Hi malcook, I tried to run this xargs one-liner, but I keep getting a basename error - "basename: invalid option -- 'a'"
I have the latest Ubuntu coreutils (8.13-3ubuntu3.1).
I looked at the basename man page and there are no listed options, only help and version.
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Thanks malcook. I will play with this, especially the xargs -P option as I have 32 cores to play with.
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time to learn xargs?
here is a one-liner that uses xargs
Code:basename -a data/rad1/*.dat | xargs -t -I {} bash -c 'cat data/rad1/"{}" data/rad2/"{}" > data/rad3/"{}" ' \;
- this works on my mac/OSX; if you're on linux the options for xargs might be different
- also, you might need to upgrade your GNU coreutils to get the version of basename that supports -a
- xargs also supports -P for doing multiple cats in parallel if you have multiple processors this could speed things up....
- the double quotes are protection again odd characters in your filenames, if any
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Thank you Justin, that worked perfectly As you suggested, I didn't need the 'cp' command.
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Here are a couple of things I noticed.
1. dir2 should be set to /data/rad2
2. instead of $topdir/$dir1, I think it should just be $dir1 (likewise for $dir2)
3. basename includes the fastq extension, so no need to append .fastq
This would be my attempt at it:
Code:topdir=/data/rad3 dir1=/data/rad1 dir2=/data/rad2 for f in $dir1/*.fastq do outf=$topdir/`basename $f` echo $outf cp $f $outf cat $dir2/`basename $f` >> $outf done
Also, it might be more straightforward to do "cat a b > c" rather than "cp a c; cat b >> c;"
So maybe the body could be replaced with
Code:outf=$topdir/`basename $f` cat $f $dir2/`basename $f` > $outf
Justin
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Append two fastq files repeatedly
Hello, I am on an Ubuntu 12 system.
I am trying to write a bash loop to runCode:cat /data/rad1/ang_TP30124.fastq /data/rad2/ang_TP30124.fastq > /data/rad3/ang_TP30124.fastq
I have 184 files in two directories with identical file names (/data/rad1 and /data/rad2). I want to append each of the like named fastq files into a single like named file into a third directory /data/rad3.
I am just learning and have come up with:Code:topdir=/data/rad3 dir1=/data/rad1 dir2=/data/rad1 for f in $topdir/$dir1/*.fastq do outf=$topdir/`basename $f .fastq` cp $f $outf cat $topdir/$dir2/`basename $f` >> $outf done
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