Hi, I have another question with bash. In the folder, I have 400 result files. I want all result to compare with his reference file.
My file structure looks like:
resFileXXX.fasta
XXX.afa
resFileYYYYYY.fasta
YYYYYY.afa
resFileU.fasta
U.afa
I need to create script comparing this by mscore. mscore command looks that:
mscore -cftit <referenceFile> <restultFile> >output
So in my case it will be something like this:
mscore -cftit XXX.afa resFileXXX.fasta >finalXXX.txt
Can someone tell me how to create a proper script in bash? It's unfamiliar to me yet, and files are too much to do that manually.
Now my script looks like this (didn't work):
#!/bin/bash
ls *.afa | while read A; do B=`echo $A | sed 's/^file/Res/;s/.afa$//'`; ./mscore -cftit $A $B.fasta > ${B}final.txt; done
It didn't work coz it creates blank files, and they have weird names like XXXresXXX.fasta.afa As I said bash is unfamiliar to me, so I think it's a syntax error. I don't even know that script is in good convention :)
Can someone help with this problem?
is the most uninformative error message in all of science ;-) Please avoid this and expain what the problem is.
OK! I explained in edit :)
Use these for some inspiration :
Bash Script Loop Help
C: looping a list of trimed fasta files to run spades assembler