In [37]:

    

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


    

In [42]:

    

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


    

In [43]:

    

def get_genome_summary(genome_annotation=None):
    if genome_annotation == None:
        raise TypeError("No GenomeAnnotation object given.")
    elif genome_annotation.get_typestring().split('-')[0] not in biokbase.data_api.genome_annotation.TYPES:
        raise TypeError("{0} is not a recognized GenomeAnnotation type.".format(type(genome_annotation)))
        annotation_details = dict()
        annotation_details["feature_type_counts"] = genome_annotation.get_feature_type_counts(annotation_details["feature_types"])
        print(annotation_details["feature_type_counts"])
    return annotation_details


    

In [44]:

    

import pprint
import datetime

def parse_all_existing_annotations():
    annotations = dict()
    for x in object_list:
        if x.type.startswith("KBaseGenomes.Genome"):
            annotations[x.name] = x
    return annotations

b = biokbase.data_api.browse(1011)

object_list = b.ls()

melampsora = b["kb|g.3157"]
arabidopsis = b["kb|g.3899"]


    

In [45]:

    

annotations = {test.name: test.object}

start = datetime.datetime.utcnow()
for n in annotations:
    print '\n'
    print '#'*80
    print '#'*80
    print '\n'    
    
    print n
    overview = get_genome_summary(annotations[n])
    pprint.pprint(overview)
    
    print '\n'
    print '#'*80
    print '#'*80
    print '\n'
end = datetime.datetime.utcnow()

print "Total time to summarize existing Genome Annotations, Taxons, Assemblies : {0}".format(end - start)


    

    





################################################################################
################################################################################


kb|g.3157






    




---------------------------------------------------------------------------
UnboundLocalError                         Traceback (most recent call last)
<ipython-input-45-aa0e88ed6320> in <module>()
      9 
     10     print n
---> 11     overview = get_genome_summary(annotations[n])
     12     pprint.pprint(overview)
     13 

<ipython-input-43-a05675b0088d> in get_genome_summary(genome_annotation)
      7         annotation_details["feature_type_counts"] = genome_annotation.get_feature_type_counts(annotation_details["feature_types"])
      8         print(annotation_details["feature_type_counts"])
----> 9     return annotation_details

UnboundLocalError: local variable 'annotation_details' referenced before assignment

In [ ]: