Metadata-Version: 1.1
Name: rnacounter
Version: 1.2.1
Summary: Estimate abundances of genomic features from read densities
Home-page: https://github.com/delafont/rnacounter
Author: Julien Delafontaine
Author-email: julien.delafontaine@epfl.ch
License: GPL-2
Description: 
        Welcome!
        ========
        `Rnacounter` estimates abundances of genes and their different transcripts
        from read alignments. Exons and introns can also be quantified.
        
        It provides fast read counting in annotated genomic features as well as a simple,
        yet efficient solution to the quantification of isoforms from RNA-seq data.
        The method used is described in [<ref>].
        A typical run is expected to take less than 2 minutes for a 1Gb BAM file from mouse
        RNA sequencing, increasing linearly with the BAM size.
        
        For all these tasks it only requires a BAM file from a read mapping on the genome,
        and a single GTF/GFF file describing the exon structure
        such as those provided by Ensembl or GenRep.
        
        It is not meant to be used as a library, but through its command-line tool "rnacounter".
        
        The code project is hosted in Github (https://github.com/delafont/rnacounter), GPL-2 licensed.
        
        Usage:
        ======
        See "rnacounter --help" and the tutorial at
        http://bbcf.epfl.ch/bbcflib/tutorial_rnacounter.html,
        also available in the doc/ folder.
        
        Minimal example::
        
            rnacounter test.bam test.gtf
        
        Installation:
        =============
        First ensure that you have numpy installed, or install it with::
        
            sudo easy_install numpy
        
        Then install rnacounter with easy_install::
        
            sudo easy_install rnacounter
        
        Or better yet, with pip::
        
            sudo pip install numpy
            sudo pip install rnacounter
        
        It installs as a standard Python library but includes the executable
        and puts it somewhere in your $PATH. Dependencies will be added
        automatically.
        
        To uninstall with pip::
        
            sudo pip uninstall rnacounter
        
        The code is fully compatible with Python 2.7 and Python 3.
        
        Building from source:
        =====================
        This allows to modify the Cython source code (rnacounter.pyx) before rebuilding.
        
        Clone or download the repository from https://github.com/delafont/rnacounter .
        
        You need cython installed (`pip install cython`).
        
        From where rnacounter.pyx lies (rnacounter/rnacounter/), run::
        
            sudo python setup.py build_ext
        
        It will recompile to create rnacounter.c, and build it.
        Then add the executable (rnacounter/bin/rnacounter) to your $PATH,
        or install from the package root (rnacounter/) with::
        
            sudo python setup.py install
        
        Dependencies:
        =============
        Tests run with the library versions below, but may work with earlier versions.
        
        * setuptools 7.0+  (installation)
        * pysam 0.7.5+     (samtools wrapper)
        * numpy 1.6.2+     (efficient numeric arrays)
        * scipy 0.9.0+     (NNLS algorithm)
        * docopt 0.6.1+    (command-line args parsing)
        * cython 0.20+     (translate Python code to C)
        
        Testing:
        ========
        Testing files in the testfiles/ folder:
        - gapdhKO.bam: alignment on mm9 with only Gapdh covered.
        - mm9_3genes_renamed.gtf: extract of the Ensembl GTF with Gapdh, the gene before and the gene after it.
        - mm9_Gapdh_renamed.gtf: extract of the Ensembl GTF with Gapdh only.
        
        Example::
        
            rnacounter testfiles/gapdhKO.bam testfiles/mm9_3genes_renamed.gtf
        
        The BAM contains 4041 reads all aligning perfectly on Gapdh (ENSMUSG00000057666) exons,
        mostly on ENSMUSE00000487077 but also ENSMUSE00000751942 and ENSMUSE00000886744.
        Nothing on other exons, which makes it a good example of badly conditioned input data...
        
        The least squares method returns counts on the following transcripts:
        ENSMUST00000117757, ENSMUST00000118875, ENSMUST00000147954
        and nothing on ENSMUST00000073605, ENSMUST00000144205, ENSMUST00000144588 .
        
        Returns a count of 2456.87 for the gene.
        
        Troubleshooting:
        ================
        Any bug report, usage issue or feature request not listed below can be addressed to
        julien.delafontaine@epfl.ch or webmaster.bbcf@epfl.ch .
        
        
Keywords: rna-seq rnaseq count reads table sequencing genetics bioinformatics
Platform: UNKNOWN
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 2.7
Classifier: Programming Language :: Python :: 3
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Natural Language :: English
Classifier: Operating System :: OS Independent
Classifier: Development Status :: 5 - Production/Stable
