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

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


[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.legacy_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.legacy_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.legacy_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