def _compare_proteomes(meth, genome1, genome2, out_proteome_cmp):
"""Start a job to run Blast between the proteomes of two genomes.
The comparison information includes best-bidirectional hits. [17]
:param genome1: Source genome1 ID [17.1]
:type genome1: kbtypes.KBaseGenomes.Genome
:ui_name genome1: Genome1 ID
:param genome2: Source genome2 ID [17.2]
:type genome2: kbtypes.KBaseGenomes.Genome
:ui_name genome2: Genome2 ID
:param out_proteome_cmp: Output proteome comparison ID. If empty, an ID will be chosen randomly. [17.3]
:type out_proteome_cmp: kbtypes.GenomeComparison.ProteomeComparison
:ui_name out_proteome_cmp: Output Proteome Comparison ID
:return: Output Proteome Comparison ID
:rtype: kbtypes.ProteomeComparison
:output_widget: GenomeComparisonWidget
"""
meth.stages = 1 # for reporting progress
token = os.environ['KB_AUTH_TOKEN']
workspace = os.environ['KB_WORKSPACE_ID']
if not out_proteome_cmp:
out_proteome_cmp = "proteome_cmp_" + ''.join([chr(random.randrange(0, 26) + ord('A')) for _ in xrange(8)])
cmpClient = GenomeComparison(url = service.URLS.genomeCmp, token = token)
blast_proteomes_params = {
'genome1ws': workspace,
'genome1id': genome1,
'genome2ws': workspace,
'genome2id': genome2,
'output_ws': workspace,
'output_id': out_proteome_cmp,
}
job_id = cmpClient.blast_proteomes(blast_proteomes_params)
return json.dumps({'ws_name': workspace, 'ws_id': out_proteome_cmp, 'job_id': job_id})
