src/hg/makeDb/doc/sacCer2.txt 1.2
1.2 2009/02/10 22:19:18 braney
added Human Proteins
Index: src/hg/makeDb/doc/sacCer2.txt
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/makeDb/doc/sacCer2.txt,v
retrieving revision 1.1
retrieving revision 1.2
diff -b -B -U 4 -r1.1 -r1.2
--- src/hg/makeDb/doc/sacCer2.txt 10 Feb 2009 20:27:13 -0000 1.1
+++ src/hg/makeDb/doc/sacCer2.txt 10 Feb 2009 22:19:18 -0000 1.2
@@ -309,4 +309,168 @@
cvs ci -m "Added ce6 - C. elegans WS190" \
etc/align.dbs etc/hgwdev.dbs
make etc-update
+###########################################################################
+# HUMAN (hg18) PROTEINS TRACK (DONE 2009-02-10 braney )
+ # bash if not using bash shell already
+
+ cd /cluster/data/sacCer2
+ mkdir /cluster/data/sacCer2/blastDb
+
+ awk '{if ($2 > 1000000) print $1}' chrom.sizes > 1meg.lst
+ twoBitToFa -seqList=1meg.lst sacCer2.2bit 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 sacCer2.2bit 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
+# 14
+
+ mkdir -p /cluster/data/sacCer2/bed/tblastn.hg18KG
+ cd /cluster/data/sacCer2/bed/tblastn.hg18KG
+ echo ../../blastDb/*.nsq | xargs ls -S | sed "s/\.nsq//" > query.lst
+ wc -l query.lst
+# 14 query.lst
+
+ # we want around 50000 jobs
+ calc `wc /cluster/data/hg18/bed/blat.hg18KG/hg18KG.psl | awk '{print $1}'`/\(50000/`wc query.lst | awk '{print $1}'`\)
+
+# 36727/(50000/14) = 10.283560
+
+# chose 100 because 10 is too small
+ mkdir -p kgfa
+ split -l 100 /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
+# 368 368 4784 kg.lst
+
+ mkdir -p blastOut
+ for i in `cat kg.lst`; do mkdir blastOut/`basename $i .fa`; done
+ tcsh
+ cd /cluster/data/sacCer2/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/sacCer2/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/sacCer2/bed/tblastn.hg18KG
+ gensub2 query.lst kg.lst blastGsub blastSpec
+ para create blastSpec
+# para try, check, push, check etc.
+
+ para time
+# Completed: 5152 of 5152 jobs
+# CPU time in finished jobs: 71064s 1184.40m 19.74h 0.82d 0.002 y
+# IO & Wait Time: 16915s 281.92m 4.70h 0.20d 0.001 y
+# Average job time: 17s 0.28m 0.00h 0.00d
+# Longest finished job: 69s 1.15m 0.02h 0.00d
+# Submission to last job: 156s 2.60m 0.04h 0.00d
+
+ ssh swarm
+ cd /cluster/data/sacCer2/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 $1`.psl)
+'_EOF_'
+ chmod +x chainOne
+ ls -1dS ../blastOut/kg?? > chain.lst
+ gensub2 chain.lst single chainGsub chainSpec
+ # do the cluster run for chaining
+ para create chainSpec
+ para try, check, push, check etc.
+
+# Completed: 368 of 368 jobs
+# CPU time in finished jobs: 5s 0.09m 0.00h 0.00d 0.000 y
+# IO & Wait Time: 1487s 24.78m 0.41h 0.02d 0.000 y
+# Average job time: 4s 0.07m 0.00h 0.00d
+# Longest finished job: 10s 0.17m 0.00h 0.00d
+# Submission to last job: 37s 0.62m 0.01h 0.00d
+
+ cd /cluster/data/sacCer2/bed/tblastn.hg18KG/blastOut
+ for i in kg??
+ do
+ cat c.$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: 5050 failed: 0 errors: 0
+
+ # load table
+ ssh hgwdev
+ cd /cluster/data/sacCer2/bed/tblastn.hg18KG
+ hgLoadPsl sacCer2 blastHg18KG.psl
+
+ # check coverage
+ featureBits sacCer2 blastHg18KG
+# 1261725 bases of 12162995 (10.373%) in intersection
+
+ featureBits sacCer2 blastHg18KG sgdGene -enrichment
+# blastHg18KG 10.373%, sgdGene 72.883%, both 10.320%, cover 99.49%, enrich 1.37x
+
+ rm -rf blastOut
+#end tblastn