Metadata-Version: 2.1
Name: pyensembl
Version: 1.8.1
Summary: Python interface to ensembl reference genome metadata
Home-page: https://github.com/openvax/pyensembl
Author: Alex Rubinsteyn
Author-email: alex.rubinsteyn@mssm.edu
License: http://www.apache.org/licenses/LICENSE-2.0.html
Description: <a href="https://travis-ci.org/openvax/pyensembl">
            <img src="https://travis-ci.org/openvax/pyensembl.svg?branch=master" alt="Build Status" />
        </a>
        <a href="https://coveralls.io/github/openvax/pyensembl?branch=master">
            <img src="https://coveralls.io/repos/openvax/pyensembl/badge.svg?branch=master&service=github" alt="Coverage Status" />
        </a>
        <a href="https://pypi.python.org/pypi/pyensembl/">
            <img src="https://img.shields.io/pypi/v/pyensembl.svg?maxAge=1000" alt="PyPI" />
        </a>
        
        
        PyEnsembl
        =======
        PyEnsembl 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. 
        
        # Example Usage
        
        ```python
        from pyensembl import EnsemblRelease
        
        # release 77 uses human reference genome GRCh38
        data = EnsemblRelease(77)
        
        # will return ['HLA-A']
        gene_names = data.gene_names_at_locus(contig=6, position=29945884)
        
        # get all exons associated with HLA-A
        exon_ids  = data.exon_ids_of_gene_name('HLA-A')
        ```
        
        # Installation
        
        You can install PyEnsembl using [pip](https://pip.pypa.io/en/latest/quickstart.html):
        
        ```sh
        pip install pyensembl
        ```
        
        This should also install any required packages, such as [datacache](https://github.com/openvax/datacache) and
        [BioPython](http://biopython.org/).
        
        Before using PyEnsembl, run the following command to download and install
        Ensembl data:
        
        ```
        pyensembl install --release <list of Ensembl release numbers> --species <species-name>
        ```
        
        For example, `pyensembl install --release 75 76 --species human` will download and install all
        human reference data from Ensembl releases 75 and 76.
        
        Alternatively, you can create the `EnsemblRelease` object from inside a Python
        process and call `ensembl_object.download()` followed by `ensembl_object.index()`.
        
        ## Cache Location
        By default, PyEnsembl uses the platform-specific `Cache` folder
        and caches the files into the `pyensembl` sub-directory.
        You can override this default by setting the environment key `PYENSEMBL_CACHE_DIR`
        as your preferred location for caching:
        
        ```sh
        export PYENSEMBL_CACHE_DIR=/custom/cache/dir
        ```
        
        or
        
        ```python
        import os
        
        os.environ['PYENSEMBL_CACHE_DIR'] = '/custom/cache/dir'
        # ... PyEnsembl API usage
        ```
        
        # Non-Ensembl Data
        
        PyEnsembl also allows arbitrary genomes via the specification
        of local file paths or remote URLs to both Ensembl and non-Ensembl GTF
        and FASTA files. (Warning: GTF formats can vary, and handling of
        non-Ensembl data is still very much in development.)
        
        For example:
        
        ```python
        data = Genome(
            reference_name='GRCh38',
            annotation_name='my_genome_features',
            gtf_path_or_url='/My/local/gtf/path_to_my_genome_features.gtf')
        # parse GTF and construct database of genomic features
        data.index()
        gene_names = data.gene_names_at_locus(contig=6, position=29945884)
        ```
        
        # API
        
        The `EnsemblRelease` object has methods to let you access all possible
        combinations of the annotation features *gene\_name*, *gene\_id*,
        *transcript\_name*, *transcript\_id*, *exon\_id* as well as the location of
        these genomic elements (contig, start position, end position, strand).
        
        ## Genes
        
        <dl>
        <dt>genes(contig=None, strand=None)</dt>
        <dd>Returns a list of Gene objects, optionally restricted to a particular contig
        or strand.</dd>
        
        <dt>genes_at_locus(contig, position, end=None, strand=None)</dt>
        <dd>Returns a list of Gene objects overlapping a particular position on a contig,
        optionally extend into a range with the end parameter and restrict to
        forward or backward strand by passing strand='+' or strand='-'.</dd>
        
        <dt>gene_by_id(gene_id)</dt>
        <dd>Return a Gene object for given Ensembl gene ID (e.g. "ENSG00000068793").</dd>
        
        <dt>gene_names(contig=None, strand=None)</dt>
        <dd>Returns all gene names in the annotation database, optionally restricted
        to a particular contig or strand.</dd>
        
        <dt>genes_by_name(gene_name)</dt>
        <dd>Get all the unqiue genes with the given name (there might be multiple
        due to copies in the genome), return a list containing a Gene object for each
        distinct ID.</dd>
        
        <dt>gene_by_protein_id(protein_id)</dt>
        <dd>Find Gene associated with the given Ensembl protein ID (e.g. "ENSP00000350283")</dd>
        
        <dt>gene_names_at_locus(contig, position, end=None, strand=None)
        </dt>
        <dd>Names of genes overlapping with the given locus, optionally restricted by strand.
        (returns a list to account for overlapping genes)</dd>
        
        <dt>gene_name_of_gene_id(gene_id)
        </dt>
        <dd>Returns name of gene with given genen ID.</dd>
        
        <dt>gene_name_of_transcript_id(transcript_id)
        </dt><dd>Returns name of gene associated with given transcript ID.</dd>
        
        <dt>gene_name_of_transcript_name(transcript_name)
        </dt>
        <dd>Returns name of gene associated with given transcript name.</dd>
        
        <dt>gene_name_of_exon_id(exon_id)
        </dt><dd>Returns name of gene associated with given exon ID.</dd>
        
        <dt>gene_ids(contig=None, strand=None)
        </dt>
        <dd>Return all gene IDs in the annotation database, optionally restricted by
        chromosome name or strand.</dd>
        
        <dt>gene_ids_of_gene_name(gene_name)
        </dt>
        <dd>Returns all Ensembl gene IDs with the given name.</dd>
        
        </dl>
        
        ## Transcripts
        
        <dl>
        <dt>transcripts(contig=None, strand=None)</dt>
        <dd>Returns a list of Transcript objects for all transcript entries in the
        Ensembl database, optionally restricted to a particular contig or strand.</dd>
        
        <dt>transcript_by_id(transcript_id)</dt>
        <dd>Construct a Transcript object for given Ensembl transcript ID (e.g. "ENST00000369985")</dd>
        
        <dt>transcripts_by_name(transcript_name)</dt>
        <dd>Returns a list of Transcript objects for every transcript matching the given name.</dd>
        
        <dt>transcript_names(contig=None, strand=None)</dt>
        <dd>Returns all transcript names in the annotation database.</dd>
        
        <dt>transcript_ids(contig=None, strand=None)</dt>
        <dd>Returns all transcript IDs in the annotation database.</dd>
        
        <dt>transcript_ids_of_gene_id(gene_id)</dt>
        <dd>Return IDs of all transcripts associated with given gene ID.</dd>
        
        <dt>transcript_ids_of_gene_name(gene_name)</dt>
        <dd>Return IDs of all transcripts associated with given gene name.</dd>
        
        <dt>transcript_ids_of_transcript_name(transcript_name)</dt>
        <dd>Find all Ensembl transcript IDs with the given name.</dd>
        
        <dt>transcript_ids_of_exon_id(exon_id)</dt>
        <dd>Return IDs of all transcripts associatd with given exon ID.</dd>
        </dl>
        
        ## Exons
        
        <dl>
        <dt>exon_ids(contig=None, strand=None)</dt>
        <dd>Returns a list of exons IDs in the annotation database, optionally restricted
        by the given chromosome and strand.</dd>
        
        <dt>exon_ids_of_gene_id(gene_id)</dt>
        <dd>Returns a list of exon IDs associated with a given gene ID.</dd>
        
        <dt>exon_ids_of_gene_name(gene_name)</dt>
        <dd>Returns a list of exon IDs associated with a given gene name.</dd>
        
        <dt>exon_ids_of_transcript_id(transcript_id)</dt>
        <dd>Returns a list of exon IDs associated with a given transcript ID.</dd>
        
        <dt>exon_ids_of_transcript_name(transcript_name)</dt>
        <dd>Returns a list of exon IDs associated with a given transcript name.</dd>
        </dl>
        
Platform: UNKNOWN
Classifier: Development Status :: 3 - Alpha
Classifier: Environment :: Console
Classifier: Operating System :: OS Independent
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: Apache Software License
Classifier: Programming Language :: Python
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Description-Content-Type: text/markdown
