CODEWITHSUNDEEP
awk
Elisabet_E
Elisabet_E

Reputation: 11

Using awk on a folder and adding file name to output rows

I should start by thanking you all for all the work you put into the answers on this site. I have spent many hours reading through them but have not found anything fitting my question yet. Hence my own post.

I have a folder with multiple subfolders and txt-files within those. In column 7 of those files, there are gene names (I do genetics for a living :)). These are the string I am trying to extract. Shortly, I would like to search the whole folder for any rows within any of the files that contain a particular gene name/string. I have been using grep for this, writing something like:

grep -r GENE . > GENE.txt

Simple, but I need to be able to tweak the search further and it seems that then awk is the way to go.

So I tried using awk. I wrote something like this:

awk '$7 == "GENENAME"' FOLDER/* > GENENAME.txt

This works well (and now I can specify that the string has to be in a particular column, this I can not do with grep, right?). However, in contrast to grep, which writes the file name at the start of each row, I now can not directly see which file which row in my output file comes from (which mostly defeats the point of the search). This, adding the name of the origin file somewhere to each row, seems like something that should absolutely be doable, but I am not able to figure it out.

The files I am searching within change (or rather get more numerous), but otherwise my search will always be for some specific string in column 7 of the same big folder. How can I get this working?

Thank you in advance, Elisabet E

Upvotes: 1

Views: 1015

Answers (2)

Ed Morton
Ed Morton

Reputation: 204558

Sounds like you're looking for:

awk '$7 == "GENENAME"{print FILENAME, $0}' FOLDER/*

If not then edit your question to clarify with sample input and expected output.

Upvotes: 0

Haifeng Zhang
Haifeng Zhang

Reputation: 31925

You can use FNR (FNR means file number of record) to print the row number and FILENAME to print the file's name, then you get the matching lines from which file and which row, for instance:

sample.csv:

aaa 123
bbb 456
aaa 789

command:

awk '$1 =="aaa"{print $0, FNR, FILENAME}' sample.csv

The output is:

aaa 123 1 sample.csv
aaa 789 3 sample.csv

Upvotes: 3

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