src/hg/makeDb/doc/susScr1.txt 1.2
1.2 2009/11/16 19:44:04 braney
started Human Proteins
Index: src/hg/makeDb/doc/susScr1.txt
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/makeDb/doc/susScr1.txt,v
retrieving revision 1.1
retrieving revision 1.2
diff -b -B -U 4 -r1.1 -r1.2
--- src/hg/makeDb/doc/susScr1.txt 16 Nov 2009 19:40:42 -0000 1.1
+++ src/hg/makeDb/doc/susScr1.txt 16 Nov 2009 19:44:04 -0000 1.2
@@ -194,4 +194,168 @@
cvs ci -m "Added susScr1 - Tetraodon Nigirividis" \
etc/align.dbs etc/hgwdev.dbs
make etc-update
+##########################################################################
+# HUMAN (hg18) PROTEINS TRACK (Working...
+ # bash if not using bash shell already
+
+ cd /cluster/data/susScr1
+ mkdir /cluster/data/susScr1/blastDb
+
+ awk '{if ($2 > 1000000) print $1}' chrom.sizes > 1meg.lst
+ twoBitToFa -seqList=1meg.lst susScr1.2bit temp.fa
+ faSplit gap temp.fa 1000000 blastDb/x -lift=blastDb.lft
+ rm temp.fa 1meg.lst
+
+ awk '{if ($2 <= 1000000) print $1}' chrom.sizes > less1meg.lst
+ twoBitToFa -seqList=less1meg.lst susScr1.2bit temp.fa
+ faSplit about temp.fa 1000000 blastDb/y
+ rm temp.fa less1meg.lst
+
+ cd blastDb
+ for i in *.fa
+ do
+ /hive/data/outside/blast229/formatdb -i $i -p F
+ done
+ rm *.fa
+ ls *.nsq | wc -l
+# 2915
+
+ mkdir -p /cluster/data/susScr1/bed/tblastn.hg18KG
+ cd /cluster/data/susScr1/bed/tblastn.hg18KG
+ echo ../../blastDb/*.nsq | xargs ls -S | sed "s/\.nsq//" > query.lst
+ wc -l query.lst
+# 2915 query.lst
+
+ # we want around 200000 jobs
+ calc `wc /cluster/data/hg18/bed/blat.hg18KG/hg18KG.psl | awk '{print $1}'`/\(200000/`wc query.lst | awk '{print $1}'`\)
+
+# 36727/(200000/2915) = 535.296025
+
+ mkdir -p kgfa
+ split -l 535 /cluster/data/hg18/bed/blat.hg18KG/hg18KG.psl kgfa/kg
+ cd kgfa
+ for i in *; do
+ nice pslxToFa $i $i.fa;
+ rm $i;
+ done
+ cd ..
+ ls -1S kgfa/*.fa > kg.lst
+ wc kg.lst
+# 69 69 897 kg.lst
+
+
+ mkdir -p blastOut
+ for i in `cat kg.lst`; do mkdir blastOut/`basename $i .fa`; done
+ tcsh
+ cd /cluster/data/susScr1/bed/tblastn.hg18KG
+ cat << '_EOF_' > blastGsub
+#LOOP
+blastSome $(path1) {check in line $(path2)} {check out exists blastOut/$(root2)/q.$(root1).psl }
+#ENDLOOP
+'_EOF_'
+
+ cat << '_EOF_' > blastSome
+#!/bin/sh
+BLASTMAT=/hive/data/outside/blast229/data
+export BLASTMAT
+g=`basename $2`
+f=/tmp/`basename $3`.$g
+for eVal in 0.01 0.001 0.0001 0.00001 0.000001 1E-09 1E-11
+do
+if /hive/data/outside/blast229/blastall -M BLOSUM80 -m 0 -F no -e $eVal -p tblastn -d $1 -i $2 -o $f.8
+then
+ mv $f.8 $f.1
+ break;
+fi
+done
+if test -f $f.1
+then
+ if /cluster/bin/i386/blastToPsl $f.1 $f.2
+ then
+ liftUp -nosort -type=".psl" -nohead $f.3 /cluster/data/susScr1/blastDb.lft carry $f.2
+ liftUp -nosort -type=".psl" -pslQ -nohead $3.tmp /cluster/data/hg18/bed/blat.hg18KG/protein.lft warn $f.3
+ if pslCheck -prot $3.tmp
+ then
+ mv $3.tmp $3
+ rm -f $f.1 $f.2 $f.3 $f.4
+ fi
+ exit 0
+ fi
+fi
+rm -f $f.1 $f.2 $3.tmp $f.8 $f.3 $f.4
+exit 1
+'_EOF_'
+ # << happy emacs
+ chmod +x blastSome
+ exit
+
+ ssh swarm
+ cd /cluster/data/susScr1/bed/tblastn.hg18KG
+ gensub2 query.lst kg.lst blastGsub blastSpec
+ para create blastSpec
+# para try, check, push, check etc.
+
+ para time
+# Completed: 201135 of 201135 jobs
+# CPU time in finished jobs: 13017817s 216963.62m 3616.06h 150.67d 0.413 y
+# IO & Wait Time: 1450739s 24178.98m 402.98h 16.79d 0.046 y
+# Average job time: 72s 1.20m 0.02h 0.00d
+# Longest finished job: 244s 4.07m 0.07h 0.00d
+# Submission to last job: 18278s 304.63m 5.08h 0.21d
+
+
+ ssh swarm
+ cd /cluster/data/susScr1/bed/tblastn.hg18KG
+ mkdir chainRun
+ cd chainRun
+ tcsh
+ cat << '_EOF_' > chainGsub
+#LOOP
+chainOne $(path1)
+#ENDLOOP
+'_EOF_'
+
+ cat << '_EOF_' > chainOne
+(cd $1; cat q.*.psl | simpleChain -prot -outPsl -maxGap=12000 stdin ../c.`basename $1`.psl)
+'_EOF_'
+ chmod +x chainOne
+ ls -1dS ../blastOut/kg?? > chain.lst
+ gensub2 chain.lst single chainGsub chainSpec
+ # do the cluster run for chaining
+ para create chainSpec
+ para try, check, push, check etc.
+
+# Completed: 64 of 64 jobs
+# CPU time in finished jobs: 29478s 491.30m 8.19h 0.34d 0.001 y
+# IO & Wait Time: 19822s 330.37m 5.51h 0.23d 0.001 y
+# Average job time: 770s 12.84m 0.21h 0.01d
+# Longest finished job: 2868s 47.80m 0.80h 0.03d
+# Submission to last job: 2882s 48.03m 0.80h 0.03d
+
+ cd /cluster/data/susScr1/bed/tblastn.hg18KG/blastOut
+ for i in kg??
+ do
+ cat c.$i.psl | awk "(\$13 - \$12)/\$11 > 0.6 {print}" > c60.$i.psl
+ sort -rn c60.$i.psl | pslUniq stdin u.$i.psl
+ awk "((\$1 / \$11) ) > 0.60 { print }" c60.$i.psl > m60.$i.psl
+ echo $i
+ done
+ sort u.*.psl m60* | uniq | sort -T /tmp -k 14,14 -k 16,16n -k 17,17n > ../blastHg18KG.psl
+ cd ..
+ pslCheck blastHg18KG.psl
+# checked: 43305 failed: 0 errors: 0
+
+ # load table
+ ssh hgwdev
+ cd /cluster/data/susScr1/bed/tblastn.hg18KG
+ hgLoadPsl susScr1 blastHg18KG.psl
+
+ # check coverage
+ featureBits susScr1 blastHg18KG
+# 42480830 bases of 3118565340 (1.362%) in intersection
+
+ featureBits susScr1 blastHg18KG xenoRefGene -enrichment
+# blastHg18KG 1.362%, xenoRefGene 1.615%, both 0.695%, cover 51.03%, enrich 31.60x
+ rm -rf blastOut
+#end tblastn