Metadata-Version: 1.1
Name: rnaseqhs
Version: 0.3
Summary: Tool for analysis of RNA-seq data.
Home-page: https://upload.pypi.org/legacy/
Author: Zhi Zhang
Author-email: zzjerryzhang@gmail.com
License: MIT
Download-URL: https://git-r3lab.uni.lu/zhi.zhang/rnaseqhs/raw/master/rnaseqhs/dist/rnaseqhs-0.2.tar.gz
Description: rnaseqhs
        =========
        
        overview
        ---------
        rnaseqhs can do bioinformatics analysis for RNA_seq data and generate clean BAM/SAM result from HISAT2, GTF result from Stringtie and featureCounts result. 
        
        rnaseqhs is available under the terms of the MIT license (see the file ``LICENSE``)
        
        pre-requirements
        -----------------
        1. 'gzip','fastx_trimmer','fastqc','cutadapt','fastq_quality_filter','hisat2','stringtie','samtools (v1.3.1)','bedtools (v2.19.1)' in $PATH.
        2.  hisat2 built genome index, transcriptome index, and gtf.
        
        Installation
        -------------
        1. tar zxvf rnaseqhs-<version>.tar.gz
        2. cd rnaseqhs-<version>
        3. python setup.py install --user
        
        Usage
        ------
        1. use it as module in python console ::
        
            >>>import rnaseqhs
        
            >>>rnaseqhs.rnaseqhs.main(<Arguments>)
        
        Arguments are ::
            >>>rnaseqhs.rnaseqhs.main(NDIR,OUTDIR,PHRED,QCCHECK,TRIM,LASTKEEP,RMADAPT, LADAPTER, RADAPTER
                        ,OVERLAP,MINLEN,REMOVEN,NCUTOFF,FILTQ
                        ,MINQ,PMINQ,QCSTAT,MAPPING,HISAT2INDEX,ORIENTATIONS
                        ,RNASTRANDNESS,GTF,RAWCOVER,GENOMEBED,WINDOWSIZE])
        
        2. use it as command line in bash ::
        
            <installed-path>/rnaseqhsb <options>
        
        Options are ::
        usage: rnaseqhs [-h] [-i INDIR] [-o OUTDIR] [-P PHRED] [-Q QCCHECK] [-T TRIM]
                        [-l LASTKEEP] [-r RMADAPT] [-L LADAPTER] [-R RADAPTER]
                        [-O OVERLAP] [-m MINLEN] [-N REMOVEN] [-c NCUTOFF] [-F FILTQ]
                        [--minQ MINQ] [--pminQ PMINQ] [-q QCSTAT] [-M MAPPING]
                        [--hisat2index HISAT2INDEX] [--orientations ORIENTATIONS]
                        [--rnastrandness RNASTRANDNESS] [--gtf GTF]
                        [--drawCover DRAWCOVER] [--genomebed GENOMEBED]
                        [--windowsize WINDOWSIZE]
        
        optional arguments:
          -h, --help            show this help message and exit
          -i INDIR, --indir INDIR
                                fastq files path
          -o OUTDIR, --outdir OUTDIR
                                output path
          -P PHRED, --phred PHRED
                                phred score used in platform [33]
          -Q QCCHECK, --qccheck QCCHECK
                                do quality check [true]
          -T TRIM, --trim TRIM  trim given fastq short reads as --lastkeep defined
          -l LASTKEEP, --lastkeep LASTKEEP
                                with "trim" option, last bases to keep
          -r RMADAPT, --rmadapt RMADAPT
                                remove adapter [true]
          -L LADAPTER, --ladapter LADAPTER
                                left adapter [AGATCGGAAGAGC]
          -R RADAPTER, --radapter RADAPTER
                                right adapter [AGATCGGAAGAGC]
          -O OVERLAP, --overlap OVERLAP
                                If the overlap between the read and adapter is shorter
                                than the overlap length, the read will NOT be
                                modified. [6]
          -m MINLEN, --minlen MINLEN
                                Discard trimmed reads that are shorter than "minlen"
                                [75]
          -N REMOVEN, --removeN REMOVEN
                                remove "N" bases [true]
          -c NCUTOFF, --Ncutoff NCUTOFF
                                with "removeN" option, N cutoff [0.1]
          -F FILTQ, --filtQ FILTQ
                                Filters sequences based on quality [true]
          --minQ MINQ           Minimum quality score to keep [20]
          --pminQ PMINQ         Minimum percent of bases [80]
          -q QCSTAT, --qcStat QCSTAT
                                generate QC statistic plot for seq
          -M MAPPING, --mapping MAPPING
                                read mapping [true]
          --hisat2index HISAT2INDEX
                                hisat2 index
          --orientations ORIENTATIONS
                                orientations
          --rnastrandness RNASTRANDNESS
                                rna strandness
          --gtf GTF             gtf file for annotation
          --drawCover DRAWCOVER
                                coverage of genome region [true]
          --genomebed GENOMEBED
                                coverage genome bed file
          --windowsize WINDOWSIZE
                                coverage window size [500000]
                                
        Links
        -----
        
        * `Project homepage <https://git-r3lab.uni.lu/zhi.zhang/rnaseqhs>`_
        * `Github page <https://git-r3lab.uni.lu/zhi.zhang/rnaseqhs>`_
            written by Zhi Zhang.
        
Keywords: rnaseq main
Platform: UNKNOWN
Classifier: Development Status :: 3 - Alpha
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python :: 3.6
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
