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        "author": "Julien Delafontaine",
        "author_email": "julien.delafontaine@epfl.ch",
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            "Development Status :: 5 - Production/Stable",
            "Natural Language :: English",
            "Operating System :: OS Independent",
            "Programming Language :: Python",
            "Programming Language :: Python :: 2.7",
            "Programming Language :: Python :: 3",
            "Topic :: Scientific/Engineering :: Bio-Informatics"
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        "description": "Welcome!\n========\n`Rnacounter` estimates abundances of genes and their different transcripts\nfrom read alignments. Exons and introns can also be quantified.\n\nIt provides fast read counting in annotated genomic features as well as a simple,\nyet efficient solution to the quantification of isoforms from RNA-seq data.\nThe method used is described in [<ref>].\nA typical run is expected to take less than 2 minutes for a 1Gb BAM file from mouse\nRNA sequencing, increasing linearly with the BAM size.\n\nFor all these tasks it only requires a BAM file from a read mapping on the genome,\nand a single GTF/GFF file describing the exon structure\nsuch as those provided by Ensembl or GenRep.\n\nIt is not meant to be used as a library, but through its command-line tool \"rnacounter\".\n\nThe code project is hosted in Github (https://github.com/delafont/rnacounter), GPL-2 licensed.\n\nUsage:\n======\nSee \"rnacounter --help\" and the tutorial at\nhttp://bbcf.epfl.ch/bbcflib/tutorial_rnacounter.html,\nalso available in the doc/ folder.\n\nMinimal example::\n\n    rnacounter test.bam test.gtf\n\nInstallation:\n=============\nFirst ensure that you have numpy installed, then install rnacounter.\nWith easy_install::\n\n    sudo easy_install numpy\n    sudo easy_install rnacounter\n\nOr better yet, with pip::\n\n    sudo pip install numpy\n    sudo pip install rnacounter\n\nIt installs as a standard Python library but includes the executable\nand puts it somewhere in your $PATH. Dependencies will be added\nautomatically.\n\nCheck that it works with the `test` command::\n\n    rnacounter test\n\nIt should display something similar to this::\n\n    ID\tCount\tRPKM\tChrom\tStart\tEnd\tStrand\tGeneName\tType\tSense\tSynonym\n    ENSMUSG00000038271\t0.0\t0.0\tchr6\t125095258\t125111800\t1\tIffo1\tGene\t.\t.\n    ENSMUSG00000057666\t3956.87179487\t434612.223694\tchr6\t125111870\t125116485\t-1\tGapdh\tGene\t.\t.\n    ENSMUSG00000038252\t0.0\t0.0\tchr6\t125118026\t125141613\t-1\tNcapd2\tGene\t.\t.\n\nTo uninstall with pip::\n\n    sudo pip uninstall rnacounter\n\nThe code is fully compatible with Python 2.7 and Python 3.\n\nBuilding from source:\n=====================\nThis allows to modify the Cython source code (rnacounter.pyx) before rebuilding.\n\nClone or download the repository from https://github.com/delafont/rnacounter .\n\nYou need cython installed (`pip install cython`).\n\nFrom where rnacounter.pyx lies (rnacounter/rnacounter/), run::\n\n    sudo python setup.py build_ext\n\nIt will recompile to create rnacounter.c, and build it.\nThen add the executable (rnacounter/bin/rnacounter) to your $PATH,\nor install from the package root (rnacounter/) with::\n\n    sudo python setup.py install\n\nDependencies:\n=============\nTests run with the library versions below, but may work with earlier versions.\n\n* setuptools 7.0+  (installation)\n* pysam 0.7.5+     (samtools wrapper)\n* numpy 1.6.2+     (efficient numeric arrays)\n* scipy 0.9.0+     (NNLS algorithm)\n* docopt 0.6.1+    (command-line args parsing)\n* cython 0.20+     (translate Python code to C)\n\nTesting:\n========\nTesting files in the testfiles/ folder:\n- gapdhKO.bam: alignment on mm9 with only Gapdh covered.\n- mm9_3genes_renamed.gtf: extract of the Ensembl GTF with Gapdh, the gene before and the gene after it.\n- mm9_Gapdh_renamed.gtf: extract of the Ensembl GTF with Gapdh only.\n\nExample::\n\n    rnacounter testfiles/gapdhKO.bam testfiles/mm9_3genes_renamed.gtf\n\n(which is equivalent to what the `test` command does)::\n\n    rnacounter test\n\nThe BAM contains 4041 reads all aligning perfectly on Gapdh (ENSMUSG00000057666) exons,\nmostly on ENSMUSE00000487077 but also ENSMUSE00000751942 and ENSMUSE00000886744.\nNothing on other exons, which makes it a good example of badly conditioned input data...\n\nThe least squares method returns counts on the following transcripts:\nENSMUST00000117757, ENSMUST00000118875, ENSMUST00000147954\nand nothing on ENSMUST00000073605, ENSMUST00000144205, ENSMUST00000144588 .\n\nTroubleshooting:\n================\nAny bug report, usage issue or feature request not listed below can be addressed to\njulien.delafontaine@epfl.ch or webmaster.bbcf@epfl.ch .",
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