src/hg/makeDb/doc/methBurt1.txt 1.2
1.2 2009/11/25 21:48:41 hiram
change autoScaleDefault to autoScale
Index: src/hg/makeDb/doc/methBurt1.txt
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/makeDb/doc/methBurt1.txt,v
retrieving revision 1.1
retrieving revision 1.2
diff -b -B -U 1000000 -r1.1 -r1.2
--- src/hg/makeDb/doc/methBurt1.txt 25 Jul 2006 20:14:26 -0000 1.1
+++ src/hg/makeDb/doc/methBurt1.txt 25 Nov 2009 21:48:41 -0000 1.2
@@ -1,163 +1,163 @@
# MULTIZ with other methanogens
# DONE (10/15/05), kpollard
cd /cluster/data/methBurt1/bed
mkdir conservation
cd conservation
cp /cluster/data/methBark1/bed/conservation/HoxD55.q .
cp /cluster/data/methBark1/bed/conservation/*.nib .
cp /cluster/data/methBark1/bed/conservation/*.chr .
cp /cluster/data/methBark1/bed/conservation/methBark1.fa .
cp /cluster/data/methBark1/bed/conservation/methBurt1.fa .
faToTwoBit methBark1.fa methBark1.2bit
faToTwoBit methBurt1.fa methBurt1.2bit
sed s/chr/methBark1.chr/ methBark1.fa > temp
sed s/plas/methBark1.plas/ temp > methBark1.fa
rm temp
#chrom sizes
faSize -detailed *.chr *.fa > chrom.sizes
#split methBurt1.fa
faSplit byname methBurt1.fa ./
foreach f (methBurt1.Contig*.fa)
echo `basename $f .fa` >> contigs.txt
end
#blastz (run on kolossus)
ssh kolossus
cd /cluster/data/methBurt1/bed/conservation/
foreach f (`cat contigs.txt`)
echo $f
blastz $f.fa methBark1.fa Q=HoxD55.q > ${f}-methBark1.lav
blastz $f.fa methMaze1.chr Q=HoxD55.q > ${f}-methMaze1.lav
blastz $f.fa metAce1.chr Q=HoxD55.q > ${f}-metAce1.lav
end
foreach f (`cat contigs.txt`)
echo $f
echo "lavToAxt"
lavToAxt ${f}-methBark1.lav methBurt1.2bit methBark1.2bit ${f}-methBark1.axt
lavToAxt ${f}-methMaze1.lav methBurt1.2bit . ${f}-methMaze1.axt
lavToAxt ${f}-metAce1.lav methBurt1.2bit . ${f}-metAce1.axt
echo "axtBest"
axtBest ${f}-methBark1.axt all -winSize=500 -minScore=5000 ${f}-methBark1-best.axt
axtBest ${f}-methMaze1.axt all -winSize=500 -minScore=5000 ${f}-methMaze1-best.axt
axtBest ${f}-metAce1.axt all -winSize=500 -minScore=5000 ${f}-metAce1-best.axt
echo "axtToMaf"
axtToMaf ${f}-methBark1-best.axt chrom.sizes chrom.sizes ${f}-methBark1.maf
axtToMaf ${f}-methMaze1-best.axt chrom.sizes chrom.sizes ${f}-methMaze1.maf
axtToMaf ${f}-metAce1-best.axt chrom.sizes chrom.sizes ${f}-metAce1.maf
end
#multiz
foreach f(*.maf)
cat $f | gawk 'BEGIN{getline; print $0; getline; getline; getline; getline;}{print $0;}' > methBurt
mv methBurt $f
end
foreach f(`cat contigs.txt`)
echo $f
multiz ${f}-methBark1.maf ${f}-methMaze1.maf - > ${f}-methBark1-methMaze1.maf
multiz ${f}-metAce1.maf ${f}-methBark1-methMaze1.maf - > ${f}-methBark1-methMaze1-metAce1.maf
end
#get rid of MAF files with no data
foreach f(`cat contigs.txt`)
wc -l ${f}-methBark1-methMaze1-metAce1.maf | gawk '{if($1<4){print "rm "$2}}' >> rmjobs
end
chmod +x rmjobs
rmjobs
#phyloHMM
foreach ff(*-methBark1-methMaze1-metAce1.maf)
set f=`basename $ff -methBark1-methMaze1-metAce1.maf`
echo $f
msa_view -i MAF -M $f.fa -o SS $ff > $f.ss
cat $f.ss | gawk '{if(/^NAMES/){print "NAMES = methBurt1,methBark1,methMaze1,metAce1";} else{print $0;}}' > methBurt
mv methBurt $f.ss
phyloFit -i SS $f.ss -t "(metAce1,(methBurt1,(methBark1,methMaze1)))" -o ${f}_MbaMaMmMbu
end
#Contig57 has the largest NTUPLES (1071) so use it for starting mod
# it shows GC=0.212928+0.220304=0.433232
#add GC content to next call
foreach f(*.ss)
set b=$f:t:r
echo $b
phastCons $f methBurt1.Contig57_MbaMaMmMbu.mod \
--gc 0.4332 --target-coverage 0.7 --estimate-trees ${b} \
--expected-lengths 25 --no-post-probs --ignore-missing \
--nrates 1,1
end
cat contigs.txt | gawk '/Contig29/{getline;}{print substr($1,11,length($1));}' > cont.txt
foreach b(`cat cont.txt`)
echo $b
phastCons methBurt1.$b.ss \
methBurt1.Contig57.cons.mod,methBurt1.Contig57.noncons.mod \
--target-coverage 0.7 --expected-lengths 25 \
--viterbi ${b}_methBurt1-elements.bed --score \
--require-informative 0 --seqname $b > ${b}_cons.dat
wigEncode ${b}_cons.dat ${b}_phastCons.wig ${b}_phastCons.wib
end
#combine phastCons elements into 1 bed file
cat *elements.bed > phastCons.bed
#move data
mkdir wib
mv Contig*_phastCons.wib wib/.
mv Contig*_phastCons.wig wib/.
mkdir /gbdb/methBurt1/wib
ln -s /cluster/data/methBurt1/bed/conservation/wib/*.wib /gbdb/methBurt1/wib
mkdir /gbdb/methBurt1/pwMaf
mkdir -p otherSpp/methBark1 otherSpp/methMaze1 otherSpp/metAce1
foreach f(`cat cont.txt`)
echo $f
mv methBurt1.${f}-methBark1.maf otherSpp/methBark1/$f.maf
mv methBurt1.${f}-methMaze1.maf otherSpp/methMaze1/$f.maf
mv methBurt1.${f}-metAce1.maf otherSpp/metAce1/$f.maf
end
ln -s /cluster/data/methBurt1/bed/conservation/otherSpp/methBark1 /gbdb/methBurt1/pwMaf/methBark1_pwMaf
ln -s /cluster/data/methBurt1/bed/conservation/otherSpp/metAce1 /gbdb/methBurt1/pwMaf/metAce1_pwMaf
ln -s /cluster/data/methBurt1/bed/conservation/otherSpp/methMaze1 /gbdb/methBurt1/pwMaf/methMaze1_pwMaf
mkdir multiz
foreach f(`cat cont.txt`)
echo $f
mv methBurt1.${f}-methBark1-methMaze1-metAce1.maf multiz/$f.maf
end
ln -s /cluster/data/methBurt1/bed/conservation/multiz /gbdb/methBurt1/multizMbuMbaMmMa
#load
hgLoadWiggle methBurt1 phastCons /cluster/data/methBurt1/bed/conservation/wib/*_phastCons.wig
hgLoadMaf -warn methBurt1 multizMbuMbaMmMa
hgLoadMaf -warn methBurt1 methBark1_pwMaf -pathPrefix=/gbdb/methBurt1/pwMaf/methBark1_pwMaf
hgLoadMaf -warn methBurt1 metAce1_pwMaf -pathPrefix=/gbdb/methBurt1/pwMaf/metAce1_pwMaf
hgLoadMaf -warn methBurt1 methMaze1_pwMaf -pathPrefix=/gbdb/methBurt1/pwMaf/methMaze1_pwMaf
hgLoadBed methBurt1 phastConsElements phastCons.bed
#trackDb
cd ~/kent/src/hg/makeDb/trackDb/archae
mkdir methBurt1
cvs add methBurt1
cd methBurt1
#trackDb.ra entry
# track multizMbuMbaMmMa
# shortLabel Conservation
# longLabel Methanogen multiz alignments
# group compGeno
# priority 10.0
# visibility pack
# type wigMaf 0.0 1.0
# maxHeightPixels 100:40:11
# wiggle phastCons
# yLineOnOff Off
- # autoScaleDefault Off
+ # autoScale Off
# pairwise pwMaf
# speciesOrder methBark1 methMaze1 metAce1
cvs add trackDb.ra
cvs commit -m "New multiz track" trackDb.ra
#html page
cvs add multizMbuMbaMmMa.html
cvs commit -m "Details page for multiz track" multizMbuMbaMmMa.html