CDSmsa

Coding sequence MSA (Multiple Sequence Alignment) with optional HMM profile building

Contents Index

• MSA example
• Usage
  • Single FASTA file
  • Multiple FASTA files

MSA example

Usage

Single FASTA file use

python single_msa.py --help

usage: single_msa.py [-h] [--msafile] [--cdsfile] [--transcode] [--output] [--build_hmm]

CDS MSA tool (single)

optional arguments:
  -h, --help         show this help message and exit
  --msafile , -m     input file path, it is a MSA output file (FASTA format)
  --cdsfile , -c     nucleotide sequence file (FASTA format)
  --transcode , -t   translate code file path, default='code.csv'
  --output , -o      output file path, CDS alignment file
  --build_hmm        build HMM profile from MSA and save to output directory

Multiple FASTA file use

python batch_msa.py --help

usage: batch_msa.py [-h] [--indir] [--cdsdir] [--transcode] [--outdir] [--build_hmm]

CDS MSA tool (batch)

optional arguments:
  -h, --help         show this help message and exit
  --indir , -i       input folder path, there are MSA output files (FASTA format)
  --cdsdir , -c      save nucleotide sequence files (FASTA format), have the
                     same name with input files
  --transcode , -t   translate code file path
  --outdir , -o      output dir path, save CDS alignment files
  --build_hmm        build HMM profile from MSA and save to output directory

Output Files

The program generates the following output files:

1. MSA files (.fa or .fasta)
2. HMM profile files (.hmm) - when --build_hmm option is used
   • HMM profiles are named using the input filename as prefix
   • Saved in the same output directory as MSA files

Example Commands

# Single file with HMM profile
python single_msa.py -c input.fa -o ./output --build_hmm

# Batch processing with HMM profiles
python batch_msa.py -i ./input_dir -o ./output_dir --build_hmm