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how to run mscore in bash?

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?

bash mscore aligment
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written by MichaelTrev • MichaelTrev 
didn't work

is the most uninformative error message in all of science ;-) Please avoid this and expain what the problem is.

• 0 views • link
written by ATpoint ATpoint

1 answer

input:

$ ls
resFileU.fasta  resFileXXX.fasta  resFileYYYYYY.fasta  U.afa  XXX.afa  YYYYYY.afa

in bash:

$ for i in *.afa; do echo "mscore -cftit $i resFile$i > final${i%.afa}.txt"; done
mscore -cftit U.afa resFileU.afa > finalU.txt
mscore -cftit XXX.afa resFileXXX.afa > finalXXX.txt
mscore -cftit YYYYYY.afa resFileYYYYYY.afa > finalYYYYYY.txt

using GNU-parallel:

$ parallel --dry-run 'mscore -cftit {} resFile{} > final{.}.txt' ::: *.afa       
mscore -cftit U.afa resFileU.afa > finalU.txt
mscore -cftit XXX.afa resFileXXX.afa > finalXXX.txt
mscore -cftit YYYYYY.afa resFileYYYYYY.afa > finalYYYYYY.txt
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written by cpad0112 cpad0112

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