Merge pull request #2939 from jj-umn/patch-4

API access to genome fasta index and sequence

lib/galaxy/webapps/galaxy/api/genomes.py

@@ -43,3 +43,35 @@ class GenomesController( BaseAPIController ):
         else:
             rval = self.app.genomes.chroms( trans, dbkey=id, num=num, chrom=chrom, low=low )
         return rval
+
+    @web.expose_api_raw_anonymous
+    def indexes(self, trans, id, **kwd):
+        """
+        GET /api/genomes/{id}/indexes?type={table name}
+
+        Returns all available indexes for a genome id for type={table name}
+        For instance, /api/genomes/hg19/indexes?type=fasta_indexes
+        """
+        index_extensions = {'fasta_indexes': '.fai'}
+        id = get_id( id, kwd.get( 'format', None ) )
+        index_type = kwd.get('type', None)
+
+        tbl_entries = self.app.tool_data_tables.data_tables[index_type].data
+        index_file_name = [x[-1] for x in tbl_entries if id in x].pop()
+
+        if_open = open(index_file_name + index_extensions[index_type], mode='r')
+        return if_open.read()
+
+    @web.expose_api_raw_anonymous
+    def sequences(self, trans, id, num=None, chrom=None, low=None, high=None, **kwd ):
+        """
+        GET /api/genomes/{id}/sequences
+
+        This is a wrapper for accepting sequence requests that
+        want a raw return, not json
+        """
+        id = get_id( id, kwd.get( 'format', None ) )
+        reference = is_true( kwd.get( 'reference', False ) )
+        assert reference
+        region = self.app.genomes.reference( trans, dbkey=id, chrom=chrom, low=low, high=high )
+        return region.sequence