Metadata-Version: 1.1
Name: pyensembl
Version: 0.5.1
Summary: Python interface to ensembl reference genome metadata
Home-page: https://github.com/hammerlab/ensembl
Author: Alex Rubinsteyn
Author-email: alex {dot} rubinsteyn {at} mssm {dot} edu
License: http://www.apache.org/licenses/LICENSE-2.0.html
Description: pyensembl
        =========
        
        Python interface to Ensembl reference genome metadata (exons,
        transcripts, &c)
        
        .. code:: 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')
        
        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).
        
        Gene Names
        ----------
        
        ``gene_names()`` : returns all gene names in the annotation database
        
        ``gene_names_on_contig(contig)`` : all gene names on a particular
        chromosome/contig
        
        ``gene_names_at_locus(contig, position, end=None, strand=None)`` : names
        of genes overlapping with the given locus (returns a list to account for
        overlapping genes)
        
        ``gene_name_of_gene_id(gene_id)`` : name of gene with given ID
        
        ``gene_name_of_transcript_id(transcript_id)`` : name of gene associated
        with given transcript ID
        
        ``gene_name_of_transcript_name(transcript_name)`` : name of gene
        associated with given transcript name
        
        ``gene_name_of_exon_id(exon_id)`` : name of gene associated with given
        exon ID
        
        Gene IDs
        --------
        
        ``gene_ids(contig=None, strand=None)`` : all gene IDs in the annotation
        database
        
        ``gene_id_of_gene_name(gene_name)`` : translate Ensembl gene ID to its
        corresponding name
        
        Transcript Names
        ----------------
        
        ``transcript_names(contig=None, strand=None)`` : all transcript names in
        the annotation database
        
        Transcript IDs
        --------------
        
        ``transcript_ids(contig=None, strand=None)`` : returns all transcript
        IDs in the annotation database
        
        ``transcript_ids_of_gene_id(gene_id)`` : return IDs of all transcripts
        associated with given gene ID
        
        ``transcript_ids_of_gene_name(gene_name)`` : return IDs of all
        transcripts associated with given gene name
        
        ``transcript_id_of_transcript_name(transcript_name)`` : translate
        transcript name to its ID
        
        ``transcript_ids_of_exon_id(exon_id)`` : return IDs of all transcripts
        associatd with given exon ID
        
        Exon IDs
        --------
        
        ``exon_ids(contig=None, strand=None)`` : returns all transcript IDs in
        the annotation database
        
        ``exon_ids_of_gene_id(gene_id)``
        
        ``exon_ids_of_gene_name(gene_name)``
        
        ``exon_ids_of_transcript_name(transcript_name)``
        
        ``exon_ids_of_transcript_id(transcript_id)``
        
        Locations
        ---------
        
        These functions currently assume that each gene maps to a single unique
        location, which is invalid both with heavily copied genes (e.g.
        `U1 <http://en.wikipedia.org/wiki/U1_spliceosomal_RNA>`__) and with
        polymorphic regions (e.g. HLA genes).
        
        ``location_of_gene_name(gene_name)``
        
        ``location_of_gene_id(gene_id)``
        
        ``location_of_transcript_id(transcript_id)``
        
        ``location_of_exon_id(exon_id)``
        
        Start Codons
        ------------
        
        ``start_codon_of_transcript_id``
        
        ``start_codon_of_transcript_name``
        
        Stop Codons
        -----------
        
        ``stop_codon_of_transcript_id``
        
        ``stop_codon_of_transcript_name``
        
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
