def addStartTag(in_path, out_path):
FH_in = FastaIO(in_path)
FH_out = FastaIO(out_path, "w")
for record in FH_in:
record.string = "^" + record.string
FH_out.write(record)
FH_in.close()
FH_out.close()
def getSeqByChr(genome_path):
"""
Return by chromosome name the sequence of this chromosome.
:param genome_path: Path to the genome file (format: fasta).
:type genome_path: str
:return: By chromosome name the sequence of this chromosome in uppercase.
:rtype: dict
"""
genome_by_chr = dict()
FH_seq = FastaIO(genome_path)
for record in FH_seq:
genome_by_chr[record.id] = record.string.upper()
FH_seq.close()
return genome_by_chr
help=
'Path to the definition of the amplicons (format: Illumina manifest).')
group_output = parser.add_argument_group('Outputs') # Outputs
group_output.add_argument(
'-f',
'--fwd-barcodes',
default="fwd_barcodes.fasta",
help=
'******************************** (format: fasta). [Default: %(default)s]'
)
group_output.add_argument(
'-r',
'--rvs-barcodes',
default="rvs_barcodes.fasta",
help=
'******************************** (format: fasta). [Default: %(default)s]'
)
args = parser.parse_args()
# Process
amplicons = getAmplicons(args.input_manifest)
FH_fwd = FastaIO(args.fwd_barcodes, "w")
FH_rvs = FastaIO(args.rvs_barcodes, "w")
for ampl in amplicons:
record_fwd = Sequence(ampl.name, ampl.up_primer)
FH_fwd.write(record_fwd)
record_rvs = Sequence(ampl.name, revcom(ampl.down_primer))
FH_rvs.write(record_rvs)
FH_fwd.close()
FH_rvs.close()