Read Genome

import modelseedpy
from modelseedpy.core.msgenome import MSGenome
from modelseedpy.core.rast_client import RastClient

genome = MS

rast = RastClient()

genome = MSGenome.from_fasta('GCF_000005845.2.faa', split=' ')

print('Number of features:', len(genome.features))

Number of features: 3

for f in genome.features:
    print(f.id, len(f.seq), f.description)

rast.annotate_genome(genome)

[{'execution_time': 1622756127.36331,
  'tool_name': 'kmer_search',
  'hostname': 'pear',
  'parameters': ['-a',
   '-g',
   200,
   '-m',
   5,
   '-d',
   '/opt/patric-common/data/kmer_metadata_v2',
   '-u',
   'http://pear.mcs.anl.gov:6100/query'],
  'id': '9CCA6D20-C4B3-11EB-A893-36A8BEF382BD'},
 {'parameters': ['annotate_hypothetical_only=1',
   'dataset_name=Release70',
   'kmer_size=8'],
  'hostname': 'pear',
  'tool_name': 'KmerAnnotationByFigfam',
  'id': '9CE3769E-C4B3-11EB-A893-36A8BEF382BD',
  'execution_time': 1622756127.52738},
 {'execute_time': 1622756127.88296,
  'hostname': 'pear',
  'parameters': [],
  'tool_name': 'annotate_proteins_similarity',
  'id': '9D19B7EA-C4B3-11EB-9714-71B3BDF382BD'}]

Equivalent call from the client it self

#genome, res = rast.annotate_genome_from_fasta('GCF_000005845.2_ASM584v2_protein.faa', split=' ')
#res

feature = genome.features.get_by_id('YP_588478.1')

feature.ontology_terms

{'RAST': 'DUF1435 domain-containing protein YjjZ [Escherichia coli str. K-12 substr. MG1655]'}

feature.add_ontology_term('')