{ "info": { "author": "Matthew Laird", "author_email": "lairdm@ebi.ac.uk", "bugtrack_url": null, "classifiers": [ "Development Status :: 4 - Beta", "Intended Audience :: Developers", "License :: OSI Approved :: Apache Software License", "Programming Language :: Python :: 2", "Programming Language :: Python :: 2.7", "Programming Language :: Python :: 3", "Programming Language :: Python :: 3.4", "Programming Language :: Python :: 3.5", "Programming Language :: Python :: 3.6", "Programming Language :: Python :: 3.7" ], "description": ".. image:: https://travis-ci.com/Ensembl/sam-alignment-reconstructor.svg?branch=master\n :target: https://travis-ci.com/Ensembl/sam-alignment-reconstructor\n.. image:: https://codecov.io/gh/Ensembl/sam-alignment-reconstructor/branch/master/graph/badge.svg\n :target: https://codecov.io/gh/Ensembl/sam-alignment-reconstructor\n.. image:: https://readthedocs.org/projects/sam-alignment-reconstructor/badge/?version=latest\n :target: https://sam-alignment-reconstructor.readthedocs.io/en/latest/?badge=latest\n :alt: Documentation Status\n\nOverview\n########\n\nThis package is design to reconstruct pairwise alignments from SAM files using the CIGAR string and MD:Z tag\n\nIt can be used as a standalone command line tool, or as a library when given the three elements above.\n\nUsage\n#####\n\nTo install the package, enable the virtual environment where it's going to be used and run\n\n::\n\n $ pip install sam-alignment-reconstructor\n $ cat file.sam | sam-alignment-reconstructor\n\n MS2007487-600V3:1:2109:08999:01136\n TTCGAAATCTCACGCTCTTTACTGAAGACCCAGATAGAGCTTATCCTAAT\n |||||||||||||||||||||||||||||||||:||||||||||||||||\n TTCGAAATCTCACGCTCTTTACTGAAGACCCAGNTAGAGCTTATCCTAAT\n\n CAGGATACTGTGTGGGAGAGGTTCGAGCAGGTATTTTTAGTGGCCTATG-\n |||||||||||||||||:||:|||||||||||||||||||||:|||||| \n CAGGATACTGTGTGGGANAGNTTCGAGCAGGTATTTTTAGTGNCCTATGC\n\n ----GGTTGGTCACTTATGCCCCTGTCTTTAAAGACTACCTCTATGAAGG\n :::|||||||||||||||||||||||||||||||||||||||||||\n CCCACTATGGTCACTTATGCCCCTGTCTTTAAAGACTACCTCTATGAAGG\n\n TCTCCGACAGTTTTATGAGGACAACATCATGTATGTGGAGATCAGAGCAC\n |||||||||||||||||||||||||||||:|||||||||:||||||||||\n TCTCCGACAGTTTTATGAGGACAACATCACGTATGTGGAAATCAGAGCAC\n\n\nDeveloping\n##########\n\nTo prepare the environment for developing the library, create a virtual environment, go to project root and then run:\n\n::\n\n $ pip install -e .[dev]\n\nTesting\n#######\nThe recommended way is to test using detox.\nThis allows for testing in all the supported python versions using virtual environments effortlessly.\nTo use, install it, then run in the project root:\n\n::\n\n $ pip install detox\n $ detox\n\nAlternatively, testing can be done in the same environment as the dev one by installing it's dependencies, then running pytest:\n\n::\n\n $ pip install -e .[test]\n $ python -m pytest -s\n\n\n", "description_content_type": "", "docs_url": null, "download_url": "", "downloads": { "last_day": 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