Metadata-Version: 1.1
Name: prapi
Version: 5.0.3
Summary: Transcriptome Analysis Pipeline for Isoform Sequencing
Home-page: http://www.bioinfor.org/tool/PRAPI/
Author: gaoyubang
Author-email: 1489582340@qq.com
License: MIT
Description: =============
        Prapi Summary
        =============
        
        |travis_badge|
        
        .. |travis_badge| image:: https://travis-ci.org/nanoporetech/tombo.svg?branch=master
            :target: https://travis-ci.org/nanoporetech/tombo
        
        PRAPI is a one-stop solution for Iso-Seq analysis of analyze alternative transcription initiation (ATI), alternative splicing (AS), alternative cleavage and polyadenylation (APA), natural antisense transcripts (NAT), and circular RNAs (circRNAs) comprehensively. 
        
        
        
        ============
        Installation
        ============
        
        |pypi_badge|
        
        .. |pypi_badge| image:: https://badge.fury.io/py/ont-tombo.svg
            :target: https://pypi.org/project/ont-tombo/
        
        Basic tombo installation (python 2.7 and 3.4+ support)
        
        ::
        
            # or install pip package (numpy install required before tombo for cython optimization)
            pip install numpy
            pip install prapi
        
        ===========
        Quick Start
        ===========
        
        Please make sure docker is installed.If you want to take DE_APA analysis,please make sure that the bam file is generated by PAS_Seq reads.If you want to take Circle analysis,please make sure that the bam file is generated by RNase R easeing reads . Before running the script, you will need to run gmap_build to make a genome reference index. Please make sure that the section info you want is right.
        ::
        
        $ path=`pwd`
        $sudo docker run -it --rm -v ${path}:/data prapi:v1 Pacbio_v16.py -c /data/conf.txt
        All parameter is stored in conf.txt.
        basic arguments
        Output_dir          Name of the output directory
        Pacbio_reads       PacBio sequence's full path and name
        GMAP_IndexesDir     Directory of genomic index files buided by gmap_build program
        GMAP_Process        Number of worker threads for GMAP
        Genome_Annotion     Reference annotation  in gpd format
        MaxIntron           Max length for one internal intron (default 200000)
        Multile_processing  Using parallel version
        other arguments
        MinDist             Minimum distance between any two poly(A) or transcripts start sites
        MinSupport          Minimum number of trusted reads supporting a poly(A) or transcripts
        start sites
        Width_of_peaks      Peak widths for searching poly(A)
        Graph arguments
        Group              Groups of different library type to specify ylim for each facet separately
        anchorLength        Min anchor Length for Tophat/Bowtie aligner
        DElib               The libraries used for differential analysis
        P value        (default 0.01)
        FDR               (default 0.01)
        
        
        
        ::
        
        
        ..
        
           See more complete tutorials on the `documentation page <http://www.bioinfor.org/tool/PRAPI/manual.php>`_.
        
        ===
        RNA
        ===
        
        
        =====================
        Further Documentation
        =====================
        
        
        ========
        Citation
        ========
        
        Gao Y, Wang H, Zhang H, Wang Y, Chen J, Gu L, (2017), PRAPI: post-transcriptional regulation analysis pipeline for Iso-Seq.Bioinformatics,Bioinformatics, btx830,https://doi.org/10.1093/bioinformatics/btx830 
        ============
        Known Issues
        ============
        
        -  The bam file provided must be sorted and indexed.
        
        
Platform: UNKNOWN
Classifier: Development Status :: 3 - Alpha
Classifier: Environment :: Console
Classifier: Intended Audience :: Science/Research
Classifier: Intended Audience :: Healthcare Industry
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: POSIX
Classifier: Programming Language :: Python
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Requires: SpliceGrapher
Requires: numpy
Requires: matplotlib
Requires: pysam
Requires: pycairo
