CODEWITHSUNDEEP
cat
user2413355
user2413355

Reputation: 1

Concatenate multiple pairs of files

I have 120 pairs of files I would like to concatenate. I have the list of pair of files and the proposed merged file name in a tab delimited file as follows

Filelist.txt

/filepath/1_first.fasta /filepath/1_second.fasta > /filepath/1_merged.fasta

/filepath/2_first.fasta /filepath/2_second.fasta > /filepath/2_merged.fasta

/filepath/3_first.fasta /filepath/3_second.fasta > /filepath/3_merged.fasta 

/filepath/4_first.fasta /filepath/4_second.fasta > /filepath/4_merged.fasta

I was trying:

$cat Filelist.txt | perl -ne 'chomp;system("cat $_;")'

with the idea of handling the Filelist.txt line by line and using the cat command on the line which for the first line should be...

/filepath/1_first.fasta /filepath/1_second.fasta > /filepath/1_merged.fasta

If I just have one pair and a single line in the Filelist.txt it works fine but with multiple lines I just get ..

/filepath/2_first.fasta: No such file or directory

$

Any clues why this might not be working for every single line? Or an alternative way to do this?

Thanks

Upvotes: 0

Views: 467

Answers (2)

twalberg
twalberg

Reputation: 62389

I would suggest this:

sed -e 's/^/cat /' Filelist.txt | bash

Assuming your Filelist.txt is really formatted that way (i.e. actually has the redirection included as shown). Maybe try the above without the | bash part first and inspect the output to make sure it looks like the right commands you want to run.

Upvotes: 1

Rijndael
Rijndael

Reputation: 3753

Try this:

cat * > merged_file

This will CAT all files in the directory and the output will be outputted into the merged_file.

Upvotes: 0

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