e0fa53bc686c9aed8e712e76638a00933e3a560f
braney
  Sun May 19 16:48:21 2024 -0700
ongoing work on pair browser

diff --git src/hg/utils/buildPairAssembly/makePair src/hg/utils/buildPairAssembly/makePair
index 5dad53e..efa37ed 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
+buildPairAssembly $filterChain $pairRefSeq $pairRefDb2bit $pairQuerySeq $pairQueryDb2bit out.fa query.psl target.psl map.bed dup.bed miss.bed baseTarget.bed baseQuery.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
@@ -33,30 +33,43 @@
 hgLoadChain -noBin -test hg38 bigChain  target.chain
 sed 's/\.000000//' chain.tab | awk 'BEGIN {OFS="\t"} {print $2, $4, $5, $11, 1000, $8, $3, $6, $7, $9, $10, $1}' > targetChain.bigChain
 bedToBigBed -type=bed6+6 -as=$HOME/kent/src/hg/lib/bigChain.as -tab targetChain.bigChain  hub/buildPair.sizes.txt hub/targetChain.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/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
+
+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
+
 
 cat << _EOF_ > hub/hub.txt
 hub buildPair
 longLabel buildPair
 email braney@ucsc.edu
 shortLabel buildPair
 useOneFile on
 
 genome buildPair
 defaultPos buildPair:1-2
 organism buildPair
 twoBitPath buildPair.2bit
 
 track map
 type bigBed 9
@@ -86,21 +99,42 @@
 bigDataUrl  /gbdb/hg38/ncbiRefSeq/ncbiRefSeq.bb
 longLabel NCBI RefSeq genes, curated and predicted sets (NM_*, XM_*, NR_*, XR_*,
  NP_* or YP_*)
 baseColorUseCds given
 baseColorDefault genomicCodons
 priority 1
 quickLiftUrl targetChain.bb
 canPack 1
 
 track dups
 type bigBed 4
 bigDataUrl dups.bb
 shortLabel dups
 longLabel dups
 
+track baseTarget
+type bigBed 4
+bigDataUrl baseTarget.bb
+shortLabel baseTarget
+longLabel baseTarget
+
 track mismatch
 type bigBed 4
 bigDataUrl mismatch.bb
 shortLabel mismatch
 longLabel mismatch
+
+track rmsk
+type bigBed
+shortLabel Query Rmsk
+longLabel Query Rmsk
+bigDataUrl $rmskBb
+quickLiftUrl queryChain.bb
+
+track ensGeneQuery
+type bigGenePred
+shortLabel Query Ensembl
+longLabel Query Ensembl
+bigDataUrl $ensGeneBb
+quickLiftUrl queryChain.bb
+
 _EOF_