.. PythonPackages Third-party packages ******************** This page lists the third-party packages/modules built upon the `MyVariant.info `_ services. .. _myvariant_python: MyVariant python module ----------------------- "`myvariant `_" is an easy-to-use Python wrapper to access `MyVariant.info `_ services. You can install it easily using either `pip `_ or `easy_install `_:: pip install myvariant #this is preferred or:: easy_install myvariant This is a brief example: .. code-block :: python In [1]: import myvariant In [2]: mv = myvariant.MyVariantInfo() In [3]: mv.getvariant('chr1:g.35367G>A') Out[3]: {'_id': 'chr1:g.35367G>A', '_version': 1, 'cadd': {'alt': 'A', 'annotype': 'NonCodingTranscript', 'bstatistic': 994, 'chmm': {'bivflnk': 0.0, 'enh': 0.0, 'enhbiv': 0.0, 'het': 0.0, 'quies': 1.0, 'reprpc': 0.0, 'reprpcwk': 0.0, 'tssa': 0.0, 'tssaflnk': 0.0, 'tssbiv': 0.0, 'tx': 0.0, 'txflnk': 0.0, 'txwk': 0.0, 'znfrpts': 0.0}, 'chrom': 1, 'consdetail': 'non_coding_exon,nc', 'consequence': 'NONCODING_CHANGE', 'consscore': 5, 'cpg': 0.03, 'dna': {'helt': -2.04, 'mgw': 0.01, 'prot': 1.54, 'roll': -0.63}, 'encode': {'exp': 31.46, 'h3k27ac': 23.44, 'h3k4me1': 23.8, 'h3k4me3': 8.6}, 'exon': '2/3', 'fitcons': 0.577621, 'gc': 0.48, 'gene': {'cds': {'cdna_pos': 476, 'rel_cdna_pos': 0.4}, 'feature_id': 'ENST00000417324', 'gene_id': 'ENSG00000237613', 'genename': 'FAM138A'}, 'gerp': {'n': 1.29, 's': -0.558}, 'isknownvariant': 'FALSE', 'istv': 'FALSE', 'length': 0, 'mapability': {'20bp': 0, '35bp': 0}, 'min_dist_tse': 122, 'min_dist_tss': 707, 'mutindex': 70, 'phast_cons': {'mammalian': 0.003, 'primate': 0.013, 'vertebrate': 0.003}, 'phred': 1.493, 'phylop': {'mammalian': -0.155, 'primate': 0.151, 'vertebrate': -0.128}, 'pos': 35367, 'rawscore': -0.160079, 'ref': 'G', 'scoresegdup': 0.99, 'segway': 'D', 'type': 'SNV'}, 'snpeff': {'ann': [{'effect': 'non_coding_exon_variant', 'feature_id': 'NR_026818.1', 'feature_type': 'transcript', 'gene_id': 'FAM138A', 'gene_name': 'FAM138A', 'hgvs_c': 'n.476C>T', 'putative_impact': 'MODIFIER', 'rank': '2', 'total': '3', 'transcript_biotype': 'Noncoding'}, {'effect': 'non_coding_exon_variant', 'feature_id': 'NR_026820.1.2', 'feature_type': 'transcript', 'gene_id': 'FAM138F.2', 'gene_name': 'FAM138F', 'hgvs_c': 'n.476C>T', 'putative_impact': 'MODIFIER', 'rank': '2', 'total': '3', 'transcript_biotype': 'Noncoding'}]}, 'vcf': {'alt': 'A', 'position': '35367', 'ref': 'G'}} See https://pypi.python.org/pypi/myvariant for more details. MyVariant R package ------------------- An R wrapper for the MyVariant.info API is available in Bioconductor since v3.2. To install:: source("https://bioconductor.org/biocLite.R") biocLite("myvariant") To view documentation for your installation, enter R and type:: browseVignettes("myvariant") For more information, visit the `Bioconductor myvariant page `_. MyVariant Node.js package ------------------------- `myvariantjs `_ is a `Node.js `_ wrapper for the MyVariant.info API, developed and maintained by `Larry Hengl `_. To install:: npm install myvariantjs --save Some brief usage examples:: var mv = require('myvariantjs'); mv.getvariant('chr9:g.107620835G>A'); mv.getvariant('chr9:g.107620835G>A', ['dbnsfp.genename', 'cadd.phred']); mv.getvariants("chr1:g.866422C>T,chr1:g.876664G>A,chr1:g.69635G>C"); // string of delimited ids mv.getvariants(["chr1:g.866422C>T", "chr1:g.876664G>A","chr1:g.69635G>C"]); mv.query("chr1:69000-70000", {fields:'dbnsfp.genename'}); mv.query("dbsnp.rsid:rs58991260", {fields:'dbnsfp'}); mv.querymany(['rs58991260', 'rs2500'], 'dbsnp.rsid'); mv.querymany(['RCV000083620', 'RCV000083611', 'RCV000083584'], 'clinvar.rcv_accession'); For more information, visit its `API and usage docs `_, and its `github code repository `_. You can also check out `this neat demo application `_ developed by Larry using this `myvariantjs `_ package. Another MyVariant.info python module ------------------------------------ This is another python wrapper of MyVariant.info services created by `Brian Schrader `_. The repository is available `here `_. You can install this package with `PyPI `_ like this:: pip install myvariant-api A JBrowse plugin for MyVariant.info and MyGene.info ---------------------------------------------------- `JBrowse `_ provides a fast, embeddable genome browser built completely with JavaScript and HTML5. `Colin `_ from the JBrowse team made a very nice plugin to visualize the gene and variant annotations in JBrowse Genome Browser, using the data served from both `MyGene.info `_ and `MyVariant.info `_ APIs. * Live demo To see it live, here is `the demo site `_. It has been tested with hg38, hg19, and zebrafish and has mygene.info and myvariant.info integrations * Source code https://github.com/elsiklab/myvariantviewer * A screenshot .. image:: /_static/jbrowse-plugin-screenshot-small.png :target: ../_static/jbrowse-plugin-screenshot.png :align: center .. raw:: html