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I have a data that looks like this (let's call this file submit.txt):

dir1/pmid_5409464.txt
dir1/pmid_5788247.txt
dir1/pmid_4971884.txt

What I want to do is to perform an inline file regex change so that it results in the following

perl mycode.pl /home/neversaint/dir1/pmid_5409464.txt > /home/neversaint/dir1/pmid_5409464.output
perl mycode.pl/home/neversaint/dir1/pmid_5788247.txt > /home/neversaint/dir1/pmid_5788247.output
perl mycode.pl /home/neversaint/dir1/pmid_4971884.txt > /home/neversaint/dir1/pmid_4971884.output

Is there a SED/Perl one liner to do that?

My difficulty is in capturing the input file name and then create the output file (.output) - for each line - based on that. I'm stuck with this:

sed 's/^/perl mycode.pl \/home\/neversaint\/dir1\//g' submit.txt |
sed 's/$/ >/'
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  • 1
    awk '{print "xxx/x/y/"$0 "> xxxxxxxx/$0}' list > output? good luck.
    – shellter
    Commented Jul 31, 2013 at 2:30
  • No that won't do. The point is for every line capture the pmid_xxx from pmid_xxx.txt and print the output version of that pmid_xxx.output also for each line.
    – neversaint
    Commented Jul 31, 2013 at 2:36
  • sed stackoverflow.com/questions/2777579/…
    – Ciro Santilli OurBigBook.com
    Commented Nov 19, 2015 at 8:15

3 Answers 3

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15

You can use escaped parenthesis to capture groups, and access the groups with \1, \2, etc.

sed 's/^\(.*\).txt$/perl mycode.pl \/home\/neversaint\/\1\.txt > \/home\/neversaint\/\1.output/' submit.sh

output:

perl mycode.pl /home/neversaint/dir1/pmid_5409464.txt > /home/neversaint/dir1/pmid_5409464.output
perl mycode.pl /home/neversaint/dir1/pmid_5788247.txt > /home/neversaint/dir1/pmid_5788247.output
perl mycode.pl /home/neversaint/dir1/pmid_4971884.txt > /home/neversaint/dir1/pmid_4971884.output

edit: it doesn't look like sed has a built-in in place file editing (GNU sed has the -i option). It still possible to do but this solution just prints to standard out. You could also use a Perl one liner as shown here: sed edit file in place

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  • thanks so much. BTW is there a way I can split your code into multiple lines; It's easier to read that way in my editor, later I realized.
    – neversaint
    Commented Jul 31, 2013 at 3:07
  • 1
    You're welcome! You could use shell variables to split it up, similar to this: stackoverflow.com/questions/8078872/…. Basically store the search string in one variable, and replace string in another. I don't know if this would help much since the replace string would still be pretty long. You could also put the search and replace part in a file, and call it using the sed -f option
    – hmatt1
    Commented Jul 31, 2013 at 3:17
1

You asked for a Sed one-liner, you got it.

sed 's/\([^.]*\)\.txt/perl mycode.pl \/home\/neversaint\/\1.txt > \/home\/neversaint\/\1.output/' submit.txt > output.txt

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  • Use another separator, instead of /, when you have many slashes in teh string (e.g. file names). Sed also works with _, | or :.
    – Attila O.
    Commented May 23, 2017 at 8:53
1

The perl oneliner for doing the same is

perl -pe "s@(.*?)(\.txt)@perl mycode.pl /home/neversaint/\\1\\2 > /home/neversaint/\\1.output@g" submit.txt

The above command will produce a replaced string in the console and you have to redirect the output to another file.

For replacing within the file (inline replace) you can add -i option . For eg 

perl -pe "s@(.*?)(.txt)@perl mycode.pl /home/neversaint/\1\2 > /home/neversaint/\1.output@g" -i submit.txt

The above will perform a replace within the submit.txt file itself.

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