[SOLVED] Need to concatenate many files with the same name occurring in many subdirectories

kmkocot · 11-04-2009, 06:27 PM

Hi all,

I have a "master" directory containing many subdirectories. Each subdirectory contains many files named #####.fa where # is any integer. I'm trying to write a script that will search through all of the subdirectories, find all the files with the same name, and concatenate them together into one output file of the same name in the master directory. The tricky part is that each file name doesn't necessarily occur in every folder. Do I need to make a query list for this or is there a way to specify files of the same name occurring in different directories?

Thanks!
Kevin

Tinkster · 11-04-2009, 06:52 PM

Untested ... something along those lines *should* work.

Code:

find -iname [0-9]\*.fa | xargs -i awk '{newfile=gensub( /.*\/([^\/]+)/, "\\1",1,FILENAME); print $0 >> "/path/to/aggregate/"newfile  }' {}

Cheers,
Tink

kmkocot · 11-04-2009, 07:09 PM

Tinkster,

That concatenates the contents of all of the files of interest into one file which is very close. I'm trying to only concatenate files with the same name. I'm sorry I was unclear. I feel like the first half of the script is what the doctor ordered. I'm trying to play around with xargs.

Thanks,
Kevin

chrism01 · 11-04-2009, 07:22 PM

I'd start with using find or ls -R to generate a list of all files in all dirs, pipe through sort -u (or uniq) to get a unique list, then use that to drive the concatenate process.

Tinkster · 11-04-2009, 07:38 PM

Quote:

Originally Posted by kmkocot

Tinkster,

That concatenates the contents of all of the files of interest into one file which is very close. I'm trying to only concatenate files with the same name. I'm sorry I was unclear. I feel like the first half of the script is what the doctor ordered. I'm trying to play around with xargs.

Thanks,
Kevin

Not in my installation. I just tested it (with an admittedly small
sample, two identical files of the same name each, in the main and a
sub-directory ... ) and it produces two concatenated files, each of
which matches the name of 1 pair.

Code:

$ find -name \*fa
./tmp/12345.fa
./tmp/432112345.fa
./12345.fa
./432112345.fa

My output directory is /tmp

Code:

ls -ltr /tmp/*fa
-rw-r--r-- 1 tink    tink     874 2009-11-05 14:35 /tmp/432112345.fa
-rw-r--r-- 1 tink    tink    1748 2009-11-05 14:35 /tmp/12345.fa

And that's running my snippet above unmodified.

What OS are you on, which version of awk are you running?

Cheers,
Tink

ghostdog74 · 11-04-2009, 07:58 PM

Code:

#!/bin/bash
find /path-type f -name "[0-9]*.fa" -printf "%f:%p\n" | awk -F":" 'BEGIN {master="/destination/"}
{
        filename=$1
        fullpath=$2
        while( (getline line < fullpath ) > 0 ){
                print line >> master filename
        }
        close(filename)
}'

kmkocot · 11-05-2009, 06:09 PM

Tinkster: My apologies... Operator error. I used FILENAME as the target of the print command at the end (instead of newfile) and it concatenated them all to that file. Now it is behaving as you said it should. Thank you!

ghostdog74: your script also works brilliantly.

Thank you, thank you, thank you!

kmkocot · 12-12-2009, 07:14 PM

Similar question...
I have a directory with many subdirectories each named like so: KOG0001, KOG0002, ...KOG9999.

Each of these subdirectories contain a variable number two kinds of files (nuc and prot) named like so: Capitella_sp_nuc_hits.fasta (nuc) and Capitella_sp_prot_hits.fasta (prot). The Capitella_sp part represents the name of the species and varies from file to file.

I'm trying to write a script that will go through each subdirectory and concatenate the contents of all the _prot_hits.fasta files into one file in the main directory named like KOG0001.fasta, KOG0002.fasta, and so on. I think I have it figured out except how to reference the source files that I want. Can anyone help me out?

Code:

find . -maxdepth 2 -type f -name "KOG[0-9][0-9][0-9][0-9]*_prot_hits.fasta" -printf "%p\n" | awk -F"_" '{print $1}' | sed 's/$/&.fasta/g' awk -F"/" 'BEGIN {filename=$3 while((getline line < **original_source_files** ) > 0) {print line >> filename} close(filename)}'

Thanks,
Kevin

ghostdog74 · 12-13-2009, 12:35 AM

put your code in code tags

kmkocot · 12-14-2009, 05:19 PM

Sorry about that. Is there a way I reference the original source files I want to concatenate if I set up the expression like this?

kmkocot · 12-15-2009, 10:23 AM

Nevermind... I was making it harder than it should be.

Code:

for i in KOG????;do find $i -name $i_*_prot_hits.fasta -exec cat {} >> $i.fasta \; ;done

ghostdog74 · 12-15-2009, 07:21 PM

Quote:

Originally Posted by kmkocot

Nevermind... I was making it harder than it should be.

yes you are

Quote:

Code:

for i in KOG????;do find $i -name $i_*_prot_hits.fasta -exec cat {} >> $i.fasta \; ;done

why do you want to execute find command for every KOG???? you iterate?? Let find do it for you (or have i missed something??)

Code:

find KOG???? -iname "KOG????_*_prot_hits.fasta" .......