src/hg/makeDb/doc/ailMel1.txt 1.11
1.11 2010/04/19 17:03:05 braney
starting Human Proteins
Index: src/hg/makeDb/doc/ailMel1.txt
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/makeDb/doc/ailMel1.txt,v
retrieving revision 1.10
retrieving revision 1.11
diff -b -B -U 4 -r1.10 -r1.11
--- src/hg/makeDb/doc/ailMel1.txt 16 Apr 2010 17:25:05 -0000 1.10
+++ src/hg/makeDb/doc/ailMel1.txt 19 Apr 2010 17:03:05 -0000 1.11
@@ -414,4 +414,193 @@
cat fb.ailMel1.chainRn4Link.txt
# 695366144 bases of 2245312831 (30.970%) in intersection
#########################################################################
+# HUMAN (hg18) PROTEINS TRACK (working
+ # bash if not using bash shell already
+
+ cd /cluster/data/ailMel1
+ mkdir /cluster/data/ailMel1/blastDb
+
+ awk '{if ($2 > 1000000) print $1}' chrom.sizes > 1meg.lst
+ twoBitToFa -seqList=1meg.lst ailMel1.2bit 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 ailMel1.2bit 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/ailMel1/bed/tblastn.hg18KG
+ cd /cluster/data/ailMel1/bed/tblastn.hg18KG
+ echo ../../blastDb/*.nsq | xargs ls -S | sed "s/\.nsq//" > query.lst
+ wc -l query.lst
+# 2915 query.lst
+
+ # we want around 350000 jobs
+ calc `wc /cluster/data/hg18/bed/blat.hg18KG/hg18KG.psl | awk '{print $1}'`/\(350000/`wc query.lst | awk '{print $1}'`\)
+
+# 36727/(350000/2915) = 305.883443
+
+ mkdir -p kgfa
+ split -l 306 /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
+# 121 121 1573 kg.lst
+
+ mkdir -p blastOut
+ for i in `cat kg.lst`; do mkdir blastOut/`basename $i .fa`; done
+ tcsh
+ cd /cluster/data/ailMel1/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/ailMel1/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/ailMel1/bed/tblastn.hg18KG
+ gensub2 query.lst kg.lst blastGsub blastSpec
+ para create blastSpec
+# para try, check, push, check etc.
+
+ para time
+# Completed: 352715 of 352715 jobs
+# CPU time in finished jobs: 13184770s 219746.16m 3662.44h 152.60d 0.418 y
+# IO & Wait Time: 1844130s 30735.51m 512.26h 21.34d 0.058 y
+# Average job time: 43s 0.71m 0.01h 0.00d
+# Longest finished job: 149s 2.48m 0.04h 0.00d
+# Submission to last job: 16902s 281.70m 4.70h 0.20d
+
+
+ ssh swarm
+ cd /cluster/data/ailMel1/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=150000 stdin ../c.`basename $1`.psl)
+'_EOF_'
+ chmod +x chainOne
+ ls -1dS ../blastOut/kg?? > chain.lst
+ gensub2 chain.lst single chainGsub chainSpec
+ # do the cluster run for chaining
+ para create chainSpec
+ para try, check, push, check etc.
+
+# Completed: 121 of 121 jobs
+# CPU time in finished jobs: 342462s 5707.70m 95.13h 3.96d 0.011 y
+# IO & Wait Time: 67882s 1131.37m 18.86h 0.79d 0.002 y
+# Average job time: 3391s 56.52m 0.94h 0.04d
+# Longest finished job: 13532s 225.53m 3.76h 0.16d
+# Submission to last job: 13544s 225.73m 3.76h 0.16d
+
+ cd /cluster/data/ailMel1/bed/tblastn.hg18KG/blastOut
+ for i in kg??
+ do
+ cat c.$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 $i
+ done
+ sort u.*.psl m60* | uniq | sort -T /tmp -k 14,14 -k 16,16n -k 17,17n > ../blastHg18KG.psl
+ cd ..
+ pslCheck blastHg18KG.psl
+# checked: 83553 failed: 0 errors: 0
+
+ # load table
+ ssh hgwdev
+ cd /cluster/data/ailMel1/bed/tblastn.hg18KG
+ hgLoadPsl ailMel1 blastHg18KG.psl
+
+ # check coverage
+ featureBits ailMel1 blastHg18KG
+# 36312685 bases of 2231298548 (1.627%) in intersection
+
+ featureBits ailMel1 blastHg18KG ensGene -enrichment
+# blastHg18KG 1.627%, ensGene 1.284%, both 0.845%, cover 51.91%, enrich 40.42x
+
+ rm -rf blastOut
+#end tblastn
+#############################################################################
+# N-SCAN gene predictions (nscanGene) - (2010-04-18 markd)
+
+/mblab.wustl.edu/predictions/taeGut1
+
+ # obtained NSCAN predictions from michael brent's group
+ # at WUSTL
+ cd /cluster/data/ailMel1/bed/nscan
+ wget -nv http://mblab.wustl.edu/predictions/pig/ailMel1/readme.txt
+ wget -nv http://mblab.wustl.edu/predictions/pig/ailMel1/ailMel1.fa
+ wget -nv http://mblab.wustl.edu/predictions/pig/ailMel1/ailMel1.gtf
+ gzip ailMel1.*
+ chmod a-w *
+
+ # load track
+ gtfToGenePred -genePredExt ailMel1.gtf.gz stdout | hgLoadGenePred -genePredExt ailMel1 nscanGene stdin
+ hgPepPred ailMel1 generic nscanPep ailMel1.fa.gz
+ rm *.tab
+
+ # pig/ailMel1/trackDb.ra, add:
+ track nscanGene override
+ informant Pig N-SCAN uses human (hg19) as the informant, updated with PASA clusters of pig cDNAs.
+
+ # veryify top-level search spec, should produce no results:
+ hgsql -Ne 'select name from nscanGene' ailMel1 | egrep -v '^chr[0-9a-zA-Z_]+\.([0-9]+|pasa)((\.[0-9a-z]+)?\.[0-9a-z]+)?$' |head
+############################################################################