Metadata-Version: 2.1
Name: igv-reports
Version: 1.0.1
Summary: Creates self-contained html pages for visual variant review with IGV (igv.js).
Home-page: https://github.com/igvteam/igv-reports
Author: Jim Robinson
License: MIT
Description: # igv-reports
        
        Python application to generate self-contained igv.js pages that can be opened within a browser with "file" protocol. 
        The generated html page contains all data neccessary for IGV as uuencoded blobs.  
        
        ## Installation
        
        #### Prerequisites
        
        igv-reports requires Python 3.6 or greater and pip.  As with all Python projects use of a virtual enviornment is recommended.
        Instructions for creating a virtual environment using _conda_ are [below](#creating-a-virtual-environment) 
        
        
        #### Installing igv-reports
        
        ```bash
        pip install igv-reports
        ```
        
        igv-reports requires the package _pysam_ which should be installed automatically.  However on OSX this sometimes 
        fails due to missing dependent libraries.  This can be fixed following the procedure below, from the pysam 
        [docs](https://pysam.readthedocs.io/en/latest/installation.html#installation);  
        _"The recommended way to install pysam is through conda/bioconda. 
        This will install pysam from the bioconda channel and automatically makes sure that dependencies are installed. 
        Also, compilation flags will be set automatically, which will potentially save a lot of trouble on OS X."_
        
        ```bash
        conda config --add channels r
        conda config --add channels bioconda
        conda install pysam
        ```
        
        
        ## Creating a report
        
        A report consists of a table of sites or regions and an associated igv views for each site.  Reports are created with 
        the command line script ```create_report```.  Command line arguments are described below.
        Although _--tracks_ is optional, a typical report will include at least an alignment track
        (BAM or CRAM) file from which the variants were called.  
        
        **Arguments:**
        * Required
            * sites    _vcf or bed file of genomic sites_
            * fasta   _reference fasta file, must be indexed_
        * Optional
            * --tracks _space-delimited list of track files, see below for supported formats.  If both *tracks* and *track-config* are specified *tracks* will appear first._
            * --track-confg _file containing array of json configuration objects for igv.js tracks.  see the [igv.js wiki](https://github.com/igvteam/igv.js/wiki/Tracks-2.0) for more details.  This option allows customization of track parameters._
            * --ideogram _ideogram file in UCSC cytoIdeo format_
            * --template _html template file_
            * --output _output file name default="igvjs_viewer.html"_
            * --info-columns _space delimited list of VCF info field names to include in variant table_
            * --info-columns-prefixes _space delimited list of prefixes of VCF info field names to include in variant table_
            * --sample-columns _space delimited list of VCF sample/format field names to include in variant table_
            * --flanking _genomic region to include either side of variant, default=1000_
            * --standalone _embed all javascript referenced via ```<script>``` tags in the page_
        
        **Track file formats:**
        
        Currently supported track file formats are BAM, CRAM, VCF, BED, GFF3, and GTF.  FASTA. BAM, CRAM, and VCF  files must 
        be indexed.  Tabix is supported for other file types and it is recommended that all large files be indexed.   
        
        ## Examples
        
        Data for the examples are available for [download](https://s3.amazonaws.com/igv.org.test/reports/examples.zip).
        
        #### Creating a variant report from a VCF file:  
        
        ```bash
        
        create_report examples/variants/variants.vcf.gz https://s3.amazonaws.com/igv.broadinstitute.org/genomes/seq/hg38/hg38.fa --ideogram examples/variants/cytoBandIdeo.txt --flanking 1000 --info-columns GENE TISSUE TUMOR COSMIC_ID GENE SOMATIC --tracks examples/variants/variants.vcf.gz examples/variants/recalibrated.bam examples/variants/refGene.sort.bed.gz --output igvjs_viewer.html
        
        ```
        
        #### Createing a junction report from a splice-junction bed file
        
        ```bash
        create_report examples/junctions/Introns.38.bed https://s3.dualstack.us-east-1.amazonaws.com/igv.broadinstitute.org/genomes/seq/hg38/hg38.fa --type junction --ideogram examples/junctions/cytoBandIdeo.txt --output junctions.html --track-config examples/junctions/tracks.json --info-columns TCGA GTEx variant_name --title "Sample A"
        ```
        
        #### Converting genomic files to data URIs for use in igv.js 
        
        The script ```create_datauri`` converts the contents of a file to a data uri for use in igv.js.   The datauri will be
        printed to stdout.  *NOTE* It is not neccessary to run this script explicitly to create a report, it is documented here
        for use with stand-alone igv.js.   
        
        
        
        **Convert a gzipped vcf file to a datauri.**
        
        ```bash
        create_datauri examples/variants/variants.vcf.gz
        
        ```
        
        **Convert a slice of a remote cram file to a datauri.**
        
        ```bash
        create_datauri \
        --region 8:127,738,322-127,738,508 \
        https://s3.amazonaws.com/1000genomes/data/HG00096/alignment/HG00096.alt_bwamem_GRCh38DH.20150718.GBR.low_coverage.cram 
        ```
        
        
        ## Creating a virtual environment
        
        Instructions for creating a virtual environment using ```conda``` follow.
        
        #### 1. Install Anaconda:  https://docs.anaconda.com/anaconda/
        
        #### 2. Create a virtual environment
        
        ```bash
        conda create -n myenv python=3.7.1
        conda install -n myenv pip
        conda activate
        conda install pip
        ```
        
Keywords: igv,bioinformatics,genomics,visualization,variant
Platform: UNKNOWN
Classifier: Programming Language :: Python :: 3
Classifier: Development Status :: 4 - Beta 
Classifier: Intended Audience :: Science/Research
Classifier: Intended Audience :: Developers
Classifier: License :: OSI Approved :: MIT License
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics 
Description-Content-Type: text/markdown
