pepsyn
Peptide library design
Installation
pepsyn is developed for Python 3.6+ and requires biopython. The CLI uses
click.
pip install pepsynor for the latest development version
git clone https://github.com/lasersonlab/pepsyn.git
cd pepsyn
python setup.py installTo run the tests
py.testUsage
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
Options:
-h, --help Show this message and exit.
Commands:
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
Options:
-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 - -
