Entering edit mode
2.3 years ago
Ramana
•
0
HI,
I had more than 4,500 orthologs, how do I run pal2nal.pl in batch mode. by taking two input files ?
pep.aln - OG0016582.mt.r.py.fa
nuc.fasta - all_OG0016582.fa.cds.fa
pal2nal.pl aafasta/OG0016582.mt.r.py.fa cdsfasta/all_OG0016582.fa.cds.fa -output paml > all_OG0016582.paml.fasta
I wrote a script, can some one correct my script, thanks.
for i in $(ls -1 *.fa | sed 's/\.fa//'); do pal2nal.pl aafasta/$i\.fa cdsfasta/$i\.fa -output paml > $i\.fasta ; done
Script -
You might add a check that the other file exists: