CODEWITHSUNDEEP
pythoncsv
Danny
Danny

Reputation: 87

How to merge several csv columns into one column using python 2.7?

I'm working with large set of csv data and I want to put several columns in different places into one column separated by semi-colon(;).

So what I have now is..

a   b   c   d
1   2   3   4
1   2   3   4
1   2   3   4

I want to change this like..this, So all my data is only in column d.

a   b   c   d
            a=1;b=2;c=3;d=4;
            a=1;b=2;c=3;d=4;
            a=1;b=2;c=3;d=4;

I know how to delete those empty column a,b and c but I just can't figure out a way to merge the data from column a,b,c into column d. Thanks in advance.

The code that I have so far is..

# Parsing the custom formatted data with csv module.
# reads the custom format input and spits out the output in VCF format.
import csv
# input and output
with open('1-0002', 'rb') as csvin, open('converted1','wb') as csvout:
    # reading and writing are all tab delimited
    reader = csv.reader(csvin, delimiter = '\t')
    writer = csv.writer(csvout, delimiter = '\t')
    # add headings before the for loop to prevent the heading being affected by column manipulation.
    writer.writerow(["#CHROM","POS","ID","REF","ALT","QUAL","FILTER","INFO"])

    for row in reader:
        # deleting unnecessary columns, 'del' operator must be in ascending order or else it will give range error
        # manually deleting columns since the input data is in custom format.
        del row[11]
        del row[10]
        del row[9]
        del row[8]
        del row[7]
        del row[6]
        del row[5]
        del row[1]
        del row[0]
        # inserting 1 and . in specific columns
        row.insert(0,'1')
        row.insert(2,'.')
        row.insert(5,'.')
        row.insert(7,'') # inserting empty column for INFO headings.

        # change 'YES' to 'PASS' , leaving HETERO as it is.
        if row[6] == 'YES':
                row[6] = 'PASS'

        writer.writerow(row)

So from this code above, I want to put the data from several different columns into INFO column.

Upvotes: 1

Views: 3766

Answers (3)

vk1011
vk1011

Reputation: 7179

Try pandas

import pandas as pd
df = pd.read_csv('1-0002.csv')
df['d_merged'] = df.apply(lambda row: 'a={0};b={1};c={2};d={3};'.format(row['a'],row['b'],row['c'],row['d']), axis=1)

This gives:

>>> df

   a  b  c  d          d_merged
0  1  2  3  4  a=1;b=2;c=3;d=4;
1  1  2  3  4  a=1;b=2;c=3;d=4;
2  1  2  3  4  a=1;b=2;c=3;d=4;

Now delete the columns you don't want:

df = df.drop(['a','b','c','d'], axis=1)

>>> df

           d_merged
0  a=1;b=2;c=3;d=4;
1  a=1;b=2;c=3;d=4;
2  a=1;b=2;c=3;d=4;

Now rename d_merged if you wish:

df = df.rename(columns={'d_merged':'d'})

>>> df

                  d
0  a=1;b=2;c=3;d=4;
1  a=1;b=2;c=3;d=4;
2  a=1;b=2;c=3;d=4;

(Alternatively, combine the above two steps as:

df['d'] = df.apply(lambda row: 'a={0};b={1};c={2};d={3};'.format(row['a'],row['b'],row['c'],row['d']), axis=1)

)

Then write to CSV:

df.to_csv('csvout.csv', index=False)

Upvotes: 0

Danver Braganza
Danver Braganza

Reputation: 1355

Simple answer: don't bother deleting the row, but make a NEW row for insertion that only picks what you want.

It will look like this:

# leave row alone, don't bother deleting columns in it.
new_row = ["a=%s;b=%s;c=%s;d=%s"% (row[12], row[13], row[14])] 
# new_row has only one column, with a string constructed of what you need. 

writer.writerow(new_row)

And voila, that should do it for you. You can also copy any other columns you need to new_row, and append() whatever else you might desire.

Upvotes: 3

Christian W.
Christian W.

Reputation: 2660

just read the file with a reader and write the data you read into another file. this example is assuming you want to still keep empty columns a, b and c

r = csv.readedr('filename.csv', 'r')
with open('outfile.csv') as outfile:
    w = csv.writer(outfile, 'w')
    for row in r:
        # joins the current row into string seperated by spaces
        outdata = row.join(' ')
        # leaves first three columns empty, writes old content onto fourth column
        data_to_write = ('', '', '', outdata)
        w.writerow(data_to_write)

Upvotes: 0

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