Skip to main content

SAM Alignment Reconstructor

Project description

https://travis-ci.com/Ensembl/sam-alignment-reconstructor.svg?branch=master https://codecov.io/gh/Ensembl/sam-alignment-reconstructor/branch/master/graph/badge.svg Documentation Status

Overview

This package is design to reconstruct pairwise alignments from SAM files using the CIGAR string and MD:Z tag

It can be used as a standalone command line tool, or as a library when given the three elements above.

Usage

To install the package, enable the virtual environment where it’s going to be used and run

$ pip install sam-alignment-reconstructor
$ cat file.sam | sam-alignment-reconstructor

MS2007487-600V3:1:2109:08999:01136
TTCGAAATCTCACGCTCTTTACTGAAGACCCAGATAGAGCTTATCCTAAT
|||||||||||||||||||||||||||||||||:||||||||||||||||
TTCGAAATCTCACGCTCTTTACTGAAGACCCAGNTAGAGCTTATCCTAAT

CAGGATACTGTGTGGGAGAGGTTCGAGCAGGTATTTTTAGTGGCCTATG-
|||||||||||||||||:||:|||||||||||||||||||||:||||||
CAGGATACTGTGTGGGANAGNTTCGAGCAGGTATTTTTAGTGNCCTATGC

----GGTTGGTCACTTATGCCCCTGTCTTTAAAGACTACCTCTATGAAGG
    :::|||||||||||||||||||||||||||||||||||||||||||
CCCACTATGGTCACTTATGCCCCTGTCTTTAAAGACTACCTCTATGAAGG

TCTCCGACAGTTTTATGAGGACAACATCATGTATGTGGAGATCAGAGCAC
|||||||||||||||||||||||||||||:|||||||||:||||||||||
TCTCCGACAGTTTTATGAGGACAACATCACGTATGTGGAAATCAGAGCAC

Developing

To prepare the environment for developing the library, create a virtual environment, go to project root and then run:

$ pip install -e .[dev]

Testing

The recommended way is to test using detox. This allows for testing in all the supported python versions using virtual environments effortlessly. To use, install it, then run in the project root:

$ pip install detox
$ detox

Alternatively, testing can be done in the same environment as the dev one by installing it’s dependencies, then running pytest:

$ pip install -e .[test]
$ python -m pytest -s

Project details


Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Files for sam-alignment-reconstructor, version 0.0.5
Filename, size File type Python version Upload date Hashes
Filename, size sam_alignment_reconstructor-0.0.5-py2.py3-none-any.whl (6.5 kB) File type Wheel Python version py2.py3 Upload date Hashes View hashes
Filename, size sam-alignment-reconstructor-0.0.5.tar.gz (14.3 kB) File type Source Python version None Upload date Hashes View hashes

Supported by

Elastic Elastic Search Pingdom Pingdom Monitoring Google Google BigQuery Sentry Sentry Error logging AWS AWS Cloud computing DataDog DataDog Monitoring Fastly Fastly CDN DigiCert DigiCert EV certificate StatusPage StatusPage Status page