src/hg/makeDb/doc/tetNig2.txt 1.4
1.4 2009/08/07 14:42:33 braney
make Human Proteins track. Needs re-doing to deal with chrUn correctly
Index: src/hg/makeDb/doc/tetNig2.txt
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/makeDb/doc/tetNig2.txt,v
retrieving revision 1.3
retrieving revision 1.4
diff -b -B -U 4 -r1.3 -r1.4
--- src/hg/makeDb/doc/tetNig2.txt 6 Aug 2009 22:59:01 -0000 1.3
+++ src/hg/makeDb/doc/tetNig2.txt 7 Aug 2009 14:42:33 -0000 1.4
@@ -210,4 +210,170 @@
'update dbDb set defaultPos="chr10:2797091-2804214" where name="tetNig2";' \
hgcentraltest
#########################################################################
+# HUMAN (hg18) PROTEINS TRACK (DONE 2009-08-07 braney )
+
+### !!!! needs re-doing to deal with chrUn correctly !!!!
+
+ # bash if not using bash shell already
+
+ cd /cluster/data/tetNig2
+ mkdir /cluster/data/tetNig2/blastDb
+
+ awk '{if ($2 > 1000000) print $1}' chrom.sizes > 1meg.lst
+ twoBitToFa -seqList=1meg.lst tetNig2.2bit 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 tetNig2.2bit 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
+# 394
+
+
+ mkdir -p /cluster/data/tetNig2/bed/tblastn.hg18KG
+ cd /cluster/data/tetNig2/bed/tblastn.hg18KG
+ echo ../../blastDb/*.nsq | xargs ls -S | sed "s/\.nsq//" > query.lst
+ wc -l query.lst
+# 394 query.lst
+
+ # we want around 100000 jobs
+ calc `wc /cluster/data/hg18/bed/blat.hg18KG/hg18KG.psl | awk '{print $1}'`/\(100000/`wc query.lst | awk '{print $1}'`\)
+
+# 36727/(100000/394) = 144.704380
+
+ mkdir -p kgfa
+ split -l 145 /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
+# 254 254 3302 kg.lst
+
+ mkdir -p blastOut
+ for i in `cat kg.lst`; do mkdir blastOut/`basename $i .fa`; done
+ tcsh
+ cd /cluster/data/tetNig2/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/tetNig2/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/tetNig2/bed/tblastn.hg18KG
+ gensub2 query.lst kg.lst blastGsub blastSpec
+ para create blastSpec
+# para try, check, push, check etc.
+
+ para time
+# Completed: 100076 of 100076 jobs
+# CPU time in finished jobs: 2219419s 36990.31m 616.51h 25.69d 0.070 y
+# IO & Wait Time: 445463s 7424.39m 123.74h 5.16d 0.014 y
+# Average job time: 27s 0.44m 0.01h 0.00d
+# Longest finished job: 319s 5.32m 0.09h 0.00d
+# Submission to last job: 2791s 46.52m 0.78h 0.03d
+
+ ssh swarm
+ cd /cluster/data/tetNig2/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 $1`.psl)
+'_EOF_'
+ chmod +x chainOne
+ ls -1dS ../blastOut/kg?? > chain.lst
+ gensub2 chain.lst single chainGsub chainSpec
+ # do the cluster run for chaining
+ para create chainSpec
+ para try, check, push, check etc.
+
+# Completed: 254 of 254 jobs
+# CPU time in finished jobs: 590077s 9834.62m 163.91h 6.83d 0.019 y
+# IO & Wait Time: 20749s 345.81m 5.76h 0.24d 0.001 y
+# Average job time: 2405s 40.08m 0.67h 0.03d
+# Longest finished job: 36592s 609.87m 10.16h 0.42d
+# Submission to last job: 36604s 610.07m 10.17h 0.42d
+
+ cd /cluster/data/tetNig2/bed/tblastn.hg18KG/blastOut
+ for i in kg??
+ do
+ cat c.$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: 38517 failed: 0 errors: 0
+
+ # load table
+ ssh hgwdev
+ cd /cluster/data/tetNig2/bed/tblastn.hg18KG
+ hgLoadPsl tetNig2 blastHg18KG.psl
+
+ # check coverage
+ featureBits tetNig2 blastHg18KG
+# 18646943 bases of 332311746 (5.611%) in intersection
+
+ featureBits tetNig2 blastHg18KG ensGene -enrichment
+# blastHg18KG 5.611%, ensGene 9.520%, both 4.993%, cover 88.97%, enrich 9.35x
+
+ rm -rf blastOut
+#end tblastn