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

# This file describes the browser build for
#    Ascaris suum/pig roundworm WS245 version

##############################################################################
# download sequence, create UCSC sequence (DONE - 2015-06-24 - Hiram)
    mkdir -p /hive/data/genomes/ascSuu1/genbank
    cd /hive/data/genomes/ascSuu1/genbank

    # there are three assemblies at NCBI
    rsync -L -a -P \
rsync://ftp.ncbi.nlm.nih.gov/genomes/genbank/invertebrate/Ascaris_suum/all_assembly_versions/GCA_000298755.1_AscSuum_1.0/ .

    rsync -L -a -P \
rsync://ftp.ncbi.nlm.nih.gov/genomes/genbank/invertebrate/Ascaris_suum/all_assembly_versions/GCA_000331935.2_AS1.0/ ./

    rsync -L -a -P \
rsync://ftp.ncbi.nlm.nih.gov/genomes/genbank/invertebrate/Ascaris_suum/all_assembly_versions/GCA_000187025.2_ASM18702v2/ ./

    # there are two at WormBase:
    mkdir -p /hive/data/genomes/ascSuu1/ws245
    cd /hive/data/genomes/ascSuu1/ws245

    wget --no-parent --timestamping -m -nH --cut-dirs=6 \
ftp://ftp.sanger.ac.uk/pub/wormbase/releases/WS245/species/PRJNA62057
    wget --no-parent --timestamping -m -nH --cut-dirs=6 \
ftp://ftp.sanger.ac.uk/pub/wormbase/releases/WS245/species/PRJNA80881

    # The genbank/GCA_000298755.1_AscSuum_1.0_genomic.fna.gz and
    # WormBase PRJNA80881/a_suum.PRJNA80881.WS245.genomic.fa.gz
    # seem equivalent, the large scaffolds are identical sized, but
    # have different composition ?  genbank is newer
    mkdir /hive/data/genomes/ascSuu1/ucsc
    cd /hive/data/genomes/ascSuu1/ucsc

    zcat ../genbank/GCA_000298755.1_AscSuum_1.0_assembly_structure/Primary_Assembly/unplaced_scaffolds/FASTA/unplaced.scaf.fna.gz \
        | sed -e 's/.1 Ascaris .*/v1/;' | gzip -c > ascSuu1.fa.gz

    zcat ../genbank/GCA_000298755.1_AscSuum_1.0_assembly_structure/Primary_Assembly/unplaced_scaffolds/AGP/unplaced.scaf.agp.gz \
      | sed -e 's/\.1/v1/;' > ascSuu1.agp

    # obtain photo, CDC public domain photo
    mkdir /hive/data/genomes/ascSuu1/photo
    cd /hive/data/genomes/ascSuu1/photo
    wget --timestamping \
http://www.cdc.gov/dpdx/images/ascariasis/Ascaris_female.jpg
    # this image is already 300x300 so it can go as is

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

#############################################################################
#  Initial database build (DONE - 2015-07-13 - Hiram)

    cd /hive/data/genomes/ascSuu1
    cat << '_EOF_' > ascSuu1.config.ra
# Config parameters for makeGenomeDb.pl:
db ascSuu1
clade worm
genomeCladePriority 68
scientificName Ascaris suum
commonName Pig roundworm
assemblyDate Sep. 2012
assemblyLabel Beijing Genomics Institute
assemblyShortLabel WS229/AscSuum_1.0
orderKey 16320
mitoAcc X54253.1
fastaFiles /hive/data/genomes/ascSuu1/ucsc/ascSuu1.fa.gz
agpFiles /hive/data/genomes/ascSuu1/ucsc/ascSuu1.agp
# qualFiles none
dbDbSpeciesDir worm
photoCreditURL http://www.cdc.gov/parasites/ascariasis/
photoCreditName Centers for Disease Control and Prevention
ncbiGenomeId 350
ncbiAssemblyId 426198
ncbiAssemblyName WS229/AscSuum_1.0
ncbiBioProject 80881
genBankAccessionID GCA_000298755.1
taxId 6253
'_EOF_'
    # << happy emacs

    # verify sequence and AGP are OK:
    time (makeGenomeDb.pl -workhorse=hgwdev -dbHost=hgwdev -fileServer=hgwdev \
         -stop=agp ascSuu1.config.ra) > agp.log 2>&1
    # *** All done!  (through the 'agp' step)
    # real    0m34.666s

    # then finish it off:
    time (makeGenomeDb.pl -workhorse=hgwdev -dbHost=hgwdev \
       -fileServer=hgwdev -continue=db ascSuu1.config.ra) > db.log 2>&1
    # real    2m38.873s

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

##############################################################################
# cpgIslands on UNMASKED sequence (DONE - 2015-07-13 - Hiram)
    mkdir /hive/data/genomes/ascSuu1/bed/cpgIslandsUnmasked
    cd /hive/data/genomes/ascSuu1/bed/cpgIslandsUnmasked

    time (doCpgIslands.pl -dbHost=hgwdev -bigClusterHub=ku -buildDir=`pwd` \
       -tableName=cpgIslandExtUnmasked \
          -maskedSeq=/hive/data/genomes/ascSuu1/ascSuu1.unmasked.2bit \
             -workhorse=hgwdev -smallClusterHub=ku ascSuu1) > do.log 2>&1
    # real    9m16.354s

    cat fb.ascSuu1.cpgIslandExtUnmasked.txt
    # 3040279 bases of 262604320 (1.158%) in intersection

#############################################################################
# cytoBandIdeo - (DONE - 2015-07-13 - Hiram)
    mkdir /hive/data/genomes/ascSuu1/bed/cytoBand
    cd /hive/data/genomes/ascSuu1/bed/cytoBand
    makeCytoBandIdeo.csh ascSuu1

#########################################################################
# ucscToINSDC table/track (DONE - 2015-07-13 - Hiram)
    mkdir /hive/data/genomes/ascSuu1/bed/ucscToINSDC
    cd /hive/data/genomes/ascSuu1/bed/ucscToINSDC

    # find the chrM accession:
    grep chrM ../../*.agp
# chrM    1       14284   4       F       X54253.1        1       14284   +

    # use that as the second argument here:
    ~/kent/src/hg/utils/automation/ucscToINSDC.sh \
       ../../genbank/GCA_000298755.1_AscSuum_1.0_assembly_structure/Primary_Assembly X54253.1

    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
    # 14
    # use the 14 in this sed
    sed -e "s/21/14/" $HOME/kent/src/hg/lib/ucscToINSDC.sql \
         | hgLoadSqlTab ascSuu1 ucscToINSDC stdin ucscToINSDC.bed
    checkTableCoords ascSuu1
    # should cover %100 entirely:
    featureBits -countGaps ascSuu1 ucscToINSDC
    # 269573965 bases of 269573965 (100.000%) in intersection

#########################################################################
# fixup search rule for assembly track/gold table (DONE - 2015-07-13 - Hiram)
    hgsql -N -e "select frag from gold;" ascSuu1 | sort | head -3
AMPH01000001.1
AMPH01000002.1
AMPH01000003.1

    hgsql -N -e "select frag from gold;" ascSuu1 | sort | tail -2
AMPH01030842.1
X54253.1

    # verify this rule will find them all or eliminate them all:
    hgsql -N -e "select frag from gold;" ascSuu1 | wc -l
    # 30843

    hgsql -N -e "select frag from gold;" ascSuu1 \
      | egrep -e '(AMPH010|X54253)[0-9]*(\.1)?' | wc -l
    # 30843

    hgsql -N -e "select frag from gold;" ascSuu1 \
      | egrep -v -e '(AMPH010|X54253)[0-9]*(\.1)?' | wc -l
    # 0

    # hence, add to trackDb/worm/ascSuu1/trackDb.ra
searchTable gold
shortCircuit 1
termRegex (AMPH010|X54253)[0-9]*(\.1)?
query select chrom,chromStart,chromEnd,frag from %s where frag like '%s%%'
searchPriority 8

##########################################################################
# running repeat masker (DONE - 2015-07-13 - Hiram)
    mkdir /hive/data/genomes/ascSuu1/bed/repeatMasker
    cd /hive/data/genomes/ascSuu1/bed/repeatMasker
    time (doRepeatMasker.pl -buildDir=`pwd` \
        -bigClusterHub=ku -dbHost=hgwdev -workhorse=hgwdev \
        -smallClusterHub=ku ascSuu1) > do.log 2>&1
    # real    259m36.195s

    cat faSize.rmsk.txt
    # 269573965 bases (6969646 N's 262604319 real 258927735 upper
    #    3676584 lower) in 12989 sequences in 1 files
    # Total size: mean 20754.0 sd 115105.2 min 189 (AMPH01005591v1)
    #    max 3795215 (JH878907v1) median 414
    # %1.36 masked total, %1.40 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 ascSuu1 rmsk
    # 3678296 bases of 269573965 (1.364%) in intersection
    # real    0m5.089s

##########################################################################
# running simple repeat (DONE - 2015-07-13 - Hiram)
    mkdir /hive/data/genomes/ascSuu1/bed/simpleRepeat
    cd /hive/data/genomes/ascSuu1/bed/simpleRepeat
    time (doSimpleRepeat.pl -buildDir=`pwd` -bigClusterHub=ku \
        -dbHost=hgwdev -workhorse=hgwdev -smallClusterHub=ku \
        ascSuu1) > do.log 2>&1
    # real    7m23.268s

    cat fb.simpleRepeat
    # 5752869 bases of 262604320 (2.191%) in intersection

    # using the Window Masker result as indicated below

##########################################################################
# CREATE MICROSAT TRACK (DONE - 2015-07-23 - Hiram)
     ssh hgwdev
     mkdir /cluster/data/ascSuu1/bed/microsat
     cd /cluster/data/ascSuu1/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 ascSuu1 microsat microsat.bed
    #	Read 1148 elements of size 4 from microsat.bed

##########################################################################
## WINDOWMASKER (DONE - 2015-07-14 - Hiram)
    mkdir /hive/data/genomes/ascSuu1/bed/windowMasker
    cd /hive/data/genomes/ascSuu1/bed/windowMasker
    time (doWindowMasker.pl -buildDir=`pwd` -workhorse=hgwdev \
        -dbHost=hgwdev ascSuu1) > do.log 2>&1
    # real    12m49.610s

    # Masking statistics
    cat faSize.ascSuu1.cleanWMSdust.txt
    # 269573965 bases (6969646 N's 262604319 real 206235073 upper
    #    56369246 lower) in 12989 sequences in 1 files
    # Total size: mean 20754.0 sd 115105.2 min 189 (AMPH01005591v1)
    #    max 3795215 (JH878907v1) median 414
    # %20.91 masked total, %21.47 masked real

    cat fb.ascSuu1.rmsk.windowmaskerSdust.txt
    # 2973361 bases of 269573965 (1.103%) in intersection

    # using this Window Masker result for final masking::
    cd /hive/data/genomes/ascSuu1
    #   you can safely ignore the warning about fields >= 13
    twoBitMask bed/windowMasker/ascSuu1.cleanWMSdust.2bit \
       -add bed/simpleRepeat/trfMask.bed  ascSuu1.2bit

    # measure the final masking:
    twoBitToFa ascSuu1.2bit stdout | faSize stdin > faSize.ascSuu1.2bit.txt
    cat faSize.ascSuu1.2bit.txt
    # 269573965 bases (6969646 N's 262604319 real 206195917 upper
    #    56408402 lower) in 12989 sequences in 1 files
    # Total size: mean 20754.0 sd 115105.2 min 189 (AMPH01005591v1)
    #    max 3795215 (JH878907v1) median 414
    # %20.93 masked total, %21.48 masked real

    # and reset the symlink
    rm /gbdb/ascSuu1/ascSuu1.2bit
    ln -s /hive/data/genomes/ascSuu1/ascSuu1.2bit /gbdb/ascSuu1/ascSuu1.2bit

##########################################################################
# cpgIslands - (DONE - 2015-07-15 - Hiram)
    mkdir /hive/data/genomes/ascSuu1/bed/cpgIslands
    cd /hive/data/genomes/ascSuu1/bed/cpgIslands
    time (doCpgIslands.pl -dbHost=hgwdev -bigClusterHub=ku \
      -workhorse=hgwdev -smallClusterHub=ku ascSuu1) > do.log 2>&1 &
    # real    38m40.524s

    cat fb.ascSuu1.cpgIslandExt.txt
    # 2314905 bases of 262604320 (0.882%) in intersection

#########################################################################
# augustus - (DONE - 2015-07-15 - Hiram)
    mkdir /hive/data/genomes/ascSuu1/bed/augustus
    cd /hive/data/genomes/ascSuu1/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 ascSuu1) > do.log 2>&1 &
    # real    74m28.022s

    cat fb.ascSuu1.augustusGene.txt
    # 17430033 bases of 262604320 (6.637%) in intersection

#########################################################################
# genscan - (DONE - 2015-07-15 - Hiram)
    mkdir /hive/data/genomes/ascSuu1/bed/genscan
    cd /hive/data/genomes/ascSuu1/bed/genscan
    time (doGenscan.pl -buildDir=`pwd` -workhorse=hgwdev -dbHost=hgwdev \
      -bigClusterHub=ku ascSuu1) > do.log 2>&1
    # real    28m2.072s

    cat fb.ascSuu1.genscan.txt
    #   12245917 bases of 262604320 (4.663%) in intersection

    cat fb.ascSuu1.genscanSubopt.txt
    #   12237266 bases of 262604320 (4.660%) in intersection

########################################################################
# Create kluster run files (DONE - 2015-08-18 - Hiram)

    cd /hive/data/genomes/ascSuu1
    # numerator is ascSuu1 gapless bases "real" as reported by:
    head -1 faSize.ascSuu1.2bit.txt
# 269573965 bases (6969646 N's 262604319 real 206195917 upper 56408402 lower)
#    in 12989 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 \( 262604319 / 2861349177 \) \* 1024
    # ( 262604319 / 2861349177 ) * 1024 = 93.979031

    # ==> use -repMatch=100
    cd /hive/data/genomes/ascSuu1
    time blat ascSuu1.2bit \
         /dev/null /dev/null -tileSize=11 -makeOoc=jkStuff/ascSuu1.11.ooc \
        -repMatch=100
    # Wrote 19578 overused 11-mers to jkStuff/ascSuu1.11.ooc
    #  real    0m4.766s

    # there are NO 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;' ascSuu1 \
#        | 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 ascSuu1 jkStuff/ascSuu1.nonBridged.lft \
#          -bedFile=jkStuff/ascSuu1.nonBridged.bed

    # survey sizes:
    n50.pl chrom.sizes
#       reading: chrom.sizes
#       contig count: 12989, total size: 269573965, one half size: 134786982
# cumulative    N50 count       contig  contig size
# 134535441       174     JH879080v1      414787
# 134786982 one half size
# 134948503       175     JH879081v1      413062

#############################################################################
# GENBANK AUTO UPDATE (DONE - 2015-08-19 - Hiram/Brian)
    ssh hgwdev
    cd $HOME/kent/src/hg/makeDb/genbank
    git pull
    # /cluster/data/genbank/data/organism.lst shows:
    # organism         mrnaCnt estCnt  refSeqCnt
    #  Ascaris suum    74205   56617   0

    # edit etc/genbank.conf to add ascSuu1 just before priPac3

# ascSuu1 (Pig roundworm/Ascaris suum)
ascSuu1.serverGenome = /hive/data/genomes/ascSuu1/ascSuu1.2bit
ascSuu1.clusterGenome = /hive/data/genomes/ascSuu1/ascSuu1.2bit
ascSuu1.ooc = /hive/data/genomes/ascSuu1/jkStuff/ascSuu1.11.ooc
ascSuu1.lift = no
# the nematodes have small introns
ascSuu1.maxIntron = 100000
ascSuu1.perChromTables = no
ascSuu1.refseq.mrna.native.pslCDnaFilter  = ${lowCover.refseq.mrna.native.pslCDnaFilter}
ascSuu1.refseq.mrna.xeno.pslCDnaFilter    = ${lowCover.refseq.mrna.xeno.pslCDnaFilter}
ascSuu1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter}
ascSuu1.genbank.mrna.xeno.pslCDnaFilter   = ${lowCover.genbank.mrna.xeno.pslCDnaFilter}
ascSuu1.genbank.est.native.pslCDnaFilter  = ${lowCover.genbank.est.native.pslCDnaFilter}
# refseq.mrna native and xeno are default yes
# genbank.mrna and genbank.est native are default yes, the xeno is default no
ascSuu1.downloadDir = ascSuu1

    # Edit src/lib/gbGenome.c to add new species.
    git commit -m "Added ascSuu1 - Pig roundworm/Ascaris suum refs #15209" etc/genbank.conf src/lib/gbGenome.c
    git push
    # update /cluster/data/genbank/etc/:
    make etc-update

    make install-server

    screen      #  control this business with a screen since it takes a while
    cd /cluster/data/genbank
    # had assistance from Brian on this as there were difficulties
    time ./bin/gbAlignStep -initial ascSuu1
    # logFile: var/build/logs/2015.08.19-13:09:42.ascSuu1.initalign.log
    # about 142 minutes == 2h 22m

    #   To re-do, rm these two sets first:
    #     /cluster/data/genbank/work/initial.ascSuu1
    #     /cluster/data/genbank/data/aligned/*/ascSuu1

    # load database when finished
    ssh hgwdev
    cd /cluster/data/genbank
    time ./bin/gbDbLoadStep -drop -initialLoad ascSuu1
    # logFile: var/dbload/hgwdev/logs/2015.08.19-18:03:13.ascSuu1.dbload.log
    # about 42 minutes

    # enable daily alignment and update of hgwdev
    cd ~/kent/src/hg/makeDb/genbank
    git pull
    # add ascSuu1 to:
    #   vi etc/align.dbs etc/hgwdev.dbs
    git commit -m "Added ascSuu1 - Ascaris suum/Pig roundworm 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=ascSuu1 -tableCoverage all.joiner
    joinerCheck -database=ascSuu1 -times all.joiner
    joinerCheck -database=ascSuu1 -keys all.joiner

    cd /hive/data/genomes/ascSuu1
    time makeDownloads.pl ascSuu1 > downloads.log 2>&1
    # real    13m42.027s

    #   now ready for pushQ entry
    mkdir /hive/data/genomes/ascSuu1/pushQ
    cd /hive/data/genomes/ascSuu1/pushQ
    makePushQSql.pl ascSuu1 > ascSuu1.pushQ.sql 2> stderr.out
    #   check for errors in stderr.out, some are OK, e.g.:
    # WARNING: hgwdev does not have /gbdb/ascSuu1/wib/gc5Base.wib
    # WARNING: hgwdev does not have /gbdb/ascSuu1/wib/quality.wib
    # WARNING: hgwdev does not have /gbdb/ascSuu1/bbi/qualityBw/quality.bw
    # WARNING: ascSuu1 does not have seq
    # WARNING: ascSuu1 does not have extFile
    # WARNING: ascSuu1 does not have estOrientInfo
    # WARNING: ascSuu1 does not have mrnaOrientInfo

    #   copy it to hgwbeta
    scp -p ascSuu1.pushQ.sql qateam@hgwbeta:/tmp
    ssh qateam@hgwbeta "./bin/x86_64/hgsql qapushq < /tmp/ascSuu1.pushQ.sql"

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

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