pepsyn 0.2.0

Peptide library design

# `pepsyn`
Peptide library design


**Installation**

`pepsyn` is developed for Python 3 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
removesite 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 removesite --site EcoRI --clip-left 5 --clip-right 5 - -
```