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coding sequence MSA(multiple sequence alignment)

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CDSmsa

coding sequence MSA(multiple sequence alignment)

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MSA example

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Usage

Single FASTA file use

python single_msa.py --help

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

CDS MSA tool (sigle)

optional arguments:
  -h, --help         show this help message and exit
  --msafile , -m     inputfile path, it is a MSA output file (FASTA format)
  --cdsfile , -c     uncleotide sequence file (FASTA formfat)
  --transcode , -t   translate code file path, default='code.csv'
  --output , -o      output file path, CDS alignment file

Multiple FASTA file use

python batch_msa.py --help

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

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 uncleotide sequence files (FASTA formfat), have the
                     same name with input files
  --transcode , -t   translate code file path
  --outdir , -o      output dir path, save CDS alignment files

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