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Peptide library design

Project description

# `pepsyn`
Peptide library design


`pepsyn` is developed for Python 3 and requires `biopython`. The CLI uses

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

$ 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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