This script was developed to discover coding sequences (CDS) within a transcript sequence. For example, this script could be applied to screen a transcriptome assembly. It does not work on a genome sequence, because the CDS must be continuous and introns would prevent the discovery.
Usage
python3 CDS_finder.py --in <FILE> --out <FILE>
Mandatory:
--in STR Input file
--out STR Output file
Optional:
--len INT Minimal CDS length[100]
--atg STR Enforces ATG at start [on]
--in specifies a FASTA file that contains nucleotide sequences.
--out specifies a FASTA file that contains the identified coding sequences. Only the longest sequence per input sequence is returned. Sequences below a minimal length threshold can be excluded.
--len specifies the minimal CDS length cutoff. Default: 100.
--atg specifies whether a CDS must start with an ATG. Possible values are 'on' and 'off'. Default: 'on'.
This repository.