#!/bin/bash

#echo "Grid G"
#./RandomSeqCluster.pl GridGparental.txt RescueMuXYPlasmidAssembly.fsa match.GridG_XYseq.fsa > GridGparental_randomSeq.fsa
#./cap3Dong GridGparental_randomSeq.fsa -p 90 -s 700 > GridGparental_randomSeq.fsa.Cap3Align 
#sed "s/Contig/GridGParentalContig/g" GridGparental_randomSeq.fsa.cap.contigs > GridGparentalContig.fsa
#mkvtree -v -allout -dna -pl 7 -db GridGparentalContig.fsa
#vmatch -q TIGRrepeatTrim_MFgss -d -p -l 40 -h 2 -identity 95 -showdesc 0 GridGparentalContig.fsa > MF_matchGparental.txt
#./matchMF_HCgss.pl TIGRrepeatTrim_MFgss MF_matchGparental.txt > MF_matchGparental.fsa
#vmatch -q TIGRrepeatTrim_HCgss -d -p -l 40 -h 2 -identity 95 -showdesc 0 GridGparentalContig.fsa > HC_matchGparental.txt
#./matchMF_HCgss.pl TIGRrepeatTrim_HCgss HC_matchGparental.txt > HC_matchGparental.fsa
#cat GridGparentalContig.fsa MF_matchGparental.fsa HC_matchGparental.fsa > Gparental_MF_HC.fsa
#./cap3Dong Gparental_MF_HC.fsa -p 90 -s 700 > Gparental_MF_HC.fsa.Cap3Align

echo "Grid H"
./RandomSeqCluster.pl GridHparental.txt RescueMuXYPlasmidAssembly.fsa match.GridH_XYseq.fsa > GridHparental_randomSeq.fsa
./cap3Dong GridHparental_randomSeq.fsa -p 90 -s 700 > GridHparental_randomSeq.fsa.Cap3Align
sed "s/Contig/GridHParentalContig/g" GridHparental_randomSeq.fsa.cap.contigs > GridHparentalContig.fsa
mkvtree -v -allout -dna -pl 7 -db GridHparentalContig.fsa
vmatch -q TIGRrepeatTrim_MFgss -d -p -l 40 -h 2 -identity 95 -showdesc 0 GridHparentalContig.fsa > MF_matchHparental.txt
./matchMF_HCgss.pl TIGRrepeatTrim_MFgss MF_matchHparental.txt > MF_matchHparental.fsa
vmatch -q TIGRrepeatTrim_HCgss -d -p -l 40 -h 2 -identity 95 -showdesc 0 GridHparentalContig.fsa > HC_matchHparental.txt
./matchMF_HCgss.pl TIGRrepeatTrim_HCgss HC_matchHparental.txt > HC_matchHparental.fsa
cat GridHparentalContig.fsa MF_matchHparental.fsa HC_matchHparental.fsa > Hparental_MF_HC.fsa
./cap3Dong Hparental_MF_HC.fsa -p 90 -s 700 > Hparental_MF_HC.fsa.Cap3Align


echo "Grid I"
./RandomSeqCluster.pl GridIparental.txt RescueMuXYPlasmidAssembly.fsa match.GridI_XYseq.fsa > GridIparental_randomSeq.fsa
./cap3Dong GridIparental_randomSeq.fsa -p 90 -s 700 > GridIparental_randomSeq.fsa.Cap3Align
sed "s/Contig/GridIParentalContig/g" GridIparental_randomSeq.fsa.cap.contigs > GridIparentalContig.fsa
mkvtree -v -allout -dna -pl 7 -db GridIparentalContig.fsa
vmatch -q TIGRrepeatTrim_MFgss -d -p -l 40 -h 2 -identity 95 -showdesc 0 GridIparentalContig.fsa > MF_matchIparental.txt
./matchMF_HCgss.pl TIGRrepeatTrim_MFgss MF_matchIparental.txt > MF_matchIparental.fsa
vmatch -q TIGRrepeatTrim_HCgss -d -p -l 40 -h 2 -identity 95 -showdesc 0 GridIparentalContig.fsa > HC_matchIparental.txt
./matchMF_HCgss.pl TIGRrepeatTrim_HCgss HC_matchIparental.txt > HC_matchIparental.fsa
cat GridIparentalContig.fsa MF_matchIparental.fsa HC_matchIparental.fsa > Iparental_MF_HC.fsa
./cap3Dong Iparental_MF_HC.fsa -p 90 -s 700 > Iparental_MF_HC.fsa.Cap3Align

echo "Grid K"
./RandomSeqCluster.pl GridKparental.txt RescueMuXYPlasmidAssembly.fsa match.GridK_XYseq.fsa > GridKparental_randomSeq.fsa
./cap3Dong GridKparental_randomSeq.fsa -p 90 -s 700 > GridKparental_randomSeq.fsa.Cap3Align
sed "s/Contig/GridKParentalContig/g" GridKparental_randomSeq.fsa.cap.contigs > GridKparentalContig.fsa
mkvtree -v -allout -dna -pl 7 -db GridKparentalContig.fsa
vmatch -q TIGRrepeatTrim_MFgss -d -p -l 40 -h 2 -identity 95 -showdesc 0 GridKparentalContig.fsa > MF_matchKparental.txt
./matchMF_HCgss.pl TIGRrepeatTrim_MFgss MF_matchKparental.txt > MF_matchKparental.fsa
vmatch -q TIGRrepeatTrim_HCgss -d -p -l 40 -h 2 -identity 95 -showdesc 0 GridKparentalContig.fsa > HC_matchKparental.txt
./matchMF_HCgss.pl TIGRrepeatTrim_HCgss HC_matchKparental.txt > HC_matchKparental.fsa
cat GridKparentalContig.fsa MF_matchKparental.fsa HC_matchKparental.fsa > Kparental_MF_HC.fsa
./cap3Dong Kparental_MF_HC.fsa -p 90 -s 700 > Kparental_MF_HC.fsa.Cap3Align


echo "Grid M"
./RandomSeqCluster.pl GridMparental.txt RescueMuXYPlasmidAssembly.fsa match.GridM_XYseq.fsa > GridMparental_randomSeq.fsa
./cap3Dong GridMparental_randomSeq.fsa -p 90 -s 700 > GridMparental_randomSeq.fsa.Cap3Align
sed "s/Contig/GridMParentalContig/g" GridMparental_randomSeq.fsa.cap.contigs > GridMparentalContig.fsa
mkvtree -v -allout -dna -pl 7 -db GridMparentalContig.fsa
vmatch -q TIGRrepeatTrim_MFgss -d -p -l 40 -h 2 -identity 95 -showdesc 0 GridMparentalContig.fsa > MF_matchMparental.txt
./matchMF_HCgss.pl TIGRrepeatTrim_MFgss MF_matchMparental.txt > MF_matchMparental.fsa
vmatch -q TIGRrepeatTrim_HCgss -d -p -l 40 -h 2 -identity 95 -showdesc 0 GridMparentalContig.fsa > HC_matchMparental.txt
./matchMF_HCgss.pl TIGRrepeatTrim_HCgss HC_matchMparental.txt > HC_matchMparental.fsa
cat GridMparentalContig.fsa MF_matchMparental.fsa HC_matchMparental.fsa > Mparental_MF_HC.fsa
./cap3Dong Mparental_MF_HC.fsa -p 90 -s 700 > Mparental_MF_HC.fsa.Cap3Align


echo "Grid P"
./RandomSeqCluster.pl GridPparental.txt RescueMuXYPlasmidAssembly.fsa match.GridP_XYseq.fsa > GridPparental_randomSeq.fsa
./cap3Dong GridPparental_randomSeq.fsa -p 90 -s 700 > GridPparental_randomSeq.fsa.Cap3Align
sed "s/Contig/GridGParentalContig/g" GridGparental_randomSeq.fsa.cap.contigs > GridPparentalContig.fsa
mkvtree -v -allout -dna -pl 7 -db GridPparentalContig.fsa
vmatch -q TIGRrepeatTrim_MFgss -d -p -l 40 -h 2 -identity 95 -showdesc 0 GridPparentalContig.fsa > MF_matchPparental.txt
./matchMF_HCgss.pl TIGRrepeatTrim_MFgss MF_matchPparental.txt > MF_matchPparental.fsa
vmatch -q TIGRrepeatTrim_HCgss -d -p -l 40 -h 2 -identity 95 -showdesc 0 GridPparentalContig.fsa > HC_matchPparental.txt
./matchMF_HCgss.pl TIGRrepeatTrim_HCgss HC_matchPparental.txt > HC_matchPparental.fsa
cat GridPparentalContig.fsa MF_matchPparental.fsa HC_matchPparental.fsa > Pparental_MF_HC.fsa
./cap3Dong Pparental_MF_HC.fsa -p 90 -s 700 > Pparental_MF_HC.fsa.Cap3Align