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In [1]:



    


from pygenprop.database_file_parser import parse_genome_property_file
from pygenprop.results import GenomePropertiesResults
from pygenprop.assignment_file_parser import parse_genome_property_longform_file, parse_interproscan_file
import pandas as pd



    











In [2]:



    


def generate_differential_assignments(*results):
    comparison = pd.concat(results, axis=1, sort=False)
    comparison_transposed = comparison.transpose()
    differential_assignments = comparison_transposed[[col for col in comparison_transposed if not comparison_transposed[col].nunique()==1]].transpose()
    return differential_assignments



    











In [3]:



    


with open('/Users/lee/Dropbox/RandD/Repositories/genome-properties/flatfiles/genomeProperties.txt') as genome_properties_file:
    genprop_tree = parse_genome_property_file(genome_properties_file)



    











In [4]:



    


with open('/Users/lee/Google_Drive/Neufeld_Lab/Projects/ELA_GSB_test_data_for_Lee/Jackson_InterProScan_GenProp_Results/Updated_Fall_2018/genome_properties/C_chlorochromatii_CaD3') as assignment_file:
    file_assignment_results = parse_genome_property_longform_file(assignment_file)
    genome_properties_file_result = GenomePropertiesResults(file_assignment_results, genome_properties_tree=genprop_tree)



    











In [5]:



    


with open('/Users/lee/Google_Drive/Neufeld_Lab/Projects/ELA_GSB_test_data_for_Lee/Jackson_InterProScan_GenProp_Results/Updated_Fall_2018/interproscan_results/C_chlorochromatii_CaD3.tsv') as assignment_file:
    file_assignment_results = parse_interproscan_file(assignment_file)
    file_assignment_results.sample_name = "C_chlorochromatii_CaD3_InterProScan"
    inteproscan_file_result = GenomePropertiesResults(file_assignment_results, genome_properties_tree=genprop_tree)



    











In [6]:



    


len(genprop_tree) # Number of properties in the tree.



    


















    
Out[6]:








1286

















In [7]:



    


len(genome_properties_file_result.property_results) # Number of assigned properties from genome properties assignment file.



    


















    
Out[7]:








1286

















In [8]:



    


len(inteproscan_file_result.property_results) # Number of assigned properties from InterProScan TSV file.



    


















    
Out[8]:








1286

















In [9]:



    


differential_property_assignments = generate_differential_assignments(genome_properties_file_result.property_results, inteproscan_file_result.property_results)



    











In [10]:



    


len(differential_property_assignments) # Number of differing property assignments between InterProScan file and genome properties assignment file.



    


















    
Out[10]:








37

















In [11]:



    


differential_step_assignments = generate_differential_assignments(genome_properties_file_result.step_results, inteproscan_file_result.step_results)



    











In [12]:



    


len(differential_step_assignments) # Number of differing step assignments between InterProScan file and genome properties assignment file.



    


















    
Out[12]:








87

















In [13]:



    


len(inteproscan_file_result.step_results) # Number of steps assigned.



    


















    
Out[13]:








6525

















In [14]:



    


global_leaf_genome_property_ids = {leaf.id for leaf in genprop_tree.leafs}
differential_genome_property_leaf_ids = set(differential_property_assignments.index.tolist()).intersection(global_leaf_genome_property_ids)



    











In [15]:



    


differential_leaf_genome_property_assignments = differential_property_assignments[differential_property_assignments.index.get_level_values(0).isin(differential_genome_property_leaf_ids)]



    











In [16]:



    


len(differential_leaf_genome_property_assignments) # Number of differing leaf step assignments between InterProScan file and genome properties assignment file.



    


















    
Out[16]:








22

















In [17]:



    


differential_leaf_step_assignments = differential_step_assignments[differential_step_assignments.index.get_level_values(0).isin(differential_genome_property_leaf_ids)]



    











In [18]:



    


len(differential_leaf_step_assignments)



    


















    
Out[18]:








20

Differential steps are due to genome properties perl improperly assigning yes when to steps where their are mutiple insufficent evidences and some of these are missing.

See: https://github.com/ebi-pf-team/genome-properties/issues/30





In [19]:



    


differential_leaf_step_assignments



    


















    
Out[19]:











  
    

      
      
      C_chlorochromatii_CaD3
      C_chlorochromatii_CaD3_InterProScan
    

    

      Genome_Property_ID
      Step_Number
      
      
    

  
  
    

      GenProp0457
      6
      YES
      NO
    

    

      7
      YES
      NO
    

    

      GenProp0458
      2
      YES
      NO
    

    

      GenProp0685
      1
      YES
      NO
    

    

      GenProp0701
      1
      YES
      NO
    

    

      GenProp0715
      2
      YES
      NO
    

    

      GenProp0724
      8
      YES
      NO
    

    

      GenProp0750
      1
      YES
      NO
    

    

      3
      YES
      NO
    

    

      GenProp0754
      1
      YES
      NO
    

    

      GenProp0756
      1
      YES
      NO
    

    

      GenProp0759
      2
      YES
      NO
    

    

      GenProp0839
      2
      YES
      NO
    

    

      GenProp0840
      2
      YES
      NO
    

    

      GenProp0842
      3
      YES
      NO
    

    

      GenProp0877
      1
      YES
      NO
    

    

      GenProp0917
      12
      YES
      NO
    

    

      GenProp0927
      2
      YES
      NO
    

    

      GenProp1074
      2
      YES
      NO
    

    

      GenProp1094
      3
      YES
      NO
    

  




















In [20]:



    


differential_leaf_genome_property_assignments



    


















    
Out[20]:











  
    

      
      C_chlorochromatii_CaD3
      C_chlorochromatii_CaD3_InterProScan
    

  
  
    

      GenProp0457
      PARTIAL
      NO
    

    

      GenProp0458
      PARTIAL
      NO
    

    

      GenProp0617
      PARTIAL
      NO
    

    

      GenProp0685
      PARTIAL
      NO
    

    

      GenProp0701
      PARTIAL
      NO
    

    

      GenProp0715
      PARTIAL
      NO
    

    

      GenProp0724
      PARTIAL
      NO
    

    

      GenProp0750
      YES
      PARTIAL
    

    

      GenProp0754
      YES
      NO
    

    

      GenProp0756
      PARTIAL
      NO
    

    

      GenProp0759
      PARTIAL
      NO
    

    

      GenProp0813
      PARTIAL
      NO
    

    

      GenProp0839
      YES
      PARTIAL
    

    

      GenProp0840
      YES
      PARTIAL
    

    

      GenProp0842
      YES
      PARTIAL
    

    

      GenProp0877
      YES
      PARTIAL
    

    

      GenProp0899
      PARTIAL
      NO
    

    

      GenProp0917
      PARTIAL
      NO
    

    

      GenProp0927
      YES
      PARTIAL
    

    

      GenProp1072
      PARTIAL
      NO
    

    

      GenProp1074
      YES
      NO
    

    

      GenProp1094
      PARTIAL
      NO
    

  




















In [21]:



    


differential_property_assignments_not_caused_by_leaves = set(differential_leaf_genome_property_assignments.index.tolist()).isdisjoint({property_id for property_id, step_id in differential_leaf_step_assignments.index.tolist()})



    











In [22]:



    


differential_property_assignments_not_caused_by_leaves



    


















    
Out[22]:








False

















In [26]:



    


print('Missmatched Properties: {:1.2}%'.format(len(differential_property_assignments)/len(inteproscan_file_result.property_results)*100))
print('Missmatched Steps: {:1.2}%'.format(len(differential_step_assignments)/len(inteproscan_file_result.step_results)*100))
print('Missmatched Leaf Properties: {:1.2}%'.format(len(differential_leaf_genome_property_assignments)/len(inteproscan_file_result.property_results)*100))
print('Missmatched Leaf Steps: {:1.2}%'.format(len(differential_leaf_step_assignments)/len(inteproscan_file_result.step_results)*100))
print('Missmatched Leaf Properties Not Caused By Missmatched Steps: {}'.format(differential_property_assignments_not_caused_by_leaves))



    


















    






Missmatched Properties: 2.9%
Missmatched Steps: 1.3%
Missmatched Leaf Properties: 1.7%
Missmatched Leaf Steps: 0.31%
Missmatched Leaf Properties Not Caused By Missmatched Steps: False

















In [ ]:

Content source: LeeBergstrand/pygenprop

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