This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Awk Help

Dear All,

I am new to awk programming, so I was trying to add the contents of the table. I have a table like this

e_gw1.100.18.1  244

e_gw1.100.2.1   12

e_gw1.100.2.1   433

e_gw1.100.22.1  15

e_gw1.100.24.1  151

e_gw1.100.24.1  47

e_gw1.100.33.1  326

And I want something like this:

e_gw1.100.18.1  244

e_gw1.100.2.1   445

e_gw1.100.24.1 198

e_gw1.100.33.1  326

I am trying to make this table unique by adding all its associated values. Thanks in advance.

CS

awk
• 1,846 views • link
updated by Aaronquinlan Aaronquinlan • written by CS • CS

Off topic. Difficult to understand what the OP wants.

• 0 views • link
written by Zev.Kronenberg Zev.Kronenberg

not exactly bioinformatics related, but:

awk '{ a[$1]=a[$1]+$2 } END{ for(k in a){ print k, a[k]} }'
• 73 views • link
written by brentp brentp

Sorry , but this is something I was doing to get the count of reads to features.

Thanks for your help

• 0 views • link
written by CS • CS

2 answers 

awk '{data[$1] += $2} END{for (key in data) {print key, data[key]}}' foo.txt
e_gw1.100.22.1 15
e_gw1.100.33.1 326
e_gw1.100.24.1 198
e_gw1.100.18.1 244
e_gw1.100.2.1 445

Bedtools has a groupby function for this as well (docs: http://bedtools.readthedocs.org/en/latest/content/tools/groupby.html) :

bedtools groupby -g 1 -c 2 -o sum -i foo.txt
e_gw1.100.18.1    244
e_gw1.100.2.1    445
e_gw1.100.22.1    15
e_gw1.100.24.1    198
e_gw1.100.33.1    326
• 225 views • link
written by Aaronquinlan Aaronquinlan

thanks very much

• 0 views • link
written by CS • CS

You should ask these kind of questions on a specific programming forum, like Stack Overflow.

• 0 views • link
written by Peixe Peixe

Log in to answer this question.

More posts like this