# for emacs: -*- mode: sh; -*-

# This file describes the browser build for Loa loa/eye worm WS245 version

##############################################################################
# download sequence, create UCSC sequence (DONE - 2015-06-24 - Hiram)
    # both the genbank and the WormBase releases are identical
    mkdir -p /hive/data/genomes/loaLoa1/genbank
    cd /hive/data/genomes/loaLoa1/genbank

    time rsync -L -a -P \
rsync://ftp.ncbi.nlm.nih.gov/genomes/genbank/invertebrate/Loa_loa/all_assembly_versions/GCA_000183805.3_Loa_loa_V3.1/ ./
# sent 394 bytes  received 112378513 bytes  6810842.85 bytes/sec
# total size is 112362653  speedup is 1.00
# real    0m15.630s

    mkdir -p /hive/data/genomes/loaLoa1/ws245
    cd /hive/data/genomes/loaLoa1/ws245

    wget --no-parent --timestamping -m -nH --cut-dirs=6 \
ftp://ftp.sanger.ac.uk/pub/wormbase/releases/WS245/species/PRJNA60051

    mkdir /hive/data/genomes/loaLoa1/ucsc
    cd /hive/data/genomes/loaLoa1/ucsc

    zcat ../genbank/GCA_000183805.3_Loa_loa_V3.1_assembly_structure/Primary_Assembly/unplaced_scaffolds/FASTA/unplaced.scaf.fna.gz \
        | sed -e 's/.1 Loa .*/v1/;' | gzip -c > loaLoa1.fa.gz

    zcat ../genbank/GCA_000183805.3_Loa_loa_V3.1_assembly_structure/Primary_Assembly/unplaced_scaffolds/AGP/unplaced.scaf.agp.gz \
      | sed -e 's/\.1/v1/;' > loaLoa1.agp

    # obtain photo, CDC public domain photo
    mkdir /hive/data/genomes/loaLoa1/photo
    cd /hive/data/genomes/loaLoa1/photo
    wget --timestamping \
http://www.cdc.gov/dpdx/images/loiasis/L_loa_adult_GA1.jpg
    # this image is already 381x300 so it can go as is

    # check into source tree
    #   src/hg/htdocs/images/Loa_loa.jpg
    # and copy to /usr/local/apache/htdocs/images/Loa_loa.jpg

#############################################################################
#  Initial database build (DONE - 2015-07-10 - Hiram)

    cd /hive/data/genomes/loaLoa1
    cat << '_EOF_' > loaLoa1.config.ra
# Config parameters for makeGenomeDb.pl:
db loaLoa1
clade worm
genomeCladePriority 68
scientificName Loa loa
commonName Eye worm
assemblyDate Jul. 2012
assemblyLabel Broad Institute L. loa genome project
assemblyShortLabel WS235/L_loa_Cameroon_isolate
orderKey 6000
mitoAcc HQ186250.1
fastaFiles /hive/data/genomes/loaLoa1/ucsc/loaLoa1.fa.gz
agpFiles /hive/data/genomes/loaLoa1/ucsc/loaLoa1.agp
# qualFiles none
dbDbSpeciesDir worm
photoCreditURL http://www.cdc.gov/parasites/loiasis/disease.html
photoCreditName Centers for Disease Control and Prevention
ncbiGenomeId 2686
ncbiAssemblyId 195281
ncbiAssemblyName WS235/Loa_loa_V3.1
ncbiBioProject 60051
genBankAccessionID GCA_000183805.3
taxId 7209
'_EOF_'
    # << happy emacs

    # verify sequence and AGP are OK:
    time (makeGenomeDb.pl -workhorse=hgwdev -dbHost=hgwdev -fileServer=hgwdev \
         -stop=agp loaLoa1.config.ra) > agp.log 2>&1
    # *** All done!  (through the 'agp' step)
    # real    0m21.029s

    # then finish it off:
    time (makeGenomeDb.pl -workhorse=hgwdev -dbHost=hgwdev \
       -fileServer=hgwdev -continue=db loaLoa1.config.ra) > db.log 2>&1
    # real    1m3.894s

    # check in the trackDb files created and add to trackDb/makefile

##############################################################################
# cpgIslands on UNMASKED sequence (DONE - 2015-07-10 - Hiram)
    mkdir /hive/data/genomes/loaLoa1/bed/cpgIslandsUnmasked
    cd /hive/data/genomes/loaLoa1/bed/cpgIslandsUnmasked

    time (doCpgIslands.pl -dbHost=hgwdev -bigClusterHub=ku -buildDir=`pwd` \
       -tableName=cpgIslandExtUnmasked \
          -maskedSeq=/hive/data/genomes/loaLoa1/loaLoa1.unmasked.2bit \
             -workhorse=hgwdev -smallClusterHub=ku loaLoa1) > do.log 2>&1
    # real    5m4.522s

    cat fb.loaLoa1.cpgIslandExtUnmasked.txt
    # 50875 bases of 87533141 (0.058%) in intersection

#############################################################################
# cytoBandIdeo - (DONE - 2015-07-10 - Hiram)
    mkdir /hive/data/genomes/loaLoa1/bed/cytoBand
    cd /hive/data/genomes/loaLoa1/bed/cytoBand
    makeCytoBandIdeo.csh loaLoa1

#########################################################################
# ucscToINSDC table/track (DONE - 2015-07-10 - Hiram)
    mkdir /hive/data/genomes/loaLoa1/bed/ucscToINSDC
    cd /hive/data/genomes/loaLoa1/bed/ucscToINSDC

    # find the chrM accession:
    grep chrM ../../*.agp
# chrM    1       13590   2       F       HQ186250.1      1       13590   +

    # use that as the second argument here:
    ~/kent/src/hg/utils/automation/ucscToINSDC.sh \
       ../../genbank/GCA_*_assembly_structure/Primary_Assembly HQ186250.1

    awk '{printf "%s\t0\t%d\n", $1,$2}' ../../chrom.sizes \
         | sort > name.coordinate.tab
    join name.coordinate.tab ucscToINSDC.txt | tr '[ ]' '[\t]' \
         > ucscToINSDC.bed
    # verify all names are coming through, should be same line count:
    wc -l *
    #   5765 name.coordinate.tab
    #   5765 ucscToINSDC.bed
    #   5765 ucscToINSDC.txt

    cut -f1 ucscToINSDC.bed | awk '{print length($0)}' | sort -n | tail -1
    # 10
    # use the 10 in this sed
    sed -e "s/21/10/" $HOME/kent/src/hg/lib/ucscToINSDC.sql \
         | hgLoadSqlTab loaLoa1 ucscToINSDC stdin ucscToINSDC.bed
    checkTableCoords loaLoa1
    # should cover %100 entirely:
    featureBits -countGaps loaLoa1 ucscToINSDC
    # 91379422 bases of 91379422 (100.000%) in intersection

#########################################################################
# fixup search rule for assembly track/gold table (DONE - 2015-07-10 - Hiram)
    hgsql -N -e "select frag from gold;" loaLoa1 | sort | head -3
ADBU02000001.1
ADBU02000002.1
ADBU02000003.1

    hgsql -N -e "select frag from gold;" loaLoa1 | sort | tail -2
ADBU02014333.1
HQ186250.1

    # verify this rule will find them all or eliminate them all:
    hgsql -N -e "select frag from gold;" loaLoa1 | wc -l
    # 14324

    hgsql -N -e "select frag from gold;" loaLoa1 \
      | egrep -e '(ADBU020|HQ186250)[0-9]*(\.1)?' | wc -l
    # 14324

    hgsql -N -e "select frag from gold;" loaLoa1 \
      | egrep -v -e '(ADBU020|HQ186250)[0-9]*(\.1)?' | wc -l
    # 0

    # hence, add to trackDb/worm/loaLoa1/trackDb.ra
searchTable gold
shortCircuit 1
termRegex (ADBU020|HQ186250)[0-9]*(\.1)?
query select chrom,chromStart,chromEnd,frag from %s where frag like '%s%%'
searchPriority 8

##########################################################################
# running repeat masker (DONE - 2015-07-10 - Hiram)
    mkdir /hive/data/genomes/loaLoa1/bed/repeatMasker
    cd /hive/data/genomes/loaLoa1/bed/repeatMasker
    time (doRepeatMasker.pl -buildDir=`pwd` \
        -bigClusterHub=ku -dbHost=hgwdev -workhorse=hgwdev \
        -smallClusterHub=ku loaLoa1) > do.log 2>&1
    # real    83m49.429s

    cat faSize.rmsk.txt
    # 91379422 bases (3847239 N's 87532183 real 83624537 upper 3907646 lower)
    #    in 5765 sequences in 1 files
    # Total size: mean 15850.7 sd 64640.7 min 265 (JH717805v1)
    #    max 1325655 (JH712066v1) median 1186
    # %4.28 masked total, %4.46 masked real

    egrep -i "versi|relea" do.log
    # RepeatMasker version open-4.0.5
    #    January 31 2015 (open-4-0-5) version of RepeatMasker
    # CC   RELEASE 20140131;

    time featureBits -countGaps loaLoa1 rmsk
    # 3908609 bases of 91379422 (4.277%) in intersection
    # real    0m3.289s

##########################################################################
# running simple repeat (DONE - 2015-07-10 - Hiram)
    mkdir /hive/data/genomes/loaLoa1/bed/simpleRepeat
    cd /hive/data/genomes/loaLoa1/bed/simpleRepeat
    time (doSimpleRepeat.pl -buildDir=`pwd` -bigClusterHub=ku \
        -dbHost=hgwdev -workhorse=hgwdev -smallClusterHub=ku \
        loaLoa1) > do.log 2>&1
    # real    10m57.576s

    cat fb.simpleRepeat
    # 2964793 bases of 87533141 (3.387%) in intersection

    # using the Window Masker result as indicated below

##########################################################################
# CREATE MICROSAT TRACK (DONE - 2015-07-15 - Hiram)
     ssh hgwdev
     mkdir /cluster/data/loaLoa1/bed/microsat
     cd /cluster/data/loaLoa1/bed/microsat
     awk '($5==2 || $5==3) && $6 >= 15 && $8 == 100 && $9 == 0 {printf("%s\t%s\t%s\t%dx%s\n", $1, $2, $3, $6, $16);}' \
	../simpleRepeat/simpleRepeat.bed > microsat.bed
    hgLoadBed loaLoa1 microsat microsat.bed
    #	Read 2111 elements of size 4 from microsat.bed

##########################################################################
## WINDOWMASKER (DONE - 2015-07-15 - Hiram)
    mkdir /hive/data/genomes/loaLoa1/bed/windowMasker
    cd /hive/data/genomes/loaLoa1/bed/windowMasker
    time (doWindowMasker.pl -buildDir=`pwd` -workhorse=hgwdev \
        -dbHost=hgwdev loaLoa1) > do.log 2>&1
    # real    5m3.906s

    # Masking statistics
    cat faSize.loaLoa1.cleanWMSdust.txt
    # 91379422 bases (3847239 N's 87532183 real 59418740 upper 28113443 lower)
    #   in 5765 sequences in 1 files
    # Total size: mean 15850.7 sd 64640.7 min 265 (JH717805v1)
    #   max 1325655 (JH712066v1) median 1186
    # %30.77 masked total, %32.12 masked real

    cat fb.loaLoa1.rmsk.windowmaskerSdust.txt
    # 3520248 bases of 91379422 (3.852%) in intersection

    # using this Window Masker result for final masking::
    cd /hive/data/genomes/loaLoa1
    #   you can safely ignore the warning about fields >= 13
    twoBitMask bed/windowMasker/loaLoa1.cleanWMSdust.2bit \
       -add bed/simpleRepeat/trfMask.bed  loaLoa1.2bit

    # measure the final masking:
    twoBitToFa loaLoa1.2bit stdout | faSize stdin > faSize.loaLoa1.2bit.txt
    cat faSize.loaLoa1.2bit.txt
    # 91379422 bases (3847239 N's 87532183 real 59394205 upper 28137978 lower)
    #   in 5765 sequences in 1 files
    # Total size: mean 15850.7 sd 64640.7 min 265 (JH717805v1)
    #   max 1325655 (JH712066v1) median 1186
    # %30.79 masked total, %32.15 masked real

    # and reset the symlink
    rm /gbdb/loaLoa1/loaLoa1.2bit
    ln -s /hive/data/genomes/loaLoa1/loaLoa1.2bit /gbdb/loaLoa1/loaLoa1.2bit

##########################################################################
# cpgIslands - (DONE - 2015-07-15 - Hiram)
    mkdir /hive/data/genomes/loaLoa1/bed/cpgIslands
    cd /hive/data/genomes/loaLoa1/bed/cpgIslands
    time (doCpgIslands.pl -dbHost=hgwdev -bigClusterHub=ku \
      -workhorse=hgwdev -smallClusterHub=ku loaLoa1) > do.log 2>&1 &
    # real    56m0.652s

    cat fb.loaLoa1.cpgIslandExt.txt
    # 40816 bases of 87533141 (0.047%) in intersection

#########################################################################
# augustus - (DONE - 2015-07-15 - Hiram)
    mkdir /hive/data/genomes/loaLoa1/bed/augustus
    cd /hive/data/genomes/loaLoa1/bed/augustus
    #  XXX this is not specifically correct, the species caenorhabditis
    #      is not necessarily accurate here
    time (doAugustus.pl -buildDir=`pwd` -bigClusterHub=ku \
      -species=caenorhabditis -dbHost=hgwdev \
         -workhorse=hgwdev loaLoa1) > do.log 2>&1 &
    # real    35m34.472s

    cat fb.loaLoa1.augustusGene.txt
    # 6440572 bases of 87533141 (7.358%) in intersection

#########################################################################
# genscan - (DONE - 2015-07-15 - Hiram)
    mkdir /hive/data/genomes/loaLoa1/bed/genscan
    cd /hive/data/genomes/loaLoa1/bed/genscan
    time (doGenscan.pl -buildDir=`pwd` -workhorse=hgwdev -dbHost=hgwdev \
      -bigClusterHub=ku loaLoa1) > do.log 2>&1
    # real    7m2.652s

    cat fb.loaLoa1.genscan.txt
    #   3545367 bases of 87533141 (4.050%) in intersection

    cat fb.loaLoa1.genscanSubopt.txt
    #   3368899 bases of 87533141 (3.849%) in intersection

########################################################################
# Create kluster run files (TBD - 2015-07-08 - Hiram)

    cd /hive/data/genomes/loaLoa1
    # numerator is loaLoa1 gapless bases "real" as reported by:
    head -1 faSize.loaLoa1.2bit.txt
# 94076581 bases (7759220 N's 86317361 real 53341517 upper 32975844 lower)
#    in 9780 sequences in 1 files
    # numerator is 'real' base count
    # denominator is hg19 gapless bases as reported by:
    #   featureBits -noRandom -noHap hg19 gap
    #     234344806 bases of 2861349177 (8.190%) in intersection
    # 1024 is threshold used for human -repMatch:
    calc \( 86317361 / 2861349177 \) \* 1024
    # ( 86317361 / 2861349177 ) * 1024 = 30.890665

    # ==> use -repMatch=100 since 30 or 50 masks too much
    cd /hive/data/genomes/loaLoa1
    time blat loaLoa1.2bit \
         /dev/null /dev/null -tileSize=11 -makeOoc=jkStuff/loaLoa1.11.ooc \
        -repMatch=100
    # Wrote 8527 overused 11-mers to jkStuff/loaLoa1.11.ooc
    #  real    0m1.846s

    # there are a few non-bridged gaps
    #   check non-bridged gaps to see what the typical size is:
    hgsql -N -e 'select * from gap where bridge="no" order by size;' loaLoa1 \
       | ave -tableOut -col=7 stdin
# min Q1 median Q3 max mean N sum stddev
# 78831 79056 79362 79503 79503 79162.5 4 316650 320.991

    # note the minimum non-bridged gap size is 78,831
    gapToLift -verbose=2 -minGap=50000 loaLoa1 jkStuff/loaLoa1.nonBridged.lft \
         -bedFile=jkStuff/loaLoa1.nonBridged.bed

    # survey sizes:
    n50.pl chrom.sizes
#       reading: chrom.sizes
#       contig count: 9780, total size: 94076581, one half size: 47038290
# cumulative    N50 count       contig  contig size
# 46960459        61      Bmal_v3_scaffold61      194773
# 47038290 one half size
# 47151548        62      Bmal_v3_scaffold62      191089

#############################################################################
# GENBANK AUTO UPDATE (TBD - 2015-06-09 - Hiram)
    ssh hgwdev
    cd $HOME/kent/src/hg/makeDb/genbank
    git pull
    # /cluster/data/genbank/data/organism.lst shows:
    # #organism               mrnaCnt estCnt  refSeqCnt
    #  Pristionchus pacificus  97      37470   0

    # edit etc/genbank.conf to add loaLoa1 just before priPac1

# loaLoa1 (P. pacificus)
loaLoa1.serverGenome = /hive/data/genomes/loaLoa1/loaLoa1.2bit
loaLoa1.clusterGenome = /hive/data/genomes/loaLoa1/loaLoa1.2bit
loaLoa1.ooc = /hive/data/genomes/loaLoa1/jkStuff/loaLoa1.11.ooc
loaLoa1.lift = /hive/data/genomes/loaLoa1/jkStuff/loaLoa1.nonBridged.lft
loaLoa1.refseq.mrna.native.pslCDnaFilter  = ${ordered.refseq.mrna.native.pslCDnaFilter}
loaLoa1.refseq.mrna.xeno.pslCDnaFilter    = ${ordered.refseq.mrna.xeno.pslCDnaFilter}
loaLoa1.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter}
loaLoa1.genbank.mrna.xeno.pslCDnaFilter   = ${ordered.genbank.mrna.xeno.pslCDnaFilter}
loaLoa1.genbank.est.native.pslCDnaFilter  = ${ordered.genbank.est.native.pslCDnaFilter}
loaLoa1.refseq.mrna.native.load = yes
loaLoa1.refseq.mrna.xeno.load  = yes
loaLoa1.refseq.mrna.xeno.loadDesc = yes
# DO NOT NEED genbank.mrna.xeno except for human, mouse
loaLoa1.genbank.mrna.xeno.load = no
loaLoa1.genbank.est.native.load = yes
loaLoa1.genbank.est.native.loadDesc = no
loaLoa1.downloadDir = loaLoa1
loaLoa1.perChromTables = no

    git commit -m "Added loaLoa1 - P. pacificus refs #15209" etc/genbank.conf
    git push
    # update /cluster/data/genbank/etc/:
    make etc-update

    screen      #  control this business with a screen since it takes a while
    cd /cluster/data/genbank

    time ./bin/gbAlignStep -initial loaLoa1
    # logFile: var/build/logs/2015.07.02-11:39:01.loaLoa1.initalign.log
    # real    91m20.362s

    #   To re-do, rm the dir first:
    #     /cluster/data/genbank/work/initial.loaLoa1

    # load database when finished
    ssh hgwdev
    cd /cluster/data/genbank
    time ./bin/gbDbLoadStep -drop -initialLoad loaLoa1
    # logFile: var/dbload/hgwdev/logs/2015.07.06-09:51:31.loaLoa1.dbload.log
    # real    18m34.687s

    # enable daily alignment and update of hgwdev
    cd ~/kent/src/hg/makeDb/genbank
    git pull
    # add loaLoa1 to:
    #   vi etc/align.dbs etc/hgwdev.dbs
    git commit -m "Added loaLoa1 - Pristionchus pacificus refs #15209" \
      etc/align.dbs etc/hgwdev.dbs
    git push
    make etc-update

#########################################################################
# all.joiner update, downloads and in pushQ - (TBD - 2015-06-22 - Hiram)
    cd $HOME/kent/src/hg/makeDb/schema
    # fixup all.joiner until this is a clean output
    joinerCheck -database=loaLoa1 -tableCoverage all.joiner
    joinerCheck -database=loaLoa1 -times all.joiner
    joinerCheck -database=loaLoa1 -keys all.joiner

    cd /hive/data/genomes/loaLoa1
    time makeDownloads.pl loaLoa1 > downloads.log 2>&1
    # real    13m42.027s

    #   now ready for pushQ entry
    mkdir /hive/data/genomes/loaLoa1/pushQ
    cd /hive/data/genomes/loaLoa1/pushQ
    makePushQSql.pl loaLoa1 > loaLoa1.pushQ.sql 2> stderr.out
    #   check for errors in stderr.out, some are OK, e.g.:
    # WARNING: hgwdev does not have /gbdb/loaLoa1/wib/gc5Base.wib
    # WARNING: hgwdev does not have /gbdb/loaLoa1/wib/quality.wib
    # WARNING: hgwdev does not have /gbdb/loaLoa1/bbi/qualityBw/quality.bw
    # WARNING: loaLoa1 does not have seq
    # WARNING: loaLoa1 does not have extFile
    # WARNING: loaLoa1 does not have estOrientInfo
    # WARNING: loaLoa1 does not have mrnaOrientInfo

    #   copy it to hgwbeta
    scp -p loaLoa1.pushQ.sql qateam@hgwbeta:/tmp
    ssh qateam@hgwbeta "./bin/x86_64/hgsql qapushq < /tmp/loaLoa1.pushQ.sql"

    #   in that pushQ entry walk through each entry and see if the
    #   sizes will set properly

#############################################################################
