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

# This file describes how browser build for
#     Necator americanus/hookworm WS245 version

##############################################################################
# download sequence, create UCSC sequence (DONE - 2015-06-24 - Hiram)
    mkdir -p /hive/data/genomes/necAme1/genbank
    cd /hive/data/genomes/necAme1/genbank

    rsync -L -a -P \
rsync://ftp.ncbi.nlm.nih.gov/genomes/genbank/invertebrate/Necator_americanus/all_assembly_versions/GCA_000507365.1_N_americanus_v1/ ./

    mkdir -p /hive/data/genomes/necAme1/ws245
    cd /hive/data/genomes/necAme1/ws245

    wget --no-parent --timestamping -m -nH --cut-dirs=6 \
ftp://ftp.sanger.ac.uk/pub/wormbase/releases/WS245/species/PRJNA231479

    # The genbank and WS245 sequences are identical
    mkdir /hive/data/genomes/necAme1/ucsc
    cd /hive/data/genomes/necAme1/ucsc

    zcat ../genbank/GCA_000507365.1_N_americanus_v1_assembly_structure/Primary_Assembly/unplaced_scaffolds/FASTA/unplaced.scaf.fna.gz \
       | sed -e 's/.1 Necator americanus .*/v1/;' | gzip -c > necAme1.fa.gz

    zcat ../genbank/GCA_000507365.1_N_americanus_v1_assembly_structure/Primary_Assembly/unplaced_scaffolds/AGP/unplaced.scaf.agp.gz \
      | sed -e 's/\.1/v1/;' > necAme1.agp

       | sed -e 's/.1 Necator americanus .*/v1/;' | gzip -c > necAme1.fa.gz
    zcat ../genbank/GCA_000688135.1_Acey_2013.11.30.genDNA_genomic.fna.gz \
       | sed -e 's/.1 Ancylostoma ceylanicum .*/v1/;' | gzip -c > necAme1.fa.gz


    # obtain photo, CDC public domain photo, reuse same photo from ancCey1
    wget --timestamping \
http://www.cdc.gov/dpdx/images/hookworm/Hookworm_filariform_A.jpg
    # this image is slightly larger than 400x300, reduce to 400x300:
    convert -geometry "400x300" Hookworm_filariform_A.jpg \
         Ancylostoma_ceylanicum.jpg

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

#############################################################################
#  Initial database build (DONE - 2015-07-15 - Hiram)

    cd /hive/data/genomes/necAme1
    cat << '_EOF_' > necAme1.config.ra
# Config parameters for makeGenomeDb.pl:
db necAme1
clade worm
genomeCladePriority 86
scientificName Necator americanus
commonName Hookworm
assemblyDate Dec. 2013
assemblyLabel The Genome Institute at Washington University
assemblyShortLabel WS242/N_americanus_v1
orderKey 8679
mitoAcc AJ417719.2
fastaFiles /hive/data/genomes/necAme1/ucsc/necAme1.fa.gz
agpFiles /hive/data/genomes/necAme1/ucsc/necAme1.agp
# qualFiles none
dbDbSpeciesDir worm
photoCreditURL http://www.cdc.gov/dpdx/hookworm/
hotoCreditName Centers for Disease Control and Prevention
ncbiGenomeId 770
ncbiAssemblyId 88321
ncbiAssemblyName WS242/N_americanus_v1
ncbiBioProject 72135
genBankAccessionID GCA_000507365.1
taxId 51031
'_EOF_'
    # << happy emacs

    # verify sequence and AGP are OK:
    time (makeGenomeDb.pl -workhorse=hgwdev -dbHost=hgwdev -fileServer=hgwdev \
         -stop=agp necAme1.config.ra) > agp.log 2>&1
    # *** All done!  (through the 'agp' step)
    # real    0m32.382s

    # then finish it off:
    time (makeGenomeDb.pl -workhorse=hgwdev -dbHost=hgwdev \
       -fileServer=hgwdev -continue=db necAme1.config.ra) > db.log 2>&1
    # real    2m16.737s

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

##############################################################################
# cpgIslands on UNMASKED sequence (DONE - 2015-07-15 - Hiram)
    mkdir /hive/data/genomes/necAme1/bed/cpgIslandsUnmasked
    cd /hive/data/genomes/necAme1/bed/cpgIslandsUnmasked

    time (doCpgIslands.pl -dbHost=hgwdev -bigClusterHub=ku -buildDir=`pwd` \
       -tableName=cpgIslandExtUnmasked \
          -maskedSeq=/hive/data/genomes/necAme1/necAme1.unmasked.2bit \
             -workhorse=hgwdev -smallClusterHub=ku necAme1) > do.log 2>&1
    # real    68m58.962s

    cat fb.necAme1.cpgIslandExtUnmasked.txt
    # 11575810 bases of 208187215 (5.560%) in intersection

#############################################################################
# cytoBandIdeo - (DONE - 2015-07-15 - Hiram)
    mkdir /hive/data/genomes/necAme1/bed/cytoBand
    cd /hive/data/genomes/necAme1/bed/cytoBand
    makeCytoBandIdeo.csh necAme1

#########################################################################
# ucscToINSDC table/track (DONE - 2015-07-15 - Hiram)
    mkdir /hive/data/genomes/necAme1/bed/ucscToINSDC
    cd /hive/data/genomes/necAme1/bed/ucscToINSDC

    # find the chrM accession:
    grep chrM ../../*.agp
# chrM    1       13605   2       F       AJ417719.2      1       13605   +

    # use that as the second argument here:
    ~/kent/src/hg/utils/automation/ucscToINSDC.sh \
       ../../genbank/GCA_000507365.1_N_americanus_v1_assembly_structure/Primary_Assembly AJ417719.2

    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 *
    # 11865 name.coordinate.tab
    # 11865 ucscToINSDC.bed
    # 11865 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 necAme1 ucscToINSDC stdin ucscToINSDC.bed
    checkTableCoords necAme1
    # should cover %100 entirely:
    featureBits -countGaps necAme1 ucscToINSDC
    # 244088665 bases of 244088665 (100.000%) in intersection

#########################################################################
# fixup search rule for assembly track/gold table (DONE - 2015-07-15 - Hiram)
    hgsql -N -e "select frag from gold;" necAme1 | sort | head -3
AJ417719.2
ANCG01000001.1
ANCG01000002.1


    hgsql -N -e "select frag from gold;" necAme1 | sort | tail -2
ANCG01065212.1
ANCG01065213.1


    # verify this rule will find them all or eliminate them all:
    hgsql -N -e "select frag from gold;" necAme1 | wc -l
    # 65214

    hgsql -N -e "select frag from gold;" necAme1 \
      | egrep -e '(ANCG010|AJ417719)[0-9]*(\.[12])?' | wc -l
    # 65214

    hgsql -N -e "select frag from gold;" necAme1 \
      | egrep -v -e '(ANCG010|AJ417719)[0-9]*(\.[12])?' | wc -l
    # 0

    # hence, add to trackDb/worm/necAme1/trackDb.ra
searchTable gold
shortCircuit 1
termRegex (ANCG010|AJ417719)[0-9]*(\.[12])?
query select chrom,chromStart,chromEnd,frag from %s where frag like '%s%%'
searchPriority 8

##########################################################################
# running repeat masker (DONE - 2015-07-15 - Hiram)
    mkdir /hive/data/genomes/necAme1/bed/repeatMasker
    cd /hive/data/genomes/necAme1/bed/repeatMasker
    time (doRepeatMasker.pl -buildDir=`pwd` \
        -bigClusterHub=ku -dbHost=hgwdev -workhorse=hgwdev \
        -smallClusterHub=ku necAme1) > do.log 2>&1
    # real    44m44.824s

    cat faSize.rmsk.txt
    # 244088665 bases (35901450 N's 208187215 real 205566359 upper
    #    2620856 lower) in 11865 sequences in 1 files
    # Total size: mean 20572.2 sd 82630.6 min 201 (KI658258v1)
    #    max 1890151 (KI657455v1) median 1315
    # %1.07 masked total, %1.26 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 necAme1 rmsk
    #  2620956 bases of 244088665 (1.074%) in intersection
    #  real    0m4.884s

##########################################################################
# running simple repeat (DONE - 2015-07-15 - Hiram)
    mkdir /hive/data/genomes/necAme1/bed/simpleRepeat
    cd /hive/data/genomes/necAme1/bed/simpleRepeat
    time (doSimpleRepeat.pl -buildDir=`pwd` -bigClusterHub=ku \
        -dbHost=hgwdev -workhorse=hgwdev -smallClusterHub=ku \
        necAme1) > do.log 2>&1
    # real    9m24.231s

    cat fb.simpleRepeat
    # 1474019 bases of 208187215 (0.708%) in intersection

    # using the Window Masker result as indicated below

##########################################################################
# CREATE MICROSAT TRACK (DONE - 2015-07-15 - Hiram)
     ssh hgwdev
     mkdir /cluster/data/necAme1/bed/microsat
     cd /cluster/data/necAme1/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 necAme1 microsat microsat.bed
    #	Read 409 elements of size 4 from microsat.bed

##########################################################################
## WINDOWMASKER (DONE - 2015-07-15 - Hiram)
    mkdir /hive/data/genomes/necAme1/bed/windowMasker
    cd /hive/data/genomes/necAme1/bed/windowMasker
    time (doWindowMasker.pl -buildDir=`pwd` -workhorse=hgwdev \
        -dbHost=hgwdev necAme1) > do.log 2>&1
    # real    19m24.750s

    # Masking statistics
    cat faSize.necAme1.cleanWMSdust.txt
    # 244088665 bases (35901450 N's 208187215 real 154506078 upper
    #   53681137 lower) in 11865 sequences in 1 files
    # Total size: mean 20572.2 sd 82630.6 min 201 (KI658258v1)
    #   max 1890151 (KI657455v1) median 1315
    # %21.99 masked total, %25.79 masked real

    cat fb.necAme1.rmsk.windowmaskerSdust.txt
    # 2166063 bases of 244088665 (0.887%) in intersection

    # using this Window Masker result for final masking::
    cd /hive/data/genomes/necAme1
    #   you can safely ignore the warning about fields >= 13
    twoBitMask bed/windowMasker/necAme1.cleanWMSdust.2bit \
       -add bed/simpleRepeat/trfMask.bed  necAme1.2bit

    # measure the final masking:
    twoBitToFa necAme1.2bit stdout | faSize stdin > faSize.necAme1.2bit.txt
    cat faSize.necAme1.2bit.txt
    # 244088665 bases (35901450 N's 208187215 real 154468942 upper
    #   53718273 lower) in 11865 sequences in 1 files
    # Total size: mean 20572.2 sd 82630.6 min 201 (KI658258v1)
    #   max 1890151 (KI657455v1) median 1315
    # %22.01 masked total, %25.80 masked real

    # and reset the symlink
    rm /gbdb/necAme1/necAme1.2bit
    ln -s /hive/data/genomes/necAme1/necAme1.2bit /gbdb/necAme1/necAme1.2bit

##########################################################################
# cpgIslands - (DONE - 2015-07-15 - Hiram)
    mkdir /hive/data/genomes/necAme1/bed/cpgIslands
    cd /hive/data/genomes/necAme1/bed/cpgIslands
    time (doCpgIslands.pl -dbHost=hgwdev -bigClusterHub=ku \
      -workhorse=hgwdev -smallClusterHub=ku necAme1) > do.log 2>&1 &
    # real    48m2.637s

    cat fb.necAme1.cpgIslandExt.txt
    # 2764104 bases of 208187215 (1.328%) in intersection

#########################################################################
# augustus - (DONE - 2015-07-15 - Hiram)
    mkdir /hive/data/genomes/necAme1/bed/augustus
    cd /hive/data/genomes/necAme1/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 necAme1) > do.log 2>&1 &
    # real    64m43.147s

    cat fb.necAme1.augustusGene.txt
    # 16924922 bases of 208187215 (8.130%) in intersection

#########################################################################
# genscan - (DONE - 2015-07-15 - Hiram)
    mkdir /hive/data/genomes/necAme1/bed/genscan
    cd /hive/data/genomes/necAme1/bed/genscan
    time (doGenscan.pl -buildDir=`pwd` -workhorse=hgwdev -dbHost=hgwdev \
      -bigClusterHub=ku necAme1) > do.log 2>&1
    # real    33m54.384s

    cat fb.necAme1.genscan.txt
    #   11294976 bases of 208187215 (5.425%) in intersection

    cat fb.necAme1.genscanSubopt.txt
    #   11510060 bases of 208187215 (5.529%) in intersection

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

    cd /hive/data/genomes/necAme1
    # numerator is necAme1 gapless bases "real" as reported by:
    head -1 faSize.necAme1.2bit.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/necAme1
    time blat necAme1.2bit \
         /dev/null /dev/null -tileSize=11 -makeOoc=jkStuff/necAme1.11.ooc \
        -repMatch=100
    # Wrote 8527 overused 11-mers to jkStuff/necAme1.11.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;' necAme1 \
       | 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 necAme1 jkStuff/necAme1.nonBridged.lft \
         -bedFile=jkStuff/necAme1.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 necAme1 just before priPac1

# necAme1 (P. pacificus)
necAme1.serverGenome = /hive/data/genomes/necAme1/necAme1.2bit
necAme1.clusterGenome = /hive/data/genomes/necAme1/necAme1.2bit
necAme1.ooc = /hive/data/genomes/necAme1/jkStuff/necAme1.11.ooc
necAme1.lift = /hive/data/genomes/necAme1/jkStuff/necAme1.nonBridged.lft
necAme1.refseq.mrna.native.pslCDnaFilter  = ${ordered.refseq.mrna.native.pslCDnaFilter}
necAme1.refseq.mrna.xeno.pslCDnaFilter    = ${ordered.refseq.mrna.xeno.pslCDnaFilter}
necAme1.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter}
necAme1.genbank.mrna.xeno.pslCDnaFilter   = ${ordered.genbank.mrna.xeno.pslCDnaFilter}
necAme1.genbank.est.native.pslCDnaFilter  = ${ordered.genbank.est.native.pslCDnaFilter}
necAme1.refseq.mrna.native.load = yes
necAme1.refseq.mrna.xeno.load  = yes
necAme1.refseq.mrna.xeno.loadDesc = yes
# DO NOT NEED genbank.mrna.xeno except for human, mouse
necAme1.genbank.mrna.xeno.load = no
necAme1.genbank.est.native.load = yes
necAme1.genbank.est.native.loadDesc = no
necAme1.downloadDir = necAme1
necAme1.perChromTables = no

    git commit -m "Added necAme1 - 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 necAme1
    # logFile: var/build/logs/2015.07.02-11:39:01.necAme1.initalign.log
    # real    91m20.362s

    #   To re-do, rm the dir first:
    #     /cluster/data/genbank/work/initial.necAme1

    # load database when finished
    ssh hgwdev
    cd /cluster/data/genbank
    time ./bin/gbDbLoadStep -drop -initialLoad necAme1
    # logFile: var/dbload/hgwdev/logs/2015.07.06-09:51:31.necAme1.dbload.log
    # real    18m34.687s

    # enable daily alignment and update of hgwdev
    cd ~/kent/src/hg/makeDb/genbank
    git pull
    # add necAme1 to:
    #   vi etc/align.dbs etc/hgwdev.dbs
    git commit -m "Added necAme1 - 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=necAme1 -tableCoverage all.joiner
    joinerCheck -database=necAme1 -times all.joiner
    joinerCheck -database=necAme1 -keys all.joiner

    cd /hive/data/genomes/necAme1
    time makeDownloads.pl necAme1 > downloads.log 2>&1
    # real    13m42.027s

    #   now ready for pushQ entry
    mkdir /hive/data/genomes/necAme1/pushQ
    cd /hive/data/genomes/necAme1/pushQ
    makePushQSql.pl necAme1 > necAme1.pushQ.sql 2> stderr.out
    #   check for errors in stderr.out, some are OK, e.g.:
    # WARNING: hgwdev does not have /gbdb/necAme1/wib/gc5Base.wib
    # WARNING: hgwdev does not have /gbdb/necAme1/wib/quality.wib
    # WARNING: hgwdev does not have /gbdb/necAme1/bbi/qualityBw/quality.bw
    # WARNING: necAme1 does not have seq
    # WARNING: necAme1 does not have extFile
    # WARNING: necAme1 does not have estOrientInfo
    # WARNING: necAme1 does not have mrnaOrientInfo

    #   copy it to hgwbeta
    scp -p necAme1.pushQ.sql qateam@hgwbeta:/tmp
    ssh qateam@hgwbeta "./bin/x86_64/hgsql qapushq < /tmp/necAme1.pushQ.sql"

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

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