{
"info": {
"author": "Alex Rubinsteyn",
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"classifiers": [
"Development Status :: 3 - Alpha",
"Environment :: Console",
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"License :: OSI Approved :: Apache Software License",
"Operating System :: OS Independent",
"Programming Language :: Python",
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"description": "\n ![\"Build](\"https://travis-ci.org/openvax/pyensembl.svg?branch=master\")
\n\n\n ![\"Coverage](\"https://coveralls.io/repos/openvax/pyensembl/badge.svg?branch=master&service=github\")
\n\n\n ![\"PyPI\"](\"https://img.shields.io/pypi/v/pyensembl.svg?maxAge=1000\")
\n\n\n\nPyEnsembl\n=======\nPyEnsembl is a Python interface to [Ensembl](http://www.ensembl.org) reference genome metadata such as exons and transcripts. PyEnsembl downloads [GTF](https://en.wikipedia.org/wiki/Gene_transfer_format) and [FASTA](https://en.wikipedia.org/wiki/FASTA_format) files from the [Ensembl FTP server](ftp://ftp.ensembl.org) and loads them into a local database. PyEnsembl can also work with custom reference data specified using user-supplied GTF and FASTA files. \n\n# Example Usage\n\n```python\nfrom pyensembl import EnsemblRelease\n\n# release 77 uses human reference genome GRCh38\ndata = EnsemblRelease(77)\n\n# will return ['HLA-A']\ngene_names = data.gene_names_at_locus(contig=6, position=29945884)\n\n# get all exons associated with HLA-A\nexon_ids = data.exon_ids_of_gene_name('HLA-A')\n```\n\n# Installation\n\nYou can install PyEnsembl using [pip](https://pip.pypa.io/en/latest/quickstart.html):\n\n```sh\npip install pyensembl\n```\n\nThis should also install any required packages, such as [datacache](https://github.com/openvax/datacache) and\n[BioPython](http://biopython.org/).\n\nBefore using PyEnsembl, run the following command to download and install\nEnsembl data:\n\n```\npyensembl install --release --species \n```\n\nFor example, `pyensembl install --release 75 76 --species human` will download and install all\nhuman reference data from Ensembl releases 75 and 76.\n\nAlternatively, you can create the `EnsemblRelease` object from inside a Python\nprocess and call `ensembl_object.download()` followed by `ensembl_object.index()`.\n\n## Cache Location\nBy default, PyEnsembl uses the platform-specific `Cache` folder\nand caches the files into the `pyensembl` sub-directory.\nYou can override this default by setting the environment key `PYENSEMBL_CACHE_DIR`\nas your preferred location for caching:\n\n```sh\nexport PYENSEMBL_CACHE_DIR=/custom/cache/dir\n```\n\nor\n\n```python\nimport os\n\nos.environ['PYENSEMBL_CACHE_DIR'] = '/custom/cache/dir'\n# ... PyEnsembl API usage\n```\n\n# Non-Ensembl Data\n\nPyEnsembl also allows arbitrary genomes via the specification\nof local file paths or remote URLs to both Ensembl and non-Ensembl GTF\nand FASTA files. (Warning: GTF formats can vary, and handling of\nnon-Ensembl data is still very much in development.)\n\nFor example:\n\n```python\ndata = Genome(\n reference_name='GRCh38',\n annotation_name='my_genome_features',\n gtf_path_or_url='/My/local/gtf/path_to_my_genome_features.gtf')\n# parse GTF and construct database of genomic features\ndata.index()\ngene_names = data.gene_names_at_locus(contig=6, position=29945884)\n```\n\n# API\n\nThe `EnsemblRelease` object has methods to let you access all possible\ncombinations of the annotation features *gene\\_name*, *gene\\_id*,\n*transcript\\_name*, *transcript\\_id*, *exon\\_id* as well as the location of\nthese genomic elements (contig, start position, end position, strand).\n\n## Genes\n\n\n- genes(contig=None, strand=None)
\n- Returns a list of Gene objects, optionally restricted to a particular contig\nor strand.
\n\n- genes_at_locus(contig, position, end=None, strand=None)
\n- Returns a list of Gene objects overlapping a particular position on a contig,\noptionally extend into a range with the end parameter and restrict to\nforward or backward strand by passing strand='+' or strand='-'.
\n\n- gene_by_id(gene_id)
\n- Return a Gene object for given Ensembl gene ID (e.g. \"ENSG00000068793\").
\n\n- gene_names(contig=None, strand=None)
\n- Returns all gene names in the annotation database, optionally restricted\nto a particular contig or strand.
\n\n- genes_by_name(gene_name)
\n- Get all the unqiue genes with the given name (there might be multiple\ndue to copies in the genome), return a list containing a Gene object for each\ndistinct ID.
\n\n- gene_by_protein_id(protein_id)
\n- Find Gene associated with the given Ensembl protein ID (e.g. \"ENSP00000350283\")
\n\n- gene_names_at_locus(contig, position, end=None, strand=None)\n
\n- Names of genes overlapping with the given locus, optionally restricted by strand.\n(returns a list to account for overlapping genes)
\n\n- gene_name_of_gene_id(gene_id)\n
\n- Returns name of gene with given genen ID.
\n\n- gene_name_of_transcript_id(transcript_id)\n
- Returns name of gene associated with given transcript ID.
\n\n- gene_name_of_transcript_name(transcript_name)\n
\n- Returns name of gene associated with given transcript name.
\n\n- gene_name_of_exon_id(exon_id)\n
- Returns name of gene associated with given exon ID.
\n\n- gene_ids(contig=None, strand=None)\n
\n- Return all gene IDs in the annotation database, optionally restricted by\nchromosome name or strand.
\n\n- gene_ids_of_gene_name(gene_name)\n
\n- Returns all Ensembl gene IDs with the given name.
\n\n
\n\n## Transcripts\n\n\n- transcripts(contig=None, strand=None)
\n- Returns a list of Transcript objects for all transcript entries in the\nEnsembl database, optionally restricted to a particular contig or strand.
\n\n- transcript_by_id(transcript_id)
\n- Construct a Transcript object for given Ensembl transcript ID (e.g. \"ENST00000369985\")
\n\n- transcripts_by_name(transcript_name)
\n- Returns a list of Transcript objects for every transcript matching the given name.
\n\n- transcript_names(contig=None, strand=None)
\n- Returns all transcript names in the annotation database.
\n\n- transcript_ids(contig=None, strand=None)
\n- Returns all transcript IDs in the annotation database.
\n\n- transcript_ids_of_gene_id(gene_id)
\n- Return IDs of all transcripts associated with given gene ID.
\n\n- transcript_ids_of_gene_name(gene_name)
\n- Return IDs of all transcripts associated with given gene name.
\n\n- transcript_ids_of_transcript_name(transcript_name)
\n- Find all Ensembl transcript IDs with the given name.
\n\n- transcript_ids_of_exon_id(exon_id)
\n- Return IDs of all transcripts associatd with given exon ID.
\n
\n\n## Exons\n\n\n- exon_ids(contig=None, strand=None)
\n- Returns a list of exons IDs in the annotation database, optionally restricted\nby the given chromosome and strand.
\n\n- exon_ids_of_gene_id(gene_id)
\n- Returns a list of exon IDs associated with a given gene ID.
\n\n- exon_ids_of_gene_name(gene_name)
\n- Returns a list of exon IDs associated with a given gene name.
\n\n- exon_ids_of_transcript_id(transcript_id)
\n- Returns a list of exon IDs associated with a given transcript ID.
\n\n- exon_ids_of_transcript_name(transcript_name)
\n- Returns a list of exon IDs associated with a given transcript name.
\n
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