{ "info": { "author": "Jim Robinson", "author_email": "", "bugtrack_url": null, "classifiers": [ "Development Status :: 4 - Beta", "Intended Audience :: Developers", "Intended Audience :: Science/Research", "License :: OSI Approved :: MIT License", "Programming Language :: Python :: 3", "Topic :: Scientific/Engineering :: Bio-Informatics" ], "description": "# igv-reports\n\nA Python application to generate self-contained HTML reports that consist of a table of genomic sites or regions and associated IGV views for each site.\nThe generated HTML page contains all data neccessary for IGV as uuencoded blobs. It can be opened within a web browser with the \"file\" protocol; no internet connection is required. \n\n\n## Installation\n\n#### Prerequisites\n\nigv-reports __requires Python 3.6__ or greater and __pip__. \n\nAs with all Python projects, use of a __virtual environment__ is recommended.\nInstructions for creating a virtual environment using ```conda``` follow.\n\n__1.__ Install Anaconda from https://docs.anaconda.com/anaconda/\n\n__2.__ Create a virtual environment\n\n```bash\nconda create -n igvreports python=3.7.1\nconda activate igvreports\n```\n\n#### Installing igv-reports\n\n```bash\npip install igv-reports\n```\n\nigv-reports requires the package _pysam_ which should be installed automatically. However on OSX this sometimes \nfails due to missing dependent libraries. This can be fixed following the procedure below, from the pysam \n[docs](https://pysam.readthedocs.io/en/latest/installation.html#installation); \n_\"The recommended way to install pysam is through conda/bioconda. \nThis will install pysam from the bioconda channel and automatically makes sure that dependencies are installed. \nAlso, compilation flags will be set automatically, which will potentially save a lot of trouble on OS X.\"_\n\n```bash\nconda config --add channels r\nconda config --add channels bioconda\nconda install pysam\n```\n\n## Creating a report\n\nA report consists of a table of sites or regions and an associated IGV views for each site. Reports are created with \nthe command line script ```create_report```. Command line arguments are described below.\nAlthough _--tracks_ is optional, a typical report will include at least an alignment track\n(BAM or CRAM) file from which the variants were called. \n\n**Arguments:**\n* Required\n * __sites__ VCF (tabix indexed vcf.gz file), BED, MAF, or generic tab delimited file of genomic variant sites.\n * __fasta__ Reference fasta file; must be indexed.\n\n* Required for generic tab delimited __sites__ file\n * __--begin__ INT. Column of start chromosomal position for __sites__ file. Used for generic tab delimited input.\n * __--end__ INT. Column of end chromosomal position for __sites__. Used for generic tab delimited input.\n * __--sequence__ INT. Column of sequence (chromosome) name.\n\n* Optional for generic tab delimited __sites__ file\n * __--zero-based__ Specify that the position in the __sites__ file is 0-based (e.g. UCSC files) rather than 1-based. Default is ```false```.\n\n* Optional\n * __--tracks__ LIST. Space-delimited list of track files, see below for supported formats. If both *tracks* and *track-config* are specified *tracks* will appear first by default.\n * __--track-config__ FILE. 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. When using this option, the track ```url``` and ```indexURL``` properties should be set to the paths to the respective files.\n * __--ideogram__ FILE. Ideogram file in UCSC cytoIdeo format.\n * __--template__ FILE. HTML template file.\n * __--output__ FILE. Output file name; default=\"igvjs_viewer.html\".\n * __--info-columns__ LIST. Space delimited list of field names to includ in the variant table. If __sites_ is a VCF file these are the info field names. If __sites__ is a tab delimited format these are column names.\n * __--info-columns-prefixes__ LIST. Space delimited list of prefixes of VCF info field names to include in variant table.\n * __--sample-columns__ LIST. Space delimited list of VCF sample/format field names to include in variant table.\n * __--flanking__ INT. Genomic region to include either side of variant; default=1000.\n * __--standalone__ Embed all JavaScript referenced via ```