def get_ensembl_organism_names(self, organism): """returns the specified organism name file contents, using the EnsEMBL path""" logging.info('RSAT - get_ensembl_organism_names(%s)', organism) return util.read_url("/".join([self.base_url, RsatDatabase.DIR_PATH, organism + '_EnsEMBL', RsatDatabase.ORGANISM_NAMES_PATH]))
def get_obo_url(self,version): url = 'http://viewvc.geneontology.org/viewvc/GO-SVN/ontology-releases/%s/' %(version) body = util.read_url(url) revision_pat = re.compile(r'<a href="/viewvc/GO-SVN\?view=revision&revision=(\d+)"') m = revision_pat.search(body) rev = m.group(1) obo_url = 'http://viewvc.geneontology.org/viewvc/GO-SVN/ontology-releases/%s/go-basic.obo?revision=%s' %(version,rev) return obo_url
CHECKPOINT_INTERVAL = 100 CHECKPOINT_FILE = None if __name__ == '__main__': print('cMonkey (Python port) (c) 2011-2012, Institute for Systems Biology') print('This program is licensed under the General Public License V3.') print('See README and LICENSE for details.\n') if len(sys.argv) < 3: print('Usage: ./run_cmonkey.sh <organism-code> <ratio-file> ' + '[string-file] [checkpoint-file]') else: string_file=None if len(sys.argv) > 3: string_file = sys.argv[3] if len(sys.argv) > 4: CHECKPOINT_FILE = sys.argv[4] matrix_factory = dm.DataMatrixFactory([dm.nochange_filter, dm.center_scale_filter]) matrix_filename = sys.argv[2] if matrix_filename.startswith('http://'): indata = util.read_url(matrix_filename) infile = util.DelimitedFile.create_from_text(indata, has_header=True, quote='\"') else: infile = util.DelimitedFile.read(matrix_filename, has_header=True, quote='\"') matrix = matrix_factory.create_from(infile) cmonkey_run = cmonkey_run.CMonkeyRun(sys.argv[1], matrix, string_file=string_file) # num_cluster=250 for halo_ref cmonkey_run.run()