How to get specific column in a row (csv)

Question

I have this piece of code:

with open(filepath, 'rb') as csvfile:
    reader = csv.reader(csvfile, delimiter=' ')
    for row in reader:
        print(' '.join(row))

and it returns:

Type,UniProt ID,Position
Sodium channel,P35498,1-123
Sodium channel,P35498,176-188
Sodium channel,P35498,234-239
Sodium channel,P35498,426-762
Sodium channel,P35498,823-830
Potassium channel ATP-sensitive inward rectifier,P48048,1-77

I would like to be able to put P35498 in a string to use later. How would I do this? I would also like to be able to get any of those columns but just an example with P35498 would be great, thanks!

If I do

with open(filepath, 'rb') as csvfile:
    reader = csv.reader(csvfile, delimiter=',')
    idlist = []
    for row in reader:
        idlist.append(row[1])
        print(idlist)

This is returned:

['UniProt ID']
['UniProt ID', 'P35498']
['UniProt ID', 'P35498', 'P35498']
['UniProt ID', 'P35498', 'P35498', 'P35498']
['UniProt ID', 'P35498', 'P35498', 'P35498', 'P35498']
['UniProt ID', 'P35498', 'P35498', 'P35498', 'P35498', 'P35498']
['UniProt ID', 'P35498', 'P35498', 'P35498', 'P35498', 'P35498', 'P48048']

Yes, but I would still like to print the entire row. @VigneshKalai — mkpappu
– mkpappu, Commented Jul 16, 2015 at 16:07

The6thSense · Accepted Answer · 2015-07-16 16:10:44Z

1

If you want the row which has "P35498" in column 2 you could check column 2 and print so when it is same :

with open(filepath, 'rb') as csvfile:
    reader = csv.reader(csvfile, delimiter=' ')
    for row in reader:
        if "P35498"==row[1]:
            print(' '.join(row))

answered Jul 16, 2015 at 16:10

The6thSense

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Comments

Anand S Kumar · Accepted Answer · 2015-07-16 16:14:27Z

1

row is a list, you can use indexes to get the data for the corresponding column. For example for column ID , which is the second column , so index 1 , you would use -

with open(filepath, 'rb') as csvfile:
    reader = csv.reader(csvfile, delimiter=',')
    idlist = []
    for row in reader:
        idlist.append(row[1])
    print(idlist)

At the end, idlist would be a list of all ids in the csv.

Also, according to your example , you should use , as the delimiter.

As said in the question comments, If the ask is to print a row with a specific id you can use -

with open(filepath, 'rb') as csvfile:
    reader = csv.reader(csvfile, delimiter=',')
    for row in reader:
        if 'P35498' in row[1]:
            print(' '.join(row))

edited Jul 16, 2015 at 16:14

answered Jul 16, 2015 at 16:07

Anand S Kumar

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7 Comments

Sam CD Over a year ago

I think the actual ID is UniProt ID, which is column 2, and would be index 1, so row[1]

Anand S Kumar Over a year ago

Yes thanks, the delimiter according to example should be , not space.

The6thSense Over a year ago

@AnandSKumar correct me if I am wrong but he said all row right

Anand S Kumar Over a year ago

@VigneshKalai Not sure i thought the ask was to get the column , but anyway added that to the answer as well. Thanks.

mkpappu Over a year ago

@AnandSKumar if you do your first answer. Look at my edit.

|

mkpappu · Accepted Answer · 2015-07-16 16:35:38Z

0

Actually, just doing

    with open(filepath, 'rb') as csvfile:
    reader = csv.reader(csvfile, delimiter=',')
    for row in reader:
        uniprot_id = row[1]
        print uniprot_id

works.

edited Jul 16, 2015 at 16:35

answered Jul 16, 2015 at 16:17

mkpappu

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2 Comments

Anand S Kumar Over a year ago

That code is exactly same as - unitprot_id = row[1]; print uniprot_id , why you using the soooo big route?

mkpappu Over a year ago

@AnandSKumar I was going to create a list with all of the ids but I decided against it and just didn't edit it...and I put uniprot_id_list = [] in the wrong place... thanks for reminding me, I would've actually kept it there!

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