How to count elements with a specific condition in csv file using python

I am still learning python language. I have a table in csv format with n columns where the header is Tax_id and every column contains species names like this

  9606                  9606.1               508771  
    0                root                root                  root    
    1  cellular organisms  cellular organisms    cellular organisms
    2           Eukaryota           Eukaryota             Eukaryota
    3        Opisthokonta        Opisthokonta                   Sar
    4             Metazoa             Metazoa             Alveolata
    5           Eumetazoa           Eumetazoa           Apicomplexa
    6           Bilateria           Bilateria           Conoidasida
    7       Deuterostomia       Deuterostomia              Coccidia
    8            Chordata            Chordata        Eucoccidiorida
    9            Craniata            Craniata           Eimeriorina

I am struggling to write a python code that counts each species with their occurrence only for columns that contains species named "Metazoa".

 #to return something like

        Eumetazoa 2
        Bilateria 2
        Craniata  2

code python csv

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updated 5.1 years ago by Ram

• written 5.3 years ago by mumdooh •

2 answers

You may want to use a dictionary and loop through the column in question, or use pandas and some sort of group-by function. For the pandas approach, see this post on StackOverflow.

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written 5.3 years ago by Ram

Here's one way, perhaps:

#!/usr/bin/env python

'''
so9467093.py
'''

import io
import pandas as pd

input_str = '''9606,9606.1,508771
root,root,root
"cellular organisms","cellular organisms","cellular organisms"
Eukaryota,Eukaryota,Eukaryota
Opisthokonta,Opisthokonta,Sar
Metazoa,Metazoa,Alveolata
Eumetazoa,Eumetazoa,Apicomplexa
Bilateria,Bilateria,Conoidasida
Deuterostomia,Deuterostomia,Coccidia
Chordata,Chordata,Eucoccidiorida
Craniata,Craniata,Eimeriorina'''

input = io.StringIO(input_str)
df = pd.read_csv(input, sep=",")

filtered_column_names = (df == 'Metazoa').any(axis=0)
subset = df[df.columns[filtered_column_names]]

print(subset.stack().value_counts())

Output:

% ./so9467093.py
root                  2
Bilateria             2
Eukaryota             2
Deuterostomia         2
Chordata              2
Eumetazoa             2
Metazoa               2
cellular organisms    2
Craniata              2
Opisthokonta          2
dtype: int64

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written 5.3 years ago by Alex Reynolds