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Peptide library design

Project description


Peptide library design


pepsyn is developed for Python 3.6+ and requires biopython. The CLI uses click.

pip install pepsyn

or for the latest development version

git clone
cd pepsyn
python install

To run the tests



pepsyn can be used as a library, but also comes with a CLI.

The main CLI command is pepsyn and it can read from stdin and stdout by specifying - as the input or output. Input and output files are FASTA formatted.

$ pepsyn -h
Usage: pepsyn [OPTIONS] COMMAND [ARGS]...

  pepsyn -- peptide synthesis design

  -h, --help  Show this message and exit.

  prefix      add a prefix to each sequence
  recodesite  remove site from each sequence's CDS by...
  revtrans    reverse translate amino acid sequences into...
  stats       compute some sequence statistics
  suffix      add a suffix to each sequence
  tile        tile a set of sequences

For example, to tile a set of sequences, use the pepsyn tile command. Each subcommand has its own help message with relevant options.

$ pepsyn tile -h
Usage: pepsyn tile [OPTIONS] INPUT OUTPUT

  tile a set of sequences

  -l, --length INTEGER   Length of output oligos
  -p, --overlap INTEGER  Overlap of oligos
  -h, --help             Show this message and exit.

Commands can be piped into each other. (Note: stdin and stdout are signified with -.)

cat pepsyn/tests/proteins.fasta \
    | pepsyn tile -l 10 -p 3 - - \
    | pepsyn revtrans - - \
    | pepsyn prefix -p ACGGG - - \
    | pepsyn suffix -s TGCTG - - \
    | pepsyn recodesite --site EcoRI --clip-left 5 --clip-right 5 - -

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