src/hg/makeDb/doc/hivGne8v2.txt 1.7
1.7 2009/03/03 00:07:19 fanhsu
Added posSelection for vax004 section.
Index: src/hg/makeDb/doc/hivGne8v2.txt
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/makeDb/doc/hivGne8v2.txt,v
retrieving revision 1.6
retrieving revision 1.7
diff -b -B -U 1000000 -r1.6 -r1.7
--- src/hg/makeDb/doc/hivGne8v2.txt 14 Jan 2009 18:29:20 -0000 1.6
+++ src/hg/makeDb/doc/hivGne8v2.txt 3 Mar 2009 00:07:19 -0000 1.7
@@ -1,705 +1,709 @@
# for emacs: -*- mode: sh; -*-
#########################################################################
# hivgne8v2 DATABASE BUILD (STARTED 04/24/08, DONE 4/28/08, Fan)
ssh hiv1
mkdir -p /cluster/store12/medical/hiv/hivgne8v2
cd /cluster/store12/medical/hiv/hivgne8v2
cd /gbdb
mkdir hivgne8v2
cd hivgne8v2
cp -Rp ../hivgne8/* .
#########################################################################
# CREATING DATABASE
# Create the hivgne8v2 database.
echo 'create database hivgne8v2' | hgsql hiv1
# CREATING GRP TABLE FOR TRACK GROUPING
echo "create table grp (PRIMARY KEY(NAME)) select * from hiv1.grp" \
| hgsql hivgne8v2
#########################################################################
# MAKE HGCENTRALHIV1 ENTRY AND TRACKDB TABLE FOR HIVGNE8V2
echo 'insert into defaultDb values("HIV GNE8 (GP120) V2.0", "hivgne8v2");' \
| hgsql -h localhost hgcentralhiv1
echo 'insert into dbDb values("hivgne8v2", " Sep. 1998", \
"/gbdb/hivgne8v2/nib", "HIV GNE8 (GP120) V2.0", "chr1", 1, 2030, \
"HIV GNE8 (GP120) V2.0","Human immunodeficiency virus 1", \
"/gbdb/hivgne8v2/html/description.html", 0, 0, " sequence as of Sep., 1998");' \
| hgsql hgcentralhiv1 -h localhost
echo 'insert into genomeClade values("HIV GNE8 (GP120) V2.0", "other", 110);'\
| hgsql hgcentralhiv1 -h localhost
#########################################################################
# COPY OVER MYSQL TABLES FROM hivgne8
cd /cluster/store12/medical/hiv/hivgne8v2
# create do1 with the following lines:
echo processing table $1 ...
#hgsql hivgne8v2 -e "drop table ${1}"
getDbTableDef hivgne8 $1 >$1.sql
hgsql hivgne8 -N -e "select * from ${1}" >$1.tab
hgsql hivgne8v2 <$1.sql
hgsql hivgne8v2 -e "load data local infile '${1}.tab' into table ${1}"
# create doall with the following lines:
do1 aaSeq
do1 chromInfo
do1 dnaSeq
do1 extFile
do1 grp
do1 gsIdXref
do1 gsidClinicRec
do1 gsidClinicRecWithSeq
do1 gsidSubjInfo
do1 hSeq
do1 hgFindSpec
do1 hgFindSpec_fanhsu
do1 history
do1 hivGene
do1 interPro
do1 seq
do1 tableDescriptions
do1 trackDb
do1 trackDb_fanhsu
do1 vax004
do1 vax004AaCons
do1 vax004Cons
do1 vax004Msa
chmod +x do*
doall
# create trackDb
cd kent/src/hg/makeDb/trackDb
# edit makefile to add hivgne8v2
vi makefile
cd hiv
mkdir hivgne8v2
cd hivgne8v2
cp -p ../hivgne8/* .
cd ../..
make alpha DBS=hivgne8v2
# Ask admin to start BLAT server process for hivgne8v2 and then
# MAKE HGCENTRALHIV1 BLATSERVERS ENTRY FOR HIVGNE8V2
echo 'insert into blatServers values("hivgne8v2", "hiv1", "17794", "1", "0"); \
insert into blatServers values("hivgne8v2", "hiv1", "17795", "0", "0");' \
| hgsql hgcentralhiv1 -h localhost
#########################################################################
# CREATE VAX003 TRACK
cd /cluster/store12/medical/hiv/hivgne8v2
# get vax003 sequences
hgsql hivgne8v2 -N -e 'select * from dnaSeq where id like "%T%"' >vax003.tab
# create .fa file
tabToFa vax003
mkdir -p /gbdb/hivgne8v2/vax003
cp -p vax003.fa /gbdb/hivgne8v2/vax003/vax003.fa
hgLoadSeq -replace hivgne8v2 /gbdb/hivgne8v2/vax003/vax003.fa
# BLAT
gfClient -minScore=200 -minIdentity=80 -nohead hiv1.cse.ucsc.edu 17795 /gbdb/hivgne8v2/nib \
-out=psl -t=dna -q=dna vax003.fa vax003.psl
# count the result
wc *.psl
cut -f 10 vax003.psl |wc
cut -f 10 vax003.psl |sort -u |wc
# load the psl result into vax003 table
hgLoadPsl hivgne8v2 vax003.psl
# hgLoadPsl has some file permission problem. Finish this by manually load the psl.tab file.
hgsql hivgne8v2 -e 'load data local infile "psl.tab" into table vax003'
#########################################################################
# COPY OVER MSA TABLES
mkdir -p /cluster/store12/medical/hiv/hivgne8v2/msa/AE
cd /cluster/store12/medical/hiv/hivgne8v2/msa/AE
# get table definition
mysqldump -d hivVax003Vax004 vax003AEMsa -u medcat -p$HGPSWD|hgsql hivgne8v2
# load the table
hgsql hivgne8v2 -e "insert into vax003AEMsa select * from hivVax003Vax004.vax003AEMsa"
#########################################################################
# CREATE MAF TRACKS FOR VAX004
mkdir -p /cluster/store12/medical/hiv/hivgne8v2/msa
cd /cluster/store12/medical/hiv/hivgne8v2/msa
# create a script file, doall
hgsql hivgne8v2 -N -e \
'select id from dnaSeq where id like "%U%"'\
|sed -e 's/ss/do1 ss/g' >doall
# create one line script file, do1, with the following line in it:
hgsql hivgne8v2 -N -e "select id, seq from vax004Msa where id='${1}'"
chmod +x do*
# run the script to get the .tab file with all MSA sequences of VAX004
doall >gne8.tab
# convert .tab into .fa file
tabToFa gne8
# grab the base alignment sequence
echo ">hivgne8v2" >gne8.aln
hgsql hivgne8v2 -N -e 'select seq from vax004Msa where id="GNE8"' >> gne8.aln
# prepare an interium file, jjAll.mfa
cat gne8.aln gne8.fa >jjAll.mfa
echo = >>jjAll.mfa
# Run xmfaToMafGne8 to create a precursor file for the final .maf
xmfaToMafGne8 jjAll.mfa j.out org1=hivgne8v2
cat j.out|sed -e 's/\./_/g'|sed -e 's/_chr/\.chr/g' >chr1.tmp
rm jjAll.mfa j.out
cat chr1.tmp |sed -e 's/ss_U/U/g' >chr1.maf
# copy .maf to /gbdb.
mkdir -p /gbdb/hivgne8v2/vax004Maf
cp chr1.maf /gbdb/hivgne8v2/vax004Maf -p
hgLoadMaf hivgne8v2 vax004Maf
# create another copy for protein MAF.
mkdir -p /gbdb/hivgne8v2/vax004AaMaf
cp -p chr1.maf /gbdb/hivgne8v2/vax004AaMaf
hgLoadMaf hivgne8v2 vax004AaMaf
#########################################################################
# CREATE CONSERVATION TRACKS FOR VAX003 AE STRAIN
mkdir -p /cluster/store12/medical/hiv/hivgne8v2/conservation/AE
cd /cluster/store12/medical/hiv/hivgne8v2/conservation/AE
# create the .wig file and .fa file of the consensus sequence.
gsidMsa hivgne8v2 vax003AEMsa GNE8-gp120-AY771703 231 vax003AECons.wig vax003AEConsensus.fa
# encode and load the wig file
wigEncode vax003AECons.wig stdout vax003AECons.wib \
| hgLoadWiggle hivgne8v2 vax003AECons stdin
# copy .wib file to /gbdb
mkdir -p /gbdb/hivgne8v2/wib
cp vax003AECons.wib /gbdb/hivgne8v2/wib
# do the same for protein conservation track
mkdir aa
cd aa
# create .wig file
gsidAaMsa2 hivgne8v2 vax003AEMsa GNE8-gp120-AY771703 231 vax003AEAaCons.wig vax003AEAaConsensus.fa
# encode and load the .wib file
wigEncode vax003AEAaCons.wig stdout vax003AEAaCons.wib \
| hgLoadWiggle hivgne8v2 vax003AEAaCons stdin
cp vax003AEAaCons.wib /gbdb/hivgne8v2/wib
#########################################################################
# CREATE MAF TRACKS FOR VAX003 AE STRAIN
mkdir -p /cluster/store12/medical/hiv/hivgne8v2/msa/AE
cd /cluster/store12/medical/hiv/hivgne8v2/msa/AE
# create a script file, doall
hgsql hivgne8v2 -N -e \
'select id from dnaSeq where id like "%T%"'\
|sed -e 's/ss/do1 ss/g' >doall
# create one line script file, do1, with the following line in it:
hgsql hivgne8v2 -N -e "select id, seq from vax003AEMsa where id='${1}'"
chmod +x do*
# run the script to get the .tab file with all MSA sequences of VAX003 AE
doall >gne8.tab
# convert .tab into .fa file
tabToFa gne8
# grab the base alignment sequence
echo ">hivgne8v2" >gne8.aln
hgsql hivgne8v2 -N -e 'select seq from vax003AEMsa where id="GNE8-gp120-AY771703"' >> gne8.aln
# prepare an interium file, jjAll.mfa
cat gne8.aln gne8.fa >jjAll.mfa
echo = >>jjAll.mfa
# Run xmfaToMafGne8 to create a precursor file for the final .maf
xmfaToMafGne8 jjAll.mfa j.out org1=hivgne8v2
cat j.out|sed -e 's/\./_/g'|sed -e 's/_chr/\.chr/g' >chr1.tmp
# rm jjAll.mfa j.out
cat chr1.tmp |sed -e 's/ss_T/T/g' >chr1.maf
# copy .maf to /gbdb.
mkdir -p /gbdb/hivgne8v2/vax003AEMaf
cp chr1.maf /gbdb/hivgne8v2/vax003AEMaf -p
hgLoadMaf hivgne8v2 vax003AEMaf
# create another copy for protein MAF.
mkdir -p /gbdb/hivgne8v2/vax003AEAaMaf
cp -p chr1.maf /gbdb/hivgne8v2/vax003AEAaMaf
hgLoadMaf hivgne8v2 vax003AEAaMaf
#########################################################################
# COPY OVER MSA TABLES FOR VAX003 B STRAIN
mkdir -p /cluster/store12/medical/hiv/hivgne8v2/msa/B
cd /cluster/store12/medical/hiv/hivgne8v2/msa/B
# get table definition
mysqldump -d hivVax003Vax004 vax003BMsa -u medcat -p$HGPSWD|hgsql hivgne8v2
# load the table
hgsql hivgne8v2 -e "insert into vax003BMsa select * from hivVax003Vax004.vax003BMsa"
#########################################################################
# CREATE CONSERVATION TRACKS FOR VAX003 B STRAIN
mkdir -p /cluster/store12/medical/hiv/hivgne8v2/conservation/B
cd /cluster/store12/medical/hiv/hivgne8v2/conservation/B
# create the .wig file and .fa file of the consensus sequence.
gsidMsa hivgne8v2 vax003BMsa GNE8-gp120-AY771703 231 vax003BCons.wig vax003BConsensus.fa
# encode and load the wig file
wigEncode vax003BCons.wig stdout vax003BCons.wib \
| hgLoadWiggle hivgne8v2 vax003BCons stdin
# copy .wib file to /gbdb
mkdir -p /gbdb/hivgne8v2/wib
cp vax003BCons.wib /gbdb/hivgne8v2/wib
# do the same for protein conservation track
mkdir aa
cd aa
# create .wig file
gsidAaMsa2 hivgne8v2 vax003BMsa GNE8-gp120-AY771703 231 vax003BAaCons.wig vax003BAaConsensus.fa
# encode and load the .wib file
wigEncode vax003BAaCons.wig stdout vax003BAaCons.wib \
| hgLoadWiggle hivgne8v2 vax003BAaCons stdin
cp vax003BAaCons.wib /gbdb/hivgne8v2/wib
#########################################################################
# CREATE MAF TRACKS FOR VAX003 B STRAIN
mkdir -p /cluster/store12/medical/hiv/hivgne8v2/msa/B
cd /cluster/store12/medical/hiv/hivgne8v2/msa/B
# create a script file, doall
hgsql hivgne8v2 -N -e \
'select id from dnaSeq where id like "%T%"'\
|sed -e 's/ss/do1 ss/g' >doall
# create one line script file, do1, with the following line in it:
hgsql hivgne8v2 -N -e "select id, seq from vax003BMsa where id='${1}'"
chmod +x do*
# run the script to get the .tab file with all MSA sequences of VAX004
doall >gne8.tab
# convert .tab into .fa file
tabToFa gne8
# grab the base alignment sequence
echo ">hivgne8v2" >gne8.aln
hgsql hivgne8v2 -N -e 'select seq from vax003BMsa where id="GNE8-gp120-AY771703"' >> gne8.aln
# prepare an interium file, jjAll.mfa
cat gne8.aln gne8.fa >jjAll.mfa
echo = >>jjAll.mfa
# Run xmfaToMafGne8B to create a precursor file for the final .maf
xmfaToMafGne8 jjAll.mfa j.out org1=hivgne8v2
cat j.out|sed -e 's/\./_/g'|sed -e 's/_chr/\.chr/g' >chr1.tmp
rm jjAll.mfa j.out
cat chr1.tmp |sed -e 's/ss_T/T/g' >chr1.maf
# copy .maf to /gbdb.
mkdir -p /gbdb/hivgne8v2/vax003BMaf
cp chr1.maf /gbdb/hivgne8v2/vax003BMaf -p
hgLoadMaf hivgne8v2 vax003BMaf
# create another copy for protein MAF.
mkdir -p /gbdb/hivgne8v2/vax003BAaMaf
cp -p chr1.maf /gbdb/hivgne8v2/vax003BAaMaf
hgLoadMaf hivgne8v2 vax003BAaMaf
#########################################################################
# CREATE VAX003 TRACK
cd ~/medical/hiv/hivgne8v2
# get vax003 sequences
hgsql hivgne8v2 -N -e 'select * from dnaSeq where id like "%T%"' >vax003.tab
# create .fa file
tabToFa vax003
mkdir -p /gbdb/hivgne8v2/vax003
cp -p vax003.fa /gbdb/hivgne8v2/vax003/vax003.fa
hgLoadSeq -replace hivgne8v2 /gbdb/hivgne8v2/vax003/vax003.fa
# BLAT
gfClient -minScore=200 -minIdentity=70 -nohead hiv1.cse.ucsc.edu 17795 \
/gbdb/hivgne8v2/nib -out=psl -t=dna -q=dna vax003.fa vax003.psl
# count the result
wc *.psl
cut -f 10 vax003.psl |wc
cut -f 10 vax003.psl |sort -u |wc
# load the psl result into vax003 table
hgLoadPsl hivgne8v2 vax003.psl
# hgLoadPsl has some file permission problem. Finish this by manually load the psl.tab file.
hgsql hivgne8v2 -e 'load data local infile "psl.tab" into table vax003'
#########################################################################
# Build the gsidSubjSeq table (used by Table View).
gsidSubjSeq hivgne8v2 dnaSeqId > j.dna
gsidSubjSeq hivgne8v2 aaSeqId > j.aa
cut -f 1 j.dna >j.1
cut -f 1 j.aa >j.2
cut -f 2 j.dna >j.3
cut -f 2 j.aa >j.4
paste j.1 j.3 j.4> gsidSubjSeq.tab
hgsql hivgne8v2 -e 'delete from gsidSubjSeq'
hgsql hivgne8v2 -e \
'load data local infile "gsidSubjSeq.tab" into table gsidSubjSeq'
rm j.1 j.2 j.3 j.4 j.dna j.aa
#########################################################################
# RE-BUILD CONSERVATION AND MSA TRACKS FOR vax003AE (Done 7/14/08, Fan)
# COPY OVER shortened MSA sequences from hivVax003Vax004
mkdir -p /cluster/store12/medical/hiv/hivgne8v2/msaNew/AE
cd /cluster/store12/medical/hiv/hivgne8v2/msaNew/AE
hgsql hivgne8v2 -e "delete from vax003AEMsa"
hgsql hivgne8v2 -e "insert into vax003AEMsa select * from hivVax003Vax004.vax003AEMsa"
# CREATE CONSERVATION TRACKS FOR AE STRAIN
mkdir -p /cluster/store12/medical/hiv/hivgne8v2/conservationNew/AE
cd /cluster/store12/medical/hiv/hivgne8v2/conservationNew/AE
# create the .wig file and .fa file of the consensus sequence.
gsidMsa hivgne8v2 vax003AEMsa GNE8-gp120-AY771703 231 vax003AECons.wig vax003AEConsensus.fa
# encode and load the wig file
wigEncode vax003AECons.wig stdout vax003AECons.wib \
| hgLoadWiggle hivgne8v2 vax003AECons stdin
# copy .wib file to /gbdb
mkdir -p /gbdb/hivgne8v2/wib
cp vax003AECons.wib /gbdb/hivgne8v2/wib
# do the same for protein conservationNew track
mkdir aa
cd aa
# create .wig file
gsidAaMsa2 hivgne8v2 vax003AEMsa GNE8-gp120-AY771703 231 vax003AEAaCons.wig vax003AEAaConsensus.fa
# encode and load the .wib file
wigEncode vax003AEAaCons.wig stdout vax003AEAaCons.wib \
| hgLoadWiggle hivgne8v2 vax003AEAaCons stdin
cp vax003AEAaCons.wib /gbdb/hivgne8v2/wib
# CREATE MAF TRACKS FOR vax003AE STRAIN
mkdir -p /cluster/store12/medical/hiv/hivgne8v2/msaNew/AE
cd /cluster/store12/medical/hiv/hivgne8v2/msaNew/AE
# create a script file, doall
hgsql hivgne8v2 -N -e \
'select id from vax003AEMsa where id like "%T%"'\
|sed -e 's/ss/do1 ss/g' >doall
# create one line script file, do1, with the following line in it:
hgsql hivgne8v2 -N -e "select id, seq from vax003AEMsa where id='${1}'"
chmod +x do*
# run the script to get the .tab file with all MSA sequences of VAX004
doall >gne8v2.tab
# convert .tab into .fa file
tabToFa gne8v2
# grab the base alignment sequence
echo ">hivgne8v2" >gne8v2.aln
hgsql hivgne8v2 -N -e 'select seq from vax003AEMsa where id="GNE8-gp120-AY771703"' >> gne8v2.aln
# prepare an interium file, jjAll.mfa
cat gne8v2.aln gne8v2.fa >jjAll.mfa
echo = >>jjAll.mfa
# Run xmfaToMafGne8 to create a precursor file for the final .maf
xmfaToMafGne8 jjAll.mfa j.out org1=hivgne8v2
cat j.out|sed -e 's/\./_/g'|sed -e 's/_chr/\.chr/g' >chr1.tmp
rm jjAll.mfa j.out
cat chr1.tmp |sed -e 's/ss_T/T/g' >chr1.maf
# copy .maf to /gbdb.
mkdir -p /gbdb/hivgne8v2/vax003AEMaf
cp chr1.maf /gbdb/hivgne8v2/vax003AEMaf -p
echo before load
hgLoadMaf hivgne8v2 vax003AEMaf
# create another copy for protein MAF.
mkdir -p /gbdb/hivgne8v2/vax003AEAaMaf
cp -p chr1.maf /gbdb/hivgne8v2/vax003AEAaMaf
hgLoadMaf hivgne8v2 vax003AEAaMaf
#########################################################################
# RE-BUILD CONSERVATION AND MSA TRACKS FOR vax003B
# COPY OVER shortened MSA sequences from hivVax003Vax004
mkdir -p /cluster/store12/medical/hiv/hivgne8v2/msaNew/B
cd /cluster/store12/medical/hiv/hivgne8v2/msaNew/B
hgsql hivgne8v2 -e "delete from vax003BMsa"
hgsql hivgne8v2 -e "insert into vax003BMsa select * from hivVax003Vax004.vax003BMsa"
# CREATE CONSERVATION TRACKS FOR B STRAIN
mkdir -p /cluster/store12/medical/hiv/hivgne8v2/conservationNew/B
cd /cluster/store12/medical/hiv/hivgne8v2/conservationNew/B
# create the .wig file and .fa file of the consensus sequence.
gsidMsa hivgne8v2 vax003BMsa GNE8-gp120-AY771703 231 vax003BCons.wig vax003BConsensus.fa
# encode and load the wig file
wigEncode vax003BCons.wig stdout vax003BCons.wib \
| hgLoadWiggle hivgne8v2 vax003BCons stdin
# copy .wib file to /gbdb
mkdir -p /gbdb/hivgne8v2/wib
cp vax003BCons.wib /gbdb/hivgne8v2/wib
# do the same for protein conservationNew track
mkdir aa
cd aa
# create .wig file
gsidAaMsa2 hivgne8v2 vax003BMsa GNE8-gp120-AY771703 231 vax003BAaCons.wig vax003BAaConsensus.fa
# encode and load the .wib file
wigEncode vax003BAaCons.wig stdout vax003BAaCons.wib \
| hgLoadWiggle hivgne8v2 vax003BAaCons stdin
cp vax003BAaCons.wib /gbdb/hivgne8v2/wib
# CREATE MAF TRACKS FOR vax003B STRAIN
mkdir -p /cluster/store12/medical/hiv/hivgne8v2/msaNew/B
cd /cluster/store12/medical/hiv/hivgne8v2/msaNew/B
# create a script file, doall
hgsql hivgne8v2 -N -e \
'select id from vax003BMsa where id like "%T%"'\
|sed -e 's/ss/do1 ss/g' >doall
# create one line script file, do1, with the following line in it:
hgsql hivgne8v2 -N -e "select id, seq from vax003BMsa where id='${1}'"
chmod +x do*
# run the script to get the .tab file with all MSA sequences of VAX004
doall >gne8v2.tab
# convert .tab into .fa file
tabToFa gne8v2
# grab the base alignment sequence
echo ">hivgne8v2" >gne8v2.aln
hgsql hivgne8v2 -N -e 'select seq from vax003BMsa where id="GNE8-gp120-AY771703"' >> gne8v2.aln
# prepare an interium file, jjAll.mfa
cat gne8v2.aln gne8v2.fa >jjAll.mfa
echo = >>jjAll.mfa
# Run xmfaToMafGne8v2B to create a precursor file for the final .maf
xmfaToMafGne8 jjAll.mfa j.out org1=hivgne8v2
cat j.out|sed -e 's/\./_/g'|sed -e 's/_chr/\.chr/g' >chr1.tmp
rm jjAll.mfa j.out
cat chr1.tmp |sed -e 's/ss_T/T/g' >chr1.maf
# copy .maf to /gbdb.
mkdir -p /gbdb/hivgne8v2/vax003BMaf
cp chr1.maf /gbdb/hivgne8v2/vax003BMaf -p
echo before load
hgLoadMaf hivgne8v2 vax003BMaf
# create another copy for protein MAF.
mkdir -p /gbdb/hivgne8v2/vax003BAaMaf
cp -p chr1.maf /gbdb/hivgne8v2/vax003BAaMaf
hgLoadMaf hivgne8v2 vax003BAaMaf
#########################################################################
# REBUILD THE gsidClinicRecWithSeq TABLE (DONE 11/03/08, Fan)
# See details in hivVax003Vax004.txt.
#########################################################################
# BUILD THE POSITIVE SELECTION TRACKS FOR VAX003 SUBTYPE B
ssh hiv1
mkdir -p /hive/groups/gsid/medical/hiv/posSelection/B/hivgne8v2
cd /hive/groups/gsid/medical/hiv/posSelection/B/hivgne8v2
# BLAT /cluster/hive/groups/gsid/medical/hiv/posSelection/B/BMsaAaConsensus.fa
# against hivgne8v2 base genome, select psl without header option
# cut and paste the result into the file BMsa.psl
hgLoadPsl -keep -table=BMsaPsl -nobin hivgne8v2 BMsa.psl
# will get the following error:
#Processing BMsa.psl
#Can't start query:
#LOAD DATA CONCURRENT INFILE
'/cluster/hive/groups/gsid/medical/hiv/hivgne8v2/posSelection/BMsa.psl' INTO
TABLE BMsaPsl
#mySQL error 13: Can't get stat of
'/cluster/hive/groups/gsid/medical/hiv/hivgne8v2/posSelection/BMsa.psl'
(Errcode: 13)
# load manually then
hgsql hivgne8v2
load data local infile "BMsa.psl" into table BMsaPsl;
quit
# build positive selection tracks for model 2 and model 8.
gsidPosSelect hivgne8v2 BMsaPsl posSelBuild pSelectBModel2 posSelBModel2.bed
hgLoadBed hivgne8v2 posSelBModel2 posSelBModel2.bed
gsidPosSelect hivgne8v2 BMsaPsl posSelBuild pSelectBModel8 posSelBModel8.bed
hgLoadBed hivgne8v2 posSelBModel8 posSelBModel8.bed
##########################################################################
# BUILD THE POSITIVE SELECTION TRACKS FOR VAX003 SUBTYPE AE
ssh hiv1
mkdir -p /hive/groups/gsid/medical/hiv/posSelection/AE/hivgne8v2
cd /hive/groups/gsid/medical/hiv/posSelection/AE/hivgne8v2
# BLAT
# /cluster/hive/groups/gsid/medical/hiv/posSelection/AE/AEMsaAaConsensus.fa
# against hivgne8v2 base genome, select psl without header option
# cut and paste the result into the file AEMsa.psl
hgLoadPsl -keep -table=AEMsaPsl -nobin hivgne8v2 AEMsa.psl
# will get the following error:
#Processing AEMsa.psl
#Can't start query:
#LOAD DATA CONCURRENT INFILE
'/cluster/hive/groups/gsid/medical/hiv/hivgne8v2/posSelection/AEMsa.psl' INTO
TABLE AEMsaPsl
#mySQL error 13: Can't get stat of
'/cluster/hive/groups/gsid/medical/hiv/hivgne8v2/posSelection/AEMsa.psl'
(Errcode: 13)
# load manually then
hgsql hivgne8v2
load data local infile "AEMsa.psl" into table AEMsaPsl;
quit
# build positive selection tracks for model 2 and model 8.
gsidPosSelect hivgne8v2 AEMsaPsl posSelBuild pSelectAEModel2
posSelAEModel2.bed
hgLoadBed hivgne8v2 posSelAEModel2 posSelAEModel2.bed
gsidPosSelect hivgne8v2 AEMsaPsl posSelBuild pSelectAEModel8
posSelAEModel8.bed
hgLoadBed hivgne8v2 posSelAEModel8 posSelAEModel8.bed
##########################################################################
+# BUILD THE POSITIVE SELECTION TRACKS FOR VAX004 (Done Fan, 3/2/09)
+
+# Please see the corresponding section in hivVax003Vax004.txt for details.
+##########################################################################