# 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. ##########################################################################