Combine separate fasta files from a list.txt

Question

I have about 10 fasta files that I need to pull from a giant folder of other fasta files (has about 100 files). I have a list of the files I need in a .txt file separated by line and I want to pull out the 10 fasta files listed and combine them into one big file.

I tried this command at first: xargs < names.txt cat > names.fasta

But it gave me this error: cat: 'read_1.fasta'$'\r': No such file or directory

For all the files except the last read in the list which it managed to add to the names.fasta .

I'm not sure what the error message means given I can find the files in my folder so they should be there. I can do this manually but I know it'll take a while to do.

EDIT: I changed the list to be separated by space and it actually pulled out all the files I needed! However, is there a way to account for reading in the names by newline instead of space??

Answer 1

This should work

xargs < names.txt cat > names.fasta

Or else try,

cat names.txt | xargs cat > newdir/names.fasta

What I think is within names.txt there's a typo or a missing file and that's what it's complaining about.

Perhaps try using

ls > tmp
cat names.txt | sort > tmp2
diff tmp tmp2

If there are any differences that should pick it up.

Answer 2

Just to address an edge case, run dos2unix names.txt first and then a modified version of @M__'s command

cat names.txt | xargs -I v_file cat v_file >> names.fasta

Based on your edit, it looks like your working platform has different line endings compared to the platform on which names.txt was last edited/saved.