18ca361b254102fc711e421c2056771598d6fc34
hiram
  Mon Jun 28 14:18:36 2021 -0700
rsync dynamic blat files to the dynablat-01 machine and add rules to test dynamic blat refs #27556

diff --git src/hg/makeDb/doc/asmHubs/testDynBlat.sh src/hg/makeDb/doc/asmHubs/testDynBlat.sh
new file mode 100755
index 0000000..83b5959
--- /dev/null
+++ src/hg/makeDb/doc/asmHubs/testDynBlat.sh
@@ -0,0 +1,64 @@
+#!/bin/bash
+
+set -beEu -o pipefail
+
+if [ $# -ne 1 ]; then
+  printf "usage: testDynBlat.sh asmId > result.json\n" 1>&2
+  exit 255
+fi
+
+export blatHost="dynablat-01"
+export blatPort="4040"
+
+export asmId=$1
+export gcX=${asmId:0:3}
+export d0=${asmId:4:3}
+export d1=${asmId:7:3}
+export d2=${asmId:10:3}
+export dataDir="$gcX/$d0/$d1/$d2/$asmId"
+export srcDir="/hive/data/genomes/asmHubs/$dataDir"
+export faaFile="/cluster/home/hiram/kent/src/hg/makeDb/doc/asmHubs/rtp1.ace2.faa.gz"
+
+time (gfClient -genome=$asmId -genomeDataDir=$dataDir -t=dnax -q=prot \
+  $blatHost $blatPort $srcDir $faaFile stdout > $asmId.rtp1.ace2.psl) 2> $asmId.dynBlat.log
+
+export realTime=`grep -w real $asmId.dynBlat.log | awk '{print $NF}'`
+export resultLines=`pslScore $asmId.rtp1.ace2.psl | wc -l`
+printf "%s\t%d\t%s\n" "${asmId}" "${resultLines}" "${realTime}"
+rm -f $asmId.rtp1.ace2.psl $asmId.dynBlat.log
+
+exit $?
+
+export hubUrl="https://hgdownload-test.gi.ucsc.edu/hubs/$gcX/$d0/$d1/$d2/$asmId/hub.txt"
+
+curl -I "$hubUrl"
+
+curl -o "$asmId.json" \
+  --data-urlencode "hubUrl=https://hgdownload-test.gi.ucsc.edu/hubs/$gcX/$d0/$d1/$d2/$asmId/hub.txt" \
+  --data-urlencode "userSeq=>hg38.RTP1.prot
+MRIFRPWRLRCPALHLPSLSVFSLRWKLPSLTTDETMCKSVTTDEWKKVFYEKMEEAKPA
+DSWDLIIDPNLKHNVLSPGWKQYLELHASGRFHCSWCWHTWQSPYVVILFHMFLDRAQRA
+GSVRMRVFKQLCYECGTARLDESSMLEENIEGLVDNLITSLREQCYGERGGQYRIHVASR
+QDNRRHRGEFCEACQEGIVHWKPSEKLLEEEATTYTFSRAPSPTKSQDQTGSGWNFCSIP
+WCLFWATVLLLIIYLQFSFRSSV
+>hg38.ACE2.prot
+MSSSSWLLLSLVAVTAAQSTIEEQAKTFLDKFNHEAEDLFYQSSLASWNYNTNITEENVQ
+NMNNAGDKWSAFLKEQSTLAQMYPLQEIQNLTVKLQLQALQQNGSSVLSEDKSKRLNTIL
+NTMSTIYSTGKVCNPDNPQECLLLEPGLNEIMANSLDYNERLWAWESWRSEVGKQLRPLY
+EEYVVLKNEMARANHYEDYGDYWRGDYEVNGVDGYDYSRGQLIEDVEHTFEEIKPLYEHL
+HAYVRAKLMNAYPSYISPIGCLPAHLLGDMWGRFWTNLYSLTVPFGQKPNIDVTDAMVDQ
+AWDAQRIFKEAEKFFVSVGLPNMTQGFWENSMLTDPGNVQKAVCHPTAWDLGKGDFRILM
+CTKVTMDDFLTAHHEMGHIQYDMAYAAQPFLLRNGANEGFHEAVGEIMSLSAATPKHLKS
+IGLLSPDFQEDNETEINFLLKQALTIVGTLPFTYMLEKWRWMVFKGEIPKDQWMKKWWEM
+KREIVGVVEPVPHDETYCDPASLFHVSNDYSFIRYYTRTLYQFQFQEALCQAAKHEGPLH
+KCDISNSTEAGQKLFNMLRLGKSEPWTLALENVVGAKNMNVRPLLNYFEPLFTWLKDQNK
+NSFVGWSTDWSPYADQSIKVRISLKSALGDKAYEWNDNEMYLFRSSVAYAMRQYFLKVKN
+QMILFGEEDVRVANLKPRISFNFFVTAPKNVSDIIPRTEVEKAIRMSRSRINDAFRLNDN
+SLEFLGIQPTLGPPNQPPVSIWLIVFGVVMGVIVVGIVILIFTGIRDRKKKNKARSGENP
+YASIDISKGENNPGFQNTDDVQTSF" \
+  --data-urlencode "db=${asmId}" \
+  --data-urlencode "type=protein" \
+  --data-urlencode "output=json" \
+    https://genome-test.gi.ucsc.edu/cgi-bin/hgBlat
+
+cat $asmId.json | python -mjson.tool > $asmId.json.txt