def _assemble_genome(meth, contig_file, out_genome):
"""This assembles a ContigSet into a Genome object in your workspace.
This should be run before trying to annotate a Genome. [2]
:param contig_file: A FASTA file with contig data [2.1]
:type contig_file: kbtypes.Unicode
:ui_name contig_file: Contig File ID
:param out_genome: Annotated output genome ID. If empty, an ID will be chosen randomly. [2.2]
:type out_genome: kbtypes.KBaseGenomes.Genome
:ui_name out_genome: Output Genome ID
:return: Assembled output genome ID
:rtype: kbtypes.KBaseGenomes.Genome
"""
# Regarding annotation, here's the latest. You want to take the fasta file that the above command
# created ("contigs.fasta"), and load it to the workspace as a contig set:
# "ga-loadfasta contigs.fasta -u MyContigs"
#
# -- this is already in the workspace by this point.
meth.stages = 4
token = os.environ['KB_AUTH_TOKEN']
workspace = os.environ['KB_WORKSPACE_ID']
# Setup invocation and double-check workspace
meth.advance("Initialize Annotation Service")
inv = InvocationService(service.URLS.invocation)
inv.run_pipeline("", "kbws-workspace " + workspace, [], 100, '/')
# Run sequence to genome.
meth.advance("Build Contig Set into a Genome")
inv.run_pipeline("", "ga-seq-to-genome " + contig_file + " --genomeid " + out_genome, [], 100, '/')
# 4. Fetch genome.
meth.advance("Fetching Genome for Display")
wsClient = workspaceService(service.URLS.workspace)
get_genome_params = {
'id': out_genome,
'type': 'Genome',
'workspace': workspace,
'auth': token,
}
genome_meta = wsClient.get_objectmeta(get_genome_params)
# 5. Pass it forward to the client.
meth.advance("Rendering Genome Information")
return json.dumps(genome_meta)
def _rm_file(f):
token = os.environ['KB_AUTH_TOKEN']
invo = InvocationService(url=URLS.invocation, token=token)
invo.remove_files("", '/', f)
return
def _mv_file(old, new):
token = os.environ['KB_AUTH_TOKEN']
invo = InvocationService(url=URLS.invocation, token=token)
invo.rename_file("", '/', old, new)
return
def _list_files(d):
token = os.environ['KB_AUTH_TOKEN']
invo = InvocationService(url=URLS.invocation, token=token)
_, files = invo.list_files("", '/', d)
return files
def _run_invo(cmd):
token = os.environ['KB_AUTH_TOKEN']
invo = InvocationService(url=URLS.invocation, token=token)
stdout, stderr = invo.run_pipeline("", cmd, [], 0, '/')
return "".join(stdout), "".join(stderr)
def _list_cmds():
token = os.environ['KB_AUTH_TOKEN']
invo = InvocationService(url=URLS.invocation, token=token)
return invo.valid_commands()
