Metadata-Version: 2.1
Name: pepsyn
Version: 0.4.1
Summary: Peptide library design
Home-page: https://github.com/lasersonlab/pepsyn
Author: Laserson Lab
License: Apache License, Version 2.0
Description: # `pepsyn`
        Peptide library design
        
        
        **Installation**
        
        `pepsyn` is developed for Python 3.6+ and requires `biopython`.  The CLI uses
        `click`.
        
        ```bash
        pip install pepsyn
        ```
        
        or for the latest development version
        
        ```bash
        git clone https://github.com/lasersonlab/pepsyn.git
        cd pepsyn
        python setup.py install
        ```
        
        To run the tests
        
        ```bash
        py.test
        ```
        
        **Usage**
        
        `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.
        
        ```bash
        $ 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.
        
        ```bash
        $ 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 `-`.)
        
        ```bash
        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 - -
        ```
        
Platform: UNKNOWN
Classifier: Programming Language :: Python :: 3
Description-Content-Type: text/markdown
