In [1]:

    

import os
os.environ['KB_AUTH_TOKEN'] = open('/tmp/kb_auth_token.txt').read().strip()


    

In [2]:

    

import biokbase
import biokbase.data_api.tests as tests
import biokbase.data_api.object
import biokbase.data_api.assembly
import biokbase.data_api.taxon
import biokbase.data_api.genome_annotation
import pandas as pd
import numpy as np
import qgrid as qg
qg.nbinstall()
import matplotlib
import matplotlib.pyplot as plt
from matplotlib.font_manager import FontProperties
%matplotlib inline


    

    




/Users/marcin/miniconda/envs/kbase-data-api/lib/python2.7/site-packages/IPython/utils/traitlets.py:5: UserWarning: IPython.utils.traitlets has moved to a top-level traitlets package.
  warn("IPython.utils.traitlets has moved to a top-level traitlets package.")

In [3]:

    

services = {
        "workspace_service_url": "https://ci.kbase.us/services/ws/",
        "shock_service_url": "https://ci.kbase.us/services/shock-api/",
    }
genome_annotation_api = biokbase.data_api.genome_annotation.GenomeAnnotationAPI(services, ref="testCondensedGenomeV2/GENOME_ANNOTATION_Escherichia_coli_K12")

###taxon api code
#taxon_ref=genome_annotation_api.get_taxon_ref()
#taxon_api = biokbase.data_api.taxon.TaxonAPI(services, ref=taxon_ref)
#gname=taxon_api(services, taxon_ref).get_scientific_name()
#print gname#genome_annotation_api.get_name()

gname=genome_annotation_api.get_name()
print gname

feature_types = genome_annotation_api.get_feature_types()
feat_count_data = np.random.random_integers(0, 1, 2)#.reshape(1, 1)
print "feat_count_data"
print feat_count_data
for i in range(1, len(feature_types)) :
    print feature_types[i]
    feature_ids=genome_annotation_api.get_feature_ids_by_type([feature_types[i]])
    feature_add=sum([len(feature_ids[x]) for x in feature_ids]) 
    feature_add =np.array([feature_add, feature_add])
    print feature_add
    feat_count_data = np.row_stack((feat_count_data, feature_add))
feat_count_data


    

    




GENOME_ANNOTATION_Escherichia_coli_K12
feat_count_data
[1 1]
opr
[649 649]
pbs
[7 7]
prm
[191 191]
rna
[170 170]
CDS
[4309 4309]






    
Out[3]:





array([[   1,    1],
       [ 649,  649],
       [   7,    7],
       [ 191,  191],
       [ 170,  170],
       [4309, 4309]])

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