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bashshellloopsfor-loopfastq

Two variable in one for loop in bash

I have a directory and inside I have two file types : *.sai and *fastq and I vant to use both variable in one shell for loop:

for j in *sai *fastq

 do bwa samse $j $j > ${j%.sai}.sam 

done;

after command do I want to load corresponding *.sai and *.fastq data in to the program (bwa samse). Could you help me please with syntax?

EXAMPLE:

in one directory is xx.fast xx.sai yy.fastq yy.sai and program bwa samse need to process in one time two corresponding files - bwa samse xx.fastq xx.sai...

Many thanks for any ideas.

Solution

  • Try doing this with bash parameter expansion:

    for j in .*sai; do  
    [[ -s ${j%.sai}.fastq ]] &&
        bwa samse "$j" "${j%.sai}.fastq" > "${j%.sai}.sam"     
done

    and please, stop killing kitties with parsing ls output. (not for you Incorigible)