diff --git a/bin/mRNAmarkup.orig b/bin/mRNAmarkup.orig index da5a04e..d82425a 100644 --- a/bin/mRNAmarkup.orig +++ b/bin/mRNAmarkup.orig @@ -3,7 +3,7 @@ # mRNAmarkup: a bash script representing a work flow for mRNA inspection and # annotation using BLAST+, MuSeqBox, and other programs. # -# Last update: April 29, 2019. Volker Brendel. +# Last update: January 28, 2022. Volker Brendel. # # Set the install directory (set this variable to the location of the @@ -1546,7 +1546,7 @@ fi if [ -e AA-"$mRNAfile".fas ]; then countP=`cat AA-"$mRNAfile".fas | egrep "^>" | wc -l` if [[ $countP > 0 ]]; then - MuSeqBox -i blastx_"$mRNAfile"-vs-HXref -n 1 -l $idsize -d $dbsize -L 240 -k $srsize -A $pid $mao $scv tmpmsbfile > /dev/null + MuSeqBox -i blastx_"$mRNAfile"-vs-$AllProteinDB -n 1 -l $idsize -d $dbsize -L 240 -k $srsize -A $pid $mao $scv tmpmsbfile > /dev/null MuSeqBox -i tmpmsbfile -n 1 -s 1 > tmpmsb4ann annotateByMuSeqBox.pl -m tmpmsb4ann -q AA-"$mRNAfile".fas -o ann-AA.fas fi @@ -1555,7 +1555,7 @@ fi if [ -e HP-"$mRNAfile".fas ]; then countP=`cat HP-"$mRNAfile".fas | egrep "^>" | wc -l` if [[ $countP > 0 ]]; then - MuSeqBox -i blastx_"$mRNAfile"-vs-HXpep -n 1 -l $idsize -d $dbsize -L 240 -k $srsize -A $pid $mao $scv tmpmsbfile > /dev/null + MuSeqBox -i blastx_"$mRNAfile"-vs-$HypotheticalProteinDB -n 1 -l $idsize -d $dbsize -L 240 -k $srsize -A $pid $mao $scv tmpmsbfile > /dev/null MuSeqBox -i tmpmsbfile -n 1 -s 1 > tmpmsb4ann annotateByMuSeqBox.pl -m tmpmsb4ann -q HP-"$mRNAfile".fas -o ann-HP.fas fi