Data

Tools

Indexes

Applications

Experiments

Open Source Science

https://github.com/cancerit/crisprreadcountspy

A tool to count reads for CRISPR.

https://github.com/cancerit/crisprreadcountspy

Science Score: 13.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ○
    .zenodo.json file
  • ○
    DOI references
  • ○
    Academic publication links
  • ○
    Academic email domains
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (12.8%) to scientific vocabulary
Last synced: 9 months ago · JSON representation

Repository

A tool to count reads for CRISPR.

Basic Info
  • Host: GitHub
  • Owner: cancerit
  • License: agpl-3.0
  • Language: Python
  • Default Branch: develop
  • Size: 176 KB
Statistics
  • Stars: 1
  • Watchers: 10
  • Forks: 1
  • Open Issues: 1
  • Releases: 0
Created almost 6 years ago · Last pushed almost 2 years ago
Metadata Files
Readme Changelog License

README.md

crisprReadCountsPy

Gets CRISPR read counts from cram files and merges readcounts from multiple read count files.

| Master | Dev | |---|---| | Build Status | Build Status |

Docker Repository on Quay

Usage

To see the full usage:

crisprReadCounts --help

Installation

VERSION=X.X.X pip install https://github.com/cancerit/crisprReadCountsPy/archive/${VERSION}.tar.gz

Development environment

Setup VirtualEnv

cd $PROJECTROOT hash virtualenv || pip3 install virtualenv virtualenv -p python3 env source env/bin/activate pip install -r requirements.txt python setup.py develop # so bin scripts can find module

For testing/coverage (./run_tests.sh)

source env/bin/activate # if not already in env pip install -r test-requirements.txt

LICENCE

Copyright (c) 2014-2020 Genome Research Ltd.

Author: CASM/Cancer IT cgphelp@sanger.ac.uk

This file is part of crisprReadCounts.

crisprReadCounts is free software: you can redistribute it and/or modify it under the terms of the GNU Affero General Public License as published by the Free Software Foundation; either version 3 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more details.

You should have received a copy of the GNU Affero General Public License along with this program. If not, see http://www.gnu.org/licenses/.

  1. The usage of a range of years within a copyright statement contained within this distribution should be interpreted as being equivalent to a list of years including the first and last year specified and all consecutive years between them. For example, a copyright statement that reads ‘Copyright (c) 2005, 2007- 2009, 2011-2012’ should be interpreted as being identical to a statement that reads ‘Copyright (c) 2005, 2007, 2008, 2009, 2011, 2012’ and a copyright statement that reads ‘Copyright (c) 2005-2012’ should be interpreted as being identical to a statement that reads ‘Copyright (c) 2005, 2006, 2007, 2008, 2009, 2010, 2011, 2012’."

Owner

  • Name: CASM IT
  • Login: cancerit
  • Kind: organization
  • Email: cgpit@sanger.ac.uk
  • Location: Hinxton, Cambridge, UK

CASM IT provide bioinformatic support for Cancer, Ageing and Somatic Mutation group at the Wellcome Sanger Institute

GitHub Events

Total
Last Year

Dependencies

Dockerfile docker
  • ubuntu 20.04 build
test-requirements.txt pypi
  • pytest * test
  • pytest-cov * test
  • radon * test