def proteins_to_fasta(ws_url='https://ci.kbase.us/services/ws/'):
"""Write FASTA file from a genome reference.
Args:
ws_url: Workspace service URL
Returns:
Full path to output file
"""
ref = "ReferenceGenomeAnnotations/kb|g.166819"
# ref = "ReferenceGenomeAnnotations/kb|g.3899"
genome_annotation = GenomeAnnotationAPI(
token=os.environ.get('KB_AUTH_TOKEN'),
services={'workspace_service_url': ws_url},
ref=ref)
# Get all the proteins with the Data API
proteins = genome_annotation.get_proteins()
# Create an output file and write to it
outfile = '/tmp/166819_prot.fasta'
with open(outfile, 'w') as f:
for fasta_line in get_fasta(proteins):
f.write(fasta_line)
return outfile
def get_proteins(self, ctx, ref):
"""
Retrieve Protein data.
@return Mapping from protein ID to data about the protein.
:param ref: instance of type "ObjectReference"
:returns: instance of mapping from String to type "Protein_data" ->
structure: parameter "protein_id" of String, parameter
"protein_amino_acid_sequence" of String, parameter
"protein_function" of String, parameter "protein_aliases" of list
of String, parameter "protein_md5" of String, parameter
"protein_domain_locations" of list of String
"""
# ctx is the context object
# return variables are: returnVal
#BEGIN get_proteins
ga = GenomeAnnotationAPI_local(self.services, ctx['token'], ref)
returnVal = ga.get_proteins()
#END get_proteins
# At some point might do deeper type checking...
if not isinstance(returnVal, dict):
raise ValueError('Method get_proteins return value ' +
'returnVal is not type dict as required.')
# return the results
return [returnVal]
def run(ws_url='https://ci.kbase.us/services/ws/'):
#an example KBase reference genome
genomeref = "ReferenceGenomeAnnotations/kb|g.166819"
#creating a new GenomeAnnotation object
genome_annotation = GenomeAnnotationAPI(services = {"workspace_service_url": ws_url}, token=os.environ.get('KB_AUTH_TOKEN'), ref=genomeref)
#return all protein objects from this genome
proteins= genome_annotation.get_proteins()
#format the proteins in FASTA format
fasta = get_protein_fasta(proteins)
outfile = '166819_prot.fasta'
with open(outfile, 'w') as f:
f.write(fasta)
def proteins_to_fasta(ws_url='https://ci.kbase.us/services/ws/'):
"""Write FASTA file from a genome reference.
Args:
ws_url: Workspace service URL
Returns:
Full path to output file
"""
ref = "ReferenceGenomeAnnotations/kb|g.166819"
# ref = "ReferenceGenomeAnnotations/kb|g.3899"
genome_annotation = GenomeAnnotationAPI(
token=os.environ.get('KB_AUTH_TOKEN'), services={
'workspace_service_url': ws_url}, ref=ref)
# Get all the proteins with the Data API
proteins = genome_annotation.get_proteins()
# Create an output file and write to it
outfile = '/tmp/166819_prot.fasta'
with open(outfile, 'w') as f:
for fasta_line in get_fasta(proteins):
f.write(fasta_line)
return outfile
gto['contigobj']['source_id'] = extsource["external_source_id"]
gto['contigobj']['name'] = extsource["external_source_id"]
gto['source'] = extsource["external_source"]
gto['source_id'] = extsource["external_source_id"]
except Exception, e:
success = 0
features = [];
success = 0;
try:
features = ga.get_features();
success = 1
except Exception, e:
success = 0
prot = ga.get_proteins();
if success == 1:
for ftrid in features.keys():
ftrdata = features[ftrid]
if 'feature_type' in ftrdata.keys():
newfeature = {'id' : ftrid,'type' : ftrdata['feature_type'],'function' : "Unknown",'location' : []}
array = ftrid.split("_");
protid = 'protein_'+array[1];
if array[0] == 'CDS' and protid in prot.keys():
newfeature['protein_translation'] = prot[protid]['protein_amino_acid_sequence']
if 'feature_ontology_terms' in ftrdata.keys():
newfeature['ontology_terms'] = ftrdata['feature_ontology_terms']
if 'feature_function' in ftrdata.keys():
newfeature['function'] = ftrdata['feature_function']
if 'feature_dna_sequence' in ftrdata.keys():
