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Bugfix: transporter prediction with mawk's awk implementation
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When mawk is used as awk-flavour, it caused that a number of transporters were not predictable with `./gapseq find-transport`. This commit fixes this bug.
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Waschina committed Aug 20, 2020
1 parent 70b4a83 commit e8da324
Showing 1 changed file with 1 addition and 1 deletion.
2 changes: 1 addition & 1 deletion src/transporter.sh
Original file line number Diff line number Diff line change
Expand Up @@ -146,7 +146,7 @@ do
subst=$(echo "$subst" | tr '_' ' ') # get space character back (was changed for look)
#echo -e $subst"\t"$type"\t"$tc"\t"$descr >> newTransporter.tbl
#exmetall=$(cat $subDB | grep -wi "$subst" | awk -F '\t' '{if ($8 != "NA") print $8}')
exmetall=$(cat $subDB | awk -F '\t' -v subst="$subst" '{IGNORECASE = 1; if ( ($1 == subst || $2 == subst) && $8 != "NA" ) print $8}')
exmetall=$(cat $subDB | awk -F '\t' -v subst="$subst" '{if ( (tolower($1) == tolower(subst) || tolower($2) == tolower(subst)) && $8 != "NA" ) print $8}')
for exmet in $exmetall
do
exid=$(cat $subDB | grep -w "$subst" | awk -F '\t' '{if ($7 != "NA") print $7}')
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