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 = biocodeutils.reverse_complement(self.residues)
return self.residues
def get_residues(self):
if len(self.locations) == 0:
raise Exception(
"ERROR: CDS.get_residues() requested but CDS {0} isn't located on anything.".format(self.id)
)
elif len(self.locations) > 1:
raise Exception(
"ERROR: CDS {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: CDS.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 = biocodeutils.reverse_complement(self.residues)
return self.residues
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 = biocodeutils.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'] = biocodeutils.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="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 = biocodeutils.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"] = biocodeutils.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 = biocodeutils.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) = biocodeutils.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 = biocodeutils.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='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 = biocodeutils.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'] = biocodeutils.reverse_complement(seq['s'])
out_fh.write(">{0} {2}\n{1}\n".format(seq_id, biocodeutils.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='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 = biocodeutils.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'] = biocodeutils.reverse_complement(seq['s'])
out_fh.write(">{0} {2}\n{1}\n".format(
seq_id, biocodeutils.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))
