Using split in python to iterate through columns

Question

I am trying to use split in python to iterate through columns but when trying to access columns I get an error that a particular list index is out of range.

This is what my file looks like:

chr1    15585711    .   A   T   45.7081 .   AB=0;ABP=0;AC=2;AF=1;AN=2;AO=3;CIGAR=1X;DP=3;DPB=3;DPRA=0;EPP=9.52472;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=0;        NS=1;NUMALT=1;ODDS=8.76405;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=78;QR=0;RO=0;RPP=9.52472;RPPR=0;RUN=1;SAF=0;SAP=9.52472;SAR=3;SRF=0;SRP=0;SRR=0;            TYPE=snp  GT:DP:RO:QR:AO:QA:GL    1/1:3:0:0:3:78:-7.28,-0.90309,0

And here is my code:

target = open('file', 'r')

for line in target:
    line = line.split('\t')
    print line[1]

When I print line it looks like a list to me, and line[0] does access chr1 which is the first column. But then when I try to access the other columns i cannot.

Are you sure its TAB separated ('\t')? It does not seem like that. Try line.split() to split on every whitespace — Gábor Erdős
– Gábor Erdős, Commented Jan 25, 2016 at 19:45
line[0] does access chr1 <- you're asking for line[1] in your code, though — inspectorG4dget
– inspectorG4dget, Commented Jan 25, 2016 at 19:46
It should be tab separated. And @Lafexlos I get the following: ['chr1', '15585711', '.', 'A', 'T', '45.7081', '.', 'AB=0;ABP=0;AC=2;AF=1;AN=2;AO=3;CIGAR=1X;DP=3;DPB=3;DPRA=0;EPP=9.52472;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=0;NS=1;NUMALT=1;ODDS=8.76405;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=78;QR=0;RO=0;RPP=9.52472;RPPR=0;RUN=1;SAF=0;SAP=9.52472;SAR=3;SRF=0;SRP=0;SRR=0;TYPE=snp', 'GT:DP:RO:QR:AO:QA:GL', '1/1:3:0:0:3:78:-7.28,-0.90309,0\n'] — The Nightman
– The Nightman, Commented Jan 25, 2016 at 19:47
You are reusing the variable line and changing it. It probably works the first time but the next time through you've already split it on tab... only one entry in that case. — AlG
– AlG, Commented Jan 25, 2016 at 19:47

midori · Accepted Answer · 2016-01-25 20:04:01Z

1

I just created a text file with data you provided and was able to split it without any problem. I would suggest to use with open it'll close your file for you when you're done:

with open('test', 'rb') as target:
    for line in target:
        print line.split()[1]

Output:

15585711

answered Jan 25, 2016 at 20:04

midori

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Eric Evans · Accepted Answer · 2016-01-25 19:54:54Z

1

The source is not using tabs. Just use:

line = line.split()

answered Jan 25, 2016 at 19:54

Eric Evans

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1 Comment

The Nightman Over a year ago

when I try this I still get the same error. However if I just paste the text into a variable and then split I do not get an error.

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