Merge pull request #38 from hammerlab/EnsemblRelease_and_README_cleanup

deleted location methods from EnsemblRelease, cleaned up...

Author: iskandr

README.md

@@ -39,13 +39,31 @@ 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
+## Genes
 
-`gene_names()`
-: returns all gene names in the annotation database
+`genes(contig=None, strand=None)`
+: returns list of Gene objects, optionally restricted to a particular contig
+or strand.
 
-`gene_names_on_contig(contig)`
-: all gene names on a particular chromosome/contig
+`genes_at_locus(contig, position, end=None, strand=None)`
+: returns 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='-'`.
+
+`gene_by_id(gene_id)`
+: return Gene object for given Ensembl gene ID (e.g. "ENSG00000068793")
+
+`gene_names(contig=None, strand=None)`
+: returns all gene names in the annotation database, optionally restricted
+to a particular contig or strand.
+
+`genes_by_name(gene_name)`
+ : 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.
+
+`gene_by_protein_id(protein_id)`
+: find Gene associated with the given Ensembl protein ID (e.g. "ENSP00000350283")
 
 `gene_names_at_locus(contig, position, end=None, strand=None)`
 : names of genes overlapping with the given locus
@@ -63,23 +81,28 @@ these genomic elements (contig, start position, end position, strand).
 `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
+`gene_ids_of_gene_name(gene_name)`
+: all Ensembl gene IDs with the given name
 
 
-## Transcript Names
+## Transcripts
+
+`transcripts(contig=None, strand=None)`
+: returns list of Transcript objects for all transcript entries in the
+Ensembl database, optionally restricted to a particular contig or strand.
+
+`transcript_by_id(transcript_id)`
+: construct Transcript object for given Ensembl transcript ID (e.g. "ENST00000369985")
+
+`transcripts_by_name(transcript_name)`
+: returns list of Transcript objects for every transcript matching the given name.
 
 `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
 
@@ -89,14 +112,14 @@ these genomic elements (contig, start position, end position, strand).
 `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_transcript_name(transcript_name)`
+: find all Ensembl transcript IDs with the given name
 
 `transcript_ids_of_exon_id(exon_id)`
 : return IDs of all transcripts associatd with given exon ID
 
 
-## Exon IDs
+## Exons
 
 `exon_ids(contig=None, strand=None)`
 : returns all transcript IDs in the annotation database
@@ -109,32 +132,3 @@ these genomic elements (contig, start position, end position, strand).
 
 `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(transcript_id)`
-
-`start_codon_of_transcript_name(transcript_id)`
-
-
-## Stop Codons
-
-`stop_codon_of_transcript_id(transcript_id)`
-
-`stop_codon_of_transcript_name(transcript_name)`

pyensembl/database.py

@@ -4,7 +4,7 @@
 import sqlite3
 
 from .common import CACHE_SUBDIR
-from .locus import normalize_chromosome, normalize_strand
+from .locus import normalize_chromosome, normalize_strand, Locus
 from .type_checks import require_integer, require_string
 
 import datacache
@@ -159,7 +159,7 @@ def column_values_at_locus(
             SELECT %s%s
             FROM ensembl
             WHERE feature = ?
-            AND seqname=?
+            AND seqname= ?
             AND start <= ?
             AND end >= ?
 
@@ -323,3 +323,66 @@ def query_distinct_on_contig(self, column_name, feature, contig):
             feature=feature,
             contig=contig,
             distinct=True)
+
+    def query_loci(self, filter_column, filter_value, feature):
+        """
+        Query for loci satisfying a given filter and feature type.
+
+
+        Parameters
+        ----------
+        filter_column : str
+            Name of column to filter results by.
+
+        filter_value : str
+            Only return loci which have this value in the their filter_column.
+
+        feature : str
+            Feature names such as 'transcript', 'gene', and 'exon'
+
+        Returns list of Locus objects
+        """
+        # list of values containing (contig, start, stop, strand)
+        result_tuples = self.query(
+            select_column_names=["seqname", "start", "end", "strand"],
+            filter_column=property_name,
+            filter_value=property_value,
+            feature=feature,
+            distinct=True,
+            required=True)
+        return [
+            Locus(contig, start, end, strand)
+            for (contig, start, end, strand)
+            in result_tuples
+        ]
+
+    def query_locus(self, filter_column, filter_value, feature):
+        """
+        Query for unique locus, raises error if missing or more than
+        one locus in the database.
+
+        Parameters
+        ----------
+        filter_column : str
+            Name of column to filter results by.
+
+        filter_value : str
+            Only return loci which have this value in the their filter_column.
+
+        feature : str
+            Feature names such as 'transcript', 'gene', and 'exon'
+
+        Returns single Locus object.
+        """
+        loci = self.query_loci(
+            filter_column=filter_column,
+            filter_value=filter_value,
+            feature=feature)
+
+        if len(loci) == 0:
+            raise ValueError("Couldn't find locus for %s with %s = %s" % (
+                feature, filter_column, filter_value))
+        elif len(loci) > 1:
+            raise ValueError("Too many loci for %s with %s = %s: %s" % (
+                feature, filter_column, filter_value, loci))
+        return loci[0]