fo argument' )
parser.add_argument('-fo', '--fasta_out', type=str, required=False, help='If passed along with -fi, the orientation-corrected sequences will be written here.' )
args = parser.parse_args()
seqs = dict()
if args.fasta_in is not None:
seqs = utils.fasta_dict_from_file(args.fasta_in)
if args.fasta_out is not None:
out_fh = open(args.fasta_out, 'w')
else:
raise Exception("ERROR: You must pass a value for -fo if you pass -fi")
total_read_mappings = 0
last_transcript_id = None
counts = { '1':{'T':0,'F':0}, '2':{'T':0,'F':0} }
transcript_count = 0
correct_orientation_count = 0
incorrect_orientation_count = 0
transcripts_to_correct = dict()
for line in open(args.sam_file):
if line.startswith('@'): continue
cols = line.split("\t")
if len(cols) < 5: continue
read_dir = cols[0][-1]
transcript_id = cols[2]
total_read_mappings += 1
flag = cols[1]
if int(flag) & 16:
seq_revcomped = 'T'
else:
seq_revcomped = 'F'
#print("DEBUG: match:{2}, SEQ_revcomped={0}, read_dir={1}".format(seq_revcomped, read_dir, transcript_id))
if transcript_id == last_transcript_id:
counts[read_dir][seq_revcomped] += 1
else:
transcript_count += 1
if last_transcript_id is not None:
## determine transcript orientation
## Given an RF library, the 1:T count should outnumber the 1:F one
if counts['1']['T'] > counts['1']['F']:
correct_orientation_count += 1
else:
incorrect_orientation_count += 1
transcripts_to_correct[last_transcript_id] = 1
## report counts
print("{0}\t1-T:{1}\t1-F:{2}\t2-T:{3}\t2-F:{4}".format(last_transcript_id, counts['1']['T'], counts['1']['F'], counts['2']['T'], counts['2']['F']))
## reset
last_transcript_id = transcript_id
counts = { '1':{'T':0,'F':0}, '2':{'T':0,'F':0} }
for seq_id in seqs:
seq = seqs[seq_id]
if seq_id in transcripts_to_correct:
seq['s'] = utils.reverse_complement(seq['s'])
out_fh.write(">{0} {2}\n{1}\n".format(seq_id, utils.wrapped_fasta(seq['s']), seq['h']))
print("Total transcripts: {0}".format(transcript_count))
print("Total reads mapped: {0}".format(total_read_mappings))
print("Transcripts in correct orientation: {0}".format(correct_orientation_count))
print("Transcripts in reverse orientation: {0}".format(incorrect_orientation_count))
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='Extract regions from a multi-FASTA file')
## output file to be written
parser.add_argument('-f',
'--fasta_file',
type=str,
required=True,
help='Path to an input FASTA file')
parser.add_argument('-c',
'--coords_file',
type=str,
required=True,
help='Path to a tab-delimited file with coordinates')
parser.add_argument('-m',
'--mol_col',
type=int,
required=True,
help='Tabdel file column with molecule identifiers')
parser.add_argument(
'-x',
'--start_coord_col',
type=int,
required=True,
help='Tabdel file column with coordinate start positions')
parser.add_argument(
'-y',
'--stop_coord_col',
type=int,
required=True,
help='Tabdel file column with coordinate stop positions')
parser.add_argument(
'-n',
'--name_col',
type=int,
required=False,
default=None,
help='Optional tabdel file column with name for exported fragment')
parser.add_argument('-o',
'--output_file',
type=str,
required=False,
default=None,
help='Optional Path to an output file to be created')
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')
seqs = utils.fasta_dict_from_file(args.fasta_file)
start_col = args.start_coord_col - 1
stop_col = args.stop_coord_col - 1
mol_col = args.mol_col - 1
for line in open(args.coords_file):
line = line.rstrip()
cols = line.split('\t')
if len(cols) < 3:
continue
(fmin, fmax,
strand) = utils.humancoords_to_0interbase(int(cols[start_col]),
int(cols[stop_col]))
mol_id = cols[mol_col]
if mol_id not in seqs:
raise Exception(
"ERROR: molecule ID ({0}) not found in FASTA file".format(
mol_id))
seq = seqs[mol_id]['s'][fmin:fmax]
seq_id = None
if args.name_col is None:
seq_id = "{0}___{1}.{2}.{3}".format(mol_id, fmin, fmax, strand)
else:
seq_id = cols[int(args.name_col) - 1]
if strand == -1:
seq = utils.reverse_complement(seq)
## write this sequence, 60bp per line
fout.write(">{0}\n".format(seq_id))
for i in range(0, len(seq), 60):
fout.write(seq[i:i + 60] + "\n")