Perl script for concatenating multiple files in aspecific order listed in a txt file

[Anonymous Monk]

Assalm o alikum everyone!

I want to concatenate 100 of FASTA file present in single directory acccording to a specfic order listed in a file by using perl kindly guide me how to do so >???

[hippo]

$ xargs cat < list > outfile

by using perl

Well you could, but then that would be more work for you and slower besides. Is this an XY Problem?

[Anonymous Monk]

Not OP, but perl scripts can be written in a way so as to be cross platform

[pryrt]

xargs is available for Windows at http://gnuwin32.sourceforge.net/packages/findutils.htm

[Your Mother]

It would be semi-trivial with Path::Tiny. You should read the stat/-X docs to know how to make it a bit more safe and robust.

Show us some code you've tried if you're having trouble getting it to work and someone will be glad to help fix or adapt it.

[Laurent_R]

To do it Perl, read the list file into an array, then loop on the array, open each file listed in turn and print what you read to the same output file.

[afoken]

To do it Perl, read the list file into an array, then loop on the array, open each file listed in turn and print what you read to the same output file.

... and don't forget to chomp off the trailing newlines.

Alexander

[Laurent_R]

Well, chomping the lines from the input files may or may not be necessary. There is no point removing the new lines if the next print statement is just adding them back. So it really depends on what the input files look like.

It may even not be necessary to read the input files line by line and possibly faster to read 4-kB blocks or so.

[BillKSmith]

Are you certain that a simple concatenate is all you need? Consider what would happen if one or more of the files did not end with a newline. Are there any other special cases?

[thanos1983]

Hello Anonymous Monk,

I see already the fellow Monks have provided you with plenty of options. I just would like to provide two more possible solutions.

But I still lost, what is the a specific order of the files in your file? Is it in numerical order?

Since you did not provide us with an example of your file and expected output I will just assume, and propose something. Why not extract all FASTA files from the file in an array and simply concatenate them with the join?

Just a suggestion if I have understand correctly.

Provide us more information so we can help you.

Solution one using File::Slurp/read_dir:

Read more... (764 Bytes)

Solution two using readdir:

Read more... (887 Bytes)

Sorry I miss understood the question.

Looking forward to your update, BR.