Warning

This document is for an old release of Galaxy. You can alternatively view this page in the latest release if it exists or view the top of the latest release's documentation.

Source code for galaxy.webapps.galaxy.api.genomes

from galaxy import web
from galaxy.web.base.controller import BaseAPIController
from galaxy.web.framework.helpers import is_true


[docs]def get_id(base, format): if format: return "%s.%s" % (base, format) else: return base
[docs]class GenomesController(BaseAPIController): """ RESTful controller for interactions with genome data. """
[docs] @web.expose_api_anonymous def index(self, trans, **kwd): """ GET /api/genomes: returns a list of installed genomes """ return self.app.genomes.get_dbkeys(trans, **kwd)
[docs] @web.json def show(self, trans, id, num=None, chrom=None, low=None, high=None, **kwd): """ GET /api/genomes/{id} Returns information about build <id> """ # Process kwds. id = get_id(id, kwd.get('format', None)) reference = is_true(kwd.get('reference', False)) # Return info. rval = None if reference: region = self.app.genomes.reference(trans, dbkey=id, chrom=chrom, low=low, high=high) rval = {'dataset_type': 'refseq', 'data': region.sequence} else: rval = self.app.genomes.chroms(trans, dbkey=id, num=num, chrom=chrom, low=low) return rval
[docs] @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()
[docs] @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