https://github.com/kdm9/parephase

5'PARE phasing
https://github.com/kdm9/parephase

Last synced: 11 days ago
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5'PARE phasing

• Host: GitHub
• URL: https://github.com/kdm9/parephase
• Owner: kdm9
• License: mpl-2.0
• Created: 2017-01-08T23:26:29.000Z (almost 8 years ago)
• Default Branch: master
• Last Pushed: 2017-05-08T02:05:51.000Z (over 7 years ago)
• Last Synced: 2024-10-11T19:22:40.425Z (about 1 month ago)
• Language: Python
• Homepage:
• Size: 35.2 KB
• Stars: 0
• Watchers: 1
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        
PAREphase

=========

Detects phasing around stop sites in 5'PARE data

Free for all users under the MPL v2, see ./LICENSE.

## Install

```bash

pip install parephase

```

## Usage

```shell

$ parephase --help

parephase -- Histogram coverage of 5' PARE data around stop sites

USAGE:

    parephase [options] -g GFF_FILE BAMFILE

OPTIONS:

    -P          Output counts per gene

    -u INT      Count INT bases upstream of the stop [default: 100]

    -d INT      Count INT bases downstream stream of the stop [default: 100]

    -g GFFFILE  GFF file describing gene models.

    -l GENIDS   File containing a list of gene models. If not given, all gene

                models are used, which can create inaccuate results. Please

                provide a list of representative gene models.

```