shell - Possible modification of nested for loop -

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i newbie, , trying modify code below takes less time run. (right takes ages.) please or give suggestions, if possible. thank beforehand.

#!/bin/sh pheno in `cat /wrk/abc/composition/results/list.txt`;   header=`head -1 /wrk/abc/composition/results/"$pheno"/meta_"$pheno".out`   echo "pheno $header" > results.txt   pheno in `cat /wrk/abc/composition/results/list.txt`;     awk -v p="$pheno" \         'nr == fnr{a[$1]; next}($3) in a{print p, $0}' \         list.txt \         /wrk/abc/composition/results/"$pheno"/meta_"$pheno".out \          >>  results.txt   done done

assuming list.txt line separated, here's same code simplified, no useless cats, (the for loops swapped while reads), , using cd reduce unreadable long paths, followed notes. should little faster, , work same before, such was:

cd /wrk/abc/composition/results/ while read pheno ;     { echo -n pheno; head -1 "$pheno"/meta_"$pheno".out ; } \        > results.txt     while read pheno ;         awk -v p="$pheno" \             'nr == fnr{a[$1]; next}($3) in a{print p, $0}' \             list.txt \             "$pheno"/meta_"$pheno".out \              >>  results.txt     done < list.txt done < list.txt cd - mv /wrk/abc/composition/results/results.txt ./

the glaring error there 2 loops, 1 nested in other; both use same variable name ($pheno), both input same file (list.txt) -- surprisingly, sort of code may function correctly, despite being confusing. must cause slowdown, since inner loop runs awk on same input file. if there 100 lines in list.txt, file might read 1,000,000 times.

then there's results.txt, inner loop appends data to, , outer loop overwrites every cycle. results.txt therefore winds being filled data last cycle.


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