6f8a50068e6c1558dbbf286b9a573800c68b1fb1
braney
  Tue May 28 17:16:22 2024 -0700
ongoing work on pair browser

diff --git src/hg/utils/buildPairAssembly/makePair src/hg/utils/buildPairAssembly/makePair
index aa96a71..748685c 100755
--- src/hg/utils/buildPairAssembly/makePair
+++ src/hg/utils/buildPairAssembly/makePair
@@ -1,30 +1,30 @@
 #!/bin/sh -ex
 
 pairRefDb=$1
 pairRefSeq=$2
 pairRefDb2bit=$3
 pairQueryDb=$4
 pairQuerySeq=$5
 pairQueryDb2bit=$6
 pairChain=$7
 
 filterChain=$pairRefSeq.$pairQuerySeq.$pairChain
 
 chainFilter -t=$pairRefSeq -q=$pairQuerySeq $pairChain > $filterChain
 
-buildPairAssembly $filterChain $pairRefSeq $pairRefDb2bit $pairQuerySeq $pairQueryDb2bit out.fa query.psl target.psl map.bed dup.bed miss.bed baseTarget.bed baseQuery.bed
+buildPairAssembly $filterChain $pairRefSeq $pairRefDb2bit $pairQuerySeq $pairQueryDb2bit out.fa query.psl target.psl map.bed dup.bed miss.bed baseTarget.bed baseQuery.bed synBlocks.bed
 
 
 rm -rf hub
 mkdir hub
 
 faToTwoBit out.fa hub/buildPair.2bit
 twoBitInfo hub/buildPair.2bit hub/buildPair.sizes.txt
 bedToBigBed  -type=bed9+4 map.bed hub/buildPair.sizes.txt hub/map.bb
 
 axtChain -psl -linearGap=medium query.psl hub/buildPair.2bit $pairQueryDb2bit query.chain
 hgLoadChain -noBin -test hg38 bigChain  query.chain
 sed 's/\.000000//' chain.tab | awk 'BEGIN {OFS="\t"} {print $2, $4, $5, $11, 1000, $8, $3, $6, $7, $9, $10, $1}' > query.bigChain
 bedToBigBed -type=bed6+6 -as=$HOME/kent/src/hg/lib/bigChain.as -tab query.bigChain  hub/buildPair.sizes.txt hub/queryChain.bb
 awk 'BEGIN {OFS="\t"} {print $1, $2, $3, $5, $4}' link.tab | sort -k1,1 -k2,2n > bigChain.bigLink
 bedToBigBed -type=bed4+1 -as=$HOME/kent/src/hg/lib/bigLink.as -tab bigChain.bigLink hub/buildPair.sizes.txt hub/queryChain.link.bb
@@ -37,30 +37,33 @@
 bedToBigBed -type=bed4+1 -as=$HOME/kent/src/hg/lib/bigLink.as -tab bigChain.bigLink hub/buildPair.sizes.txt hub/targetChain.link.bb
 
 chainSwap query.chain swap.query.chain
 chainSwap target.chain swap.target.chain
 awk '{print $1,$2,$3,$7}' dup.bed | liftOver -minMatch=0.001 stdin swap.query.chain tmp foo
 awk '{print $4,$5,$6,$7}' dup.bed | liftOver -minMatch=0.001 stdin swap.target.chain tmp2 foo
 sort tmp tmp2 > tmp3
 bedToBigBed -type=bed4 -tab tmp3 hub/buildPair.sizes.txt hub/dups.bb
 
 bedToBigBed -type=bed4 miss.bed hub/buildPair.sizes.txt hub/mismatch.bb
 
 bedToBigBed -type=bed4+1 baseTarget.bed hub/buildPair.sizes.txt hub/baseTarget.bb
 
 bedToBigBed -type=bed4+1 baseQuery.bed hub/buildPair.sizes.txt hub/baseQuery.bb
 
+sort -k1,1 -k2,2n synBlocks.bed > sorted.bed
+bedToBigBed -type=bed4 sorted.bed hub/buildPair.sizes.txt hub/synBlocks.bb
+
 genome=$pairQueryDb
 gcX="${genome:0:3}"
 d0="${genome:4:3}"
 d1="${genome:7:3}"
 d2="${genome:10:3}"
 
 tmp=`cd /usr/local/apache/htdocs/hubs; echo $gcX/$d0/$d1/$d2/$genome/bbi/*ens*.bb `
 ensGeneBb=https://hgdownload.soe.ucsc.edu/hubs/$tmp
 tmp=`cd /usr/local/apache/htdocs/hubs; echo $gcX/$d0/$d1/$d2/$genome/bbi/*rmsk.bb `
 rmskBb=https://hgdownload.soe.ucsc.edu/hubs/$tmp
 tmp=`cd /usr/local/apache/htdocs/hubs; echo $gcX/$d0/$d1/$d2/$genome/bbi/*simpleRepeat.bb `
 simpleBb=https://hgdownload.soe.ucsc.edu/hubs/$tmp
 
 
 cat << _EOF_ > hub/groups.txt
@@ -142,30 +145,38 @@
 priority 0.1
 type bigBaseView
 bigDataUrl baseQuery.bb
 shortLabel BaseView
 longLabel $pairQueryDb BaseView
 group query
 
 track baseTarget
 priority 0.1
 type bigBaseView
 bigDataUrl baseTarget.bb
 shortLabel BaseView
 longLabel $pairRefDb BaseView
 group target
 
+track synBlocks
+priority 0.1
+type bigBed 4
+bigDataUrl synBlocks.bb
+shortLabel synBlocks
+longLabel Synteny Blocks
+group map
+
 track mismatch
 type bigBed 4
 bigDataUrl mismatch.bb
 shortLabel Mismatches
 longLabel Mismatches between $pairRefDb and $pairQueryDb
 group map
 
 #track trmsk
 #type bigBed 9
 #itemRgb on
 #shortLabel Rmsk
 #longLabel $pairRefDb Rmsk
 #bigDataUrl $rmskBb
 #quickLiftUrl targetChain.bb
 #group target