unix: looping through results of find command

Question

I have a find command that outputs as I would like (it looks for files with strelka in the name and ends with .vcf):

find . -name *strelka* | grep '.vcf$'

But I want to then iterate over each and perform additional stuff.

To simply experiment, I'm just having it do a line count on each file (but ultimately I would want to do more in the end, this is just me playing around), but it already doesn't seem to work.

I have :

for i in find . -name \*strelka\* | grep '.vcf$'; do wc -l $i; done

Anyone know what is wrong with this?

Please don't improve the commands in the question or both the question and answers get pointless. — michas
– michas, Commented Mar 12, 2014 at 22:35
Several solutions fail if filenames contain spaces or other special characters. To address that issue, see stackoverflow.com/questions/7039130/… — TextGeek
– TextGeek, Commented Dec 4, 2019 at 17:30

user3392484 · Accepted Answer · 2014-03-12 21:19:16Z

3

Use find . -name '*strelka*.vcf', thereby avoiding the grep and letting you use find ... -exec

Either pipe into xargs, or use -exec:

find . -name '*strelka*.vcf' | xargs wc -l  

find . -name '*strelka*.vcf' -exec wc -l '{}' \;

Prefer the latter, for various reasons.

Your approach (with a $(...) around your find) is OK, except:

You'll have grief if there are spaces in filenames. (You'd have grief with xargs too - there's a way round that involving \0, but it's a bit arcane.)
You'll exceed the command line length limit if there are too many matching files.

answered Mar 12, 2014 at 21:19

user3392484

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2 Comments

rici Over a year ago

The xargs version will call wc many fewer times, possibly once (depending on how many files there are). The -exec version as written will call wc once per file. In the former case, you'll get possibly useful (or possibly undesired) totals from wc. You could modify the -exec case to do the same by changing the \; to +.

Lynch Over a year ago

for the first option using find and xargs I would suggest to use: find . -print0 -name '*strelka*.vcf' | xargs -0 wc -l. Its is to ensure you dont end up having problems with wierd filename containing \n or other preblematic chars.

chepner · Accepted Answer · 2014-03-13 00:36:01Z

3

Assuming you are using a recent (4.0 or greater) version of bash, you don't need to use find for this; a file pattern is sufficient, along with the globstar option.

shopt -s globstar
for i in **/*strelka*.vcf; do
    wc -l $i
done

For a small number of files, you can probably just use

wc -l **/*strelka*.vcf

For a large number of files,

find -name '*strelka*.vcf' -execdir wc -l '{}' +

is most efficient.

edited Mar 13, 2014 at 0:36

answered Mar 13, 2014 at 0:11

chepner

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Comments

michas · Accepted Answer · 2014-03-12 21:27:38Z

2

You can change your command as follows:

for i in $(find . -name \*strelka\* | grep '.vcf$'); do wc -l $i; done

or

find . -name \*strelka\* | grep '.vcf$' | while read i; do wc -l $i; done

or

find . -name \*strelka\* | grep '.vcf$' | xargs wc -l

You can also improve you find command to look for \*strelka\*.vcf to avoid the grep.

Also pay attention that files might contain spaces or even newlines. They would probably break your command. Therefore the best way is probably using:

find . -name '*strelka*.vcf' -exec wc -l '{}' \;

answered Mar 12, 2014 at 21:27

michas

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