#############################################################################
## 4-Way Multiz (DONE - 2017-04-20 - Hiram)
    ssh hgwdev
    mkdir /hive/data/genomes/galVar1/bed/multiz4way
    cd /hive/data/genomes/galVar1/bed/multiz4way

    # from the 213-way in the source tree, select out the 5 used here:
    /cluster/bin/phast/tree_doctor \
        --prune-all-but hg38,galVar1,mm10,tupChi1 \
        /cluster/home/hiram/kent/src/hg/utils/phyloTrees/213way.nh \
          > galVar1.4way.nh.0
    cat galVar1.4way.nh.0
    # ((hg38:0.143908,(tupChi1:0.120000,galVar1:0.080000):0.054937):0.002000,
    #	mm10:0.356483);

    # using TreeGraph2 tree editor on the Mac, rearrange to get galVar1
    # at the top:

    #	what that looks like:
 ~/kent/src/hg/utils/phyloTrees/asciiTree.pl galVar1.4way.nh | sed -e 's/^/# /;'
# (((galVar1:0.08,
#   tupChi1:0.12):0.054937,
#  hg38:0.143908):0.002,
# mm10:0.356483);

    # extract species list from that .nh file
    sed 's/[a-z][a-z]*_//g; s/:[0-9\.][0-9\.]*//g; s/;//; /^ *$/d' \
        galVar1.4way.nh | xargs echo | sed 's/ //g; s/,/ /g' \
        | sed 's/[()]//g; s/,/ /g' | tr '[ ]' '[\n]' > species.list.txt

    # construct db to name translation list:
    cat species.list.txt | while read DB
do
hgsql -N -e "select name,organism from dbDb where name=\"${DB}\";" hgcentraltest
done | sed -e "s/\t/->/; s/ /_/g;" | sed -e 's/$/;/' | sed -e 's/\./_/g' \
        | sed -e 's/-nosed/_nosed/; s/-eating/_eating/;' > db.to.name.txt

    # construct a common name .nh file:
    /cluster/bin/phast/tree_doctor --rename \
    "`cat db.to.name.txt`" galVar1.4way.nh | sed -e 's/00*)/)/g; s/00*,/,/g' \
       | $HOME/kent/src/hg/utils/phyloTrees/asciiTree.pl /dev/stdin \
         > galVar1.4way.commonNames.nh
    cat galVar1.4way.commonNames.nh | sed -e 's/^/# /;'
# (((Malayan_flying_lemur:0.08,
#   Chinese_tree_shrew:0.12):0.054937,
#  Human:0.143908):0.002,
# Mouse:0.356483);

#	Use this specification in the phyloGif tool:
#	http://genome.ucsc.edu/cgi-bin/phyloGif
#	to obtain a png image for src/hg/htdocs/images/phylo/galVar1_4way.png

    ~/kent/src/hg/utils/phyloTrees/asciiTree.pl galVar1.4way.nh > t.nh
    ~/kent/src/hg/utils/phyloTrees/scientificNames.sh t.nh \
       | $HOME/kent/src/hg/utils/phyloTrees/asciiTree.pl /dev/stdin \
          > galVar1.4way.scientificNames.nh
    rm -f t.nh
    cat galVar1.4way.scientificNames.nh | sed -e 's/^/# /;'
# (((Galeopterus_variegatus:0.08,
#   Tupaia_chinensis:0.12):0.054937,
#  Homo_sapiens:0.143908):0.002,
# Mus_musculus:0.356483);

    /cluster/bin/phast/all_dists galVar1.4way.nh | grep galVar1 \
        | sed -e "s/galVar1.//" | sort -k2n > 4way.distances.txt
    #	Use this output to create the table below
    cat 4way.distances.txt | sed -e 's/^/# /;'
# tupChi1       0.200000
# hg38  0.278845
# mm10  0.493420

    printf '#!/usr/bin/env perl

use strict;
use warnings;

open (FH, "<4way.distances.txt") or
        die "can not read 4way.distances.txt";

my $count = 0;
while (my $line = <FH>) {
    chomp $line;
    my ($D, $dist) = split('"'"'\\s+'"'"', $line);
    my $chain = "chain" . ucfirst($D);
    my $B="/hive/data/genomes/galVar1/bed/lastz.$D/fb.galVar1." .
        $chain . "Link.txt";
    my $chainLinkMeasure =
        `awk '"'"'{print \\$5}'"'"' ${B} 2> /dev/null | sed -e "s/(//; s/)//"`;
    chomp $chainLinkMeasure;
    $chainLinkMeasure = 0.0 if (length($chainLinkMeasure) < 1);
    $chainLinkMeasure =~ s/\\%%//;
    my $swapFile="/hive/data/genomes/${D}/bed/lastz.galVar1/fb.${D}.chainGalVar1Link.txt";
    my $swapMeasure = "N/A";
    if ( -s $swapFile ) {
	$swapMeasure =
	    `awk '"'"'{print \\$5}'"'"' ${swapFile} 2> /dev/null | sed -e "s/(//; s/)//"`;
	chomp $swapMeasure;
	$swapMeasure = 0.0 if (length($swapMeasure) < 1);
	$swapMeasure =~ s/\\%%//;
    }
    my $orgName=
    `hgsql -N -e "select organism from dbDb where name='"'"'$D'"'"';" hgcentraltest`;
    chomp $orgName;
    if (length($orgName) < 1) {
        $orgName="N/A";
    }
    ++$count;
    printf "# %%02d  %%.4f (%%%% %%06.3f) (%%%% %%06.3f) - %%s %%s\\n", $count, $dist,
        $chainLinkMeasure, $swapMeasure, $orgName, $D;
}
close (FH);
' > sizeStats.pl
    chmod +x ./sizeStats.pl
    ./sizeStats.pl

#	If you can fill in all the numbers in this table, you are ready for
#	the multiple alignment procedure

#       featureBits chainLink measures
#               chainLink
#  N distance  on galVar1  on other     other species
# 01  0.2000 (% 53.211) (% 52.252) - Chinese tree shrew tupChi1
# 02  0.2788 (% 64.881) (% 57.036) - Human hg38
# 03  0.4934 (% 35.972) (% 35.618) - Mouse mm10

# None of this concern for distances matters in building the first step, the
# maf files.  The distances will be better calibrated later.

    # create species list and stripped down tree for autoMZ
    sed 's/[a-z][a-z]*_//g; s/:[0-9\.][0-9\.]*//g; s/;//; /^ *$/d' \
	galVar1.4way.nh | xargs echo | sed 's/ //g; s/,/ /g' > tree.nh

    sed 's/[()]//g; s/,/ /g' tree.nh > species.list
    # galVar1 tupChi1 hg38 mm10

    # survey N50 for each
    for db in `cat species.list`
do
n50.pl /hive/data/genomes/$db/chrom.sizes
done
#       reading: /hive/data/genomes/galVar1/chrom.sizes
#       contig count: 179514, total size: 3187660572, one half size: 1593830286
# cumulative    N50 count       contig  contig size
1593691350      3422    NW_007730159v1  245222
1593830286 one half size
1593936539      3423    NW_007729331v1  245189
#       reading: /hive/data/genomes/tupChi1/chrom.sizes
#       contig count: 50750, total size: 2846580235, one half size: 1423290117
# cumulative    N50 count       contig  contig size
1419920836      231     KB321095        3691413
1423290117 one half size
1423590960      232     KB321106        3670124
#       reading: /hive/data/genomes/hg38/chrom.sizes
#       contig count: 455, total size: 3209286105, one half size: 1604643052
# cumulative    N50 count       contig  contig size
1547391171      8       chrX    156040895
1604643052 one half size
1692529807      9       chr8    145138636
#       reading: /hive/data/genomes/mm10/chrom.sizes
#       contig count: 66, total size: 2730871774, one half size: 1365435887
# cumulative    N50 count       contig  contig size
1312176979      8       chr7    145441459
1365435887 one half size
1442871972      9       chr10   130694993

    #	bash shell syntax here ...
    cd /hive/data/genomes/galVar1/bed/multiz4way
    export H=/hive/data/genomes/galVar1/bed
    mkdir mafLinks
    # good assemblies can use syntenic net:
    #  hg38 mm10
    for G in hg38 mm10
    do
      mkdir mafLinks/$G
      echo ln -s ${H}/lastz.$G/axtChain/galVar1.${G}.synNet.maf.gz ./mafLinks/$G
      ln -s ${H}/lastz.$G/axtChain/galVar1.${G}.synNet.maf.gz ./mafLinks/$G
    done

    # other assemblies using recip best net:
    #  tupBel1
    for G in tupChi1
    do
      mkdir mafLinks/$G
      echo ln -s ${H}/lastz.$G/mafRBestNet/galVar1.${G}.rbest.maf.gz ./mafLinks/$G
      ln -s ${H}/lastz.$G/mafRBestNet/galVar1.${G}.rbest.maf.gz ./mafLinks/$G
    done

    # verify the symLinks are good:
    ls -ogrtL mafLinks/*/* | sed -e 's/^/# /; s/-rw-rw-r-- 1//;'
#  1145536271 Apr 26  2016 mafLinks/hg38/galVar1.hg38.synNet.maf.gz
#   663877752 Apr 26  2016 mafLinks/mm10/galVar1.mm10.synNet.maf.gz
#   985551111 Mar 10 09:44 mafLinks/tupChi1/galVar1.tupChi1.rbest.maf.gz

    # split the maf files into a set of hashed named files
    # this hash named split keeps the same chr/contig names in the same
    # named hash file.
    mkdir /hive/data/genomes/galVar1/bed/multiz4way/mafSplit
    cd /hive/data/genomes/galVar1/bed/multiz4way/mafSplit
    time for D in `sed -e "s/galVar1 //" ../species.list`
do
    echo "${D}"
    mkdir $D
    cd $D
    echo "mafSplit -byTarget -useHashedName=8 /dev/null . ../../mafLinks/${D}/*.maf.gz"
    mafSplit -byTarget -useHashedName=8 /dev/null . \
	../../mafLinks/${D}/*.maf.gz
    cd ..
done
    # real    3m42.845s

    # construct a list of all possible maf file names.
    # they do not all exist in each of the species directories
    find . -type f | wc -l
    # 768
    find . -type f | grep ".maf$" | xargs -L 1 basename | sort -u > maf.list
    wc -l maf.list
    # 256 maf.list

    mkdir /hive/data/genomes/galVar1/bed/multiz4way/splitRun
    cd /hive/data/genomes/galVar1/bed/multiz4way/splitRun
    mkdir maf run
    cd run
    mkdir penn
    cp -p /cluster/bin/penn/multiz.2009-01-21_patched/multiz penn
    cp -p /cluster/bin/penn/multiz.2009-01-21_patched/maf_project penn
    cp -p /cluster/bin/penn/multiz.2009-01-21_patched/autoMZ penn

    #	verify the db and pairs settings are correct
    printf '#!/bin/csh -ef
set db = galVar1
set c = $1
set result = $2
set run = `/bin/pwd`
set tmp = /dev/shm/$db/multiz.$c
set pairs = /hive/data/genomes/galVar1/bed/multiz4way/mafSplit
/bin/rm -fr $tmp
/bin/mkdir -p $tmp
/bin/cp -p ../../tree.nh ../../species.list $tmp
pushd $tmp > /dev/null
foreach s (`/bin/sed -e "s/$db //" species.list`)
    set in = $pairs/$s/$c
    set out = $db.$s.sing.maf
    if (-e $in.gz) then
        /bin/zcat $in.gz > $out
        if (! -s $out) then
            echo "##maf version=1 scoring=autoMZ" > $out
        endif
    else if (-e $in) then
        /bin/ln -s $in $out
    else
        echo "##maf version=1 scoring=autoMZ" > $out
    endif
end
set path = ($run/penn $path); rehash
$run/penn/autoMZ + T=$tmp E=$db "`cat tree.nh`" $db.*.sing.maf $c \
        > /dev/null
popd > /dev/null
/bin/rm -f $result
/bin/cp -p $tmp/$c $result
/bin/rm -fr $tmp
' > autoMultiz.csh

    chmod +x autoMultiz.csh

    printf '#LOOP
./autoMultiz.csh $(file1) {check out line+ /hive/data/genomes/galVar1/bed/multiz4way/splitRun/maf/$(root1).maf}
#ENDLOOP
' > template

# << happy emacs

    ln -s ../../mafSplit/maf.list maf.list
    ssh ku
    cd /hive/data/genomes/galVar1/bed/multiz4way/splitRun/run
    gensub2 maf.list single template jobList
    para create jobList
    para try ... check ... push ... etc...
# Completed: 256 of 256 jobs
# CPU time in finished jobs:      34427s     573.79m     9.56h    0.40d  0.001 y
# IO & Wait Time:                   845s      14.08m     0.23h    0.01d  0.000 y
# Average job time:                 138s       2.30m     0.04h    0.00d
# Longest finished job:             224s       3.73m     0.06h    0.00d
# Submission to last job:           514s       8.57m     0.14h    0.01d

    # combine into one file  (the 1>&2 redirect sends the echo to stderr)
    cd /hive/data/genomes/galVar1/bed/multiz4way
    head -1 splitRun/maf/020.maf > multiz4way.maf
    time for F in splitRun/maf/*.maf
do
    echo "${F}" 1>&2
    egrep -v "^#" ${F}
done >> multiz4way.maf
    # real    1m0.539s

    tail -1 splitRun/maf/020.maf >> multiz4way.maf
# -rw-rw-r-- 1 7936538389 Apr 20 12:26 multiz4way.maf

    # Load into database
    ssh hgwdev
    cd /hive/data/genomes/galVar1/bed/multiz4way
    mkdir /gbdb/galVar1/multiz4way
    ln -s `pwd`/multiz4way.maf /gbdb/galVar1/multiz4way
    cd /dev/shm
    time hgLoadMaf galVar1 multiz4way
# Loaded 7945505 mafs in 1 files from /gbdb/galVar1/multiz4way
# real    2m9.253s

    time hgLoadMafSummary -verbose=2 -minSize=30000 \
	-mergeGap=1500 -maxSize=200000 galVar1 multiz4waySummary \
	/gbdb/galVar1/multiz4way/multiz4way.maf
# Created 44817 summary blocks from 1147493 components and 7945505 mafs from /gbdb/galVar1/multiz4way/multiz4way.maf
# real    1m28.388s

# -rw-rw-r-- 1 427725497 Apr 20 13:20 multiz4way.tab
# -rw-rw-r-- 1   2250192 Apr 20 13:26 multiz4waySummary.tab

    wc -l multiz4way*.tab
#   7945505 multiz4way.tab
#     44817 multiz4waySummary.tab

    rm multiz4way*.tab

##############################################################################
# GAP ANNOTATE MULTIZ4WAY MAF AND LOAD TABLES (DONE - 2017-04-20 - Hiram)
    # mafAddIRows has to be run on single chromosome maf files, it does not
    #	function correctly when more than one reference sequence
    #	are in a single file.  Need to split of the maf file into individual
    #   maf files
    mkdir -p /hive/data/genomes/galVar1/bed/multiz4way/anno/mafSplit
    cd /hive/data/genomes/galVar1/bed/multiz4way/anno/mafSplit

    time mafSplit -outDirDepth=2 -byTarget -useFullSequenceName \
        /dev/null . ../../multiz4way.maf
    #   real    2m59.091s

    find . -type f | wc -l
    #   81881

    # check for N.bed files everywhere:
    cd /hive/data/genomes/galVar1/bed/multiz4way/anno
    for DB in `cat ../species.list`
do
    if [ ! -s /hive/data/genomes/${DB}/${DB}.N.bed ]; then
        echo "MISS: ${DB}"
#         cd /hive/data/genomes/${DB}
#         twoBitInfo -nBed ${DB}.2bit ${DB}.N.bed
    else
        echo "  OK: ${DB}"
    fi
done

    cd /hive/data/genomes/galVar1/bed/multiz4way/anno
    for DB in `cat ../species.list`
do
    echo "${DB} "
    ln -s  /hive/data/genomes/${DB}/${DB}.N.bed ${DB}.bed
    echo ${DB}.bed  >> nBeds
    ln -s  /hive/data/genomes/${DB}/chrom.sizes ${DB}.len
    echo ${DB}.len  >> sizes
done
    # make sure they all are successful symLinks:
    ls -ogrtL

    screen -S gapAnno      # use a screen to control this longish job
    ssh ku
    cd /hive/data/genomes/galVar1/bed/multiz4way/anno
    mkdir result
    find ./mafSplit -type d | sed -e 's#./mafSplit/##' | while read D
do
    echo mkdir -p result/${D}
    mkdir -p result/${D}
done
    printf '#LOOP
mafAddIRows -nBeds=nBeds mafSplit/$(path1) /hive/data/genomes/galVar1/galVar1.2bit {check out exists+ result/$(path1)}
#ENDLOOP
' > template

    find ./mafSplit -type f | sed -e 's#^./mafSplit/##' > maf.list
    gensub2 maf.list single template jobList
    # limit jobs on a node with the ram=32g requirement because they go fast
    para -maxJob=50 create jobList
    para try ... check ... push ...
# Completed: 81881 of 81881 jobs
# CPU time in finished jobs:      25237s     420.61m     7.01h    0.29d  0.001 y
# IO & Wait Time:                207724s    3462.07m    57.70h    2.40d  0.007 y
# Average job time:                   3s       0.05m     0.00h    0.00d
# Longest finished job:               6s       0.10m     0.00h    0.00d
# Submission to last job:          2970s      49.50m     0.82h    0.03d

    # verify all result files have some content, look for 0 size files:
    find ./result -type f -size 0
    # should see none
    # or in this manner:
    find ./result -type f | xargs ls -og | sort -k3nr | tail

    # combine into one file  (the 1>&2 redirect sends the echo to stderr)
    head -q -n 1 result/1/3/NW_007891373v1.maf > galVar1.4way.maf
    time find ./result -type f | while read F
do
    echo "${F}" 1>&2
    grep -h -v "^#" ${F}
done >> galVar1.4way.maf
    # real    16m28.349s

    #	these maf files do not have the end marker, this does nothing:
    #	tail -q -n 1 result/4/0/NW_007804317v1.maf >> galVar1.4way.maf
    # How about an official end marker:
    echo "##eof maf" >> galVar1.4way.maf
    ls -og
# -rw-rw-r--  1 10018032961 Apr 20 15:22 galVar1.4way.maf

    du -hsc galVar1.4way.maf
    # 9.4G     galVar1.4way.maf

    # construct symlinks to get the individual maf files into gbdb:
    rm /gbdb/galVar1/multiz4way/multiz4way.maf   # remove previous results
    ln -s `pwd`/galVar1.4way.maf /gbdb/galVar1/multiz4way/multiz4way.maf

    # Load into database
    cd /dev/shm
    time hgLoadMaf -pathPrefix=/gbdb/galVar1/multiz4way galVar1 multiz4way
    #  Loaded 9225719 mafs in 1 files from /gbdb/galVar1/multiz4way
    #  real    2m53.105s

    time hgLoadMafSummary -verbose=2 -minSize=30000 \
	-mergeGap=1500 -maxSize=200000 galVar1 multiz4waySummary \
        /gbdb/galVar1/multiz4way/multiz4way.maf
    # Created 44817 summary blocks from 1147493 components and 9225719 mafs from /gbdb/galVar1/multiz4way/multiz4way.maf
    # real    1m54.667s

    # -rw-rw-r-- 1 496471344 Apr 20 15:25 multiz4way.tab
    # -rw-rw-r-- 1   2339826 Apr 20 15:28 multiz4waySummary.tab

    rm multiz4way*.tab

######################################################################
# MULTIZ4WAY MAF FRAMES (DONE - 2017-04-20 - Hiram)
    ssh hgwdev
    mkdir /hive/data/genomes/galVar1/bed/multiz4way/frames
    cd /hive/data/genomes/galVar1/bed/multiz4way/frames
#   survey all the genomes to find out what kinds of gene tracks they have
    printf '#!/bin/csh -fe
foreach db (`cat ../species.list`)
    printf "# ${db}: "
    set tables = `hgsql $db -N -e "show tables" | egrep "Gene|ncbiRefSeq"`
    foreach table ($tables)
        if ($table == "ensGene" || $table == "refGene" || \
           $table == "ncbiRefSeq" || $table == "mgcGenes" || \
           $table == "knownGene" || $table == "xenoRefGene" ) then
           set count = `hgsql $db -N -e "select count(*) from $table"`
            echo -n "${table}: ${count}, "
        endif
    end
    set orgName = `hgsql hgcentraltest -N -e \
            "select scientificName from dbDb where name='"'"'$db'"'"'"`
    set orgId = `hgsql $db -N -e \
            "select id from organism where name='"'"'$orgName'"'"'"`
    if ($orgId == "") then
        echo "Mrnas: 0"
    else
        set count = `hgsql $db -N -e "select count(*) from gbCdnaInfo where organism=$orgId"`
        echo "Mrnas: ${count}"
    endif
end
' > showGenes.csh
    # << happy emacs
    chmod +x ./showGenes.csh
    time ./showGenes.csh
# galVar1: ncbiRefSeq: 41547, xenoRefGene: 499145, Mrnas: 0
# tupChi1: refGene: 206, xenoRefGene: 343637, Mrnas: 50709
# hg38: ensGene: 208239, knownGene: 197782, mgcGenes: 35305, ncbiRefSeq: 159322, refGene: 69527, xenoRefGene: 184852, Mrnas: 11481766
# mm10: ensGene: 103734, knownGene: 63759, mgcGenes: 26777, ncbiRefSeq: 107894, refGene: 36869, xenoRefGene: 179145, Mrnas: 5367574

#  real    0m52.579s

    # from that summary, use these gene sets:
    # knownGene - hg38 mm10
    # ncbiRefSeq - galVar1
    # xenoRefGene - tupChi1
 
    mkdir genes
    #   1. knownGene: hg38 mm10
    for DB in hg38 mm10
do
    hgsql -N -e "select name,chrom,strand,txStart,txEnd,cdsStart,cdsEnd,exonCount,exonStarts,exonEnds from knownGene" ${DB} \
      | genePredSingleCover stdin stdout | gzip -2c \
        > genes/${DB}.gp.gz
    printf "# ${DB}: "
    genePredCheck -db=${DB} genes/${DB}.gp.gz
done
# hg38: checked: 21375 failed: 0
# mm10: checked: 21100 failed: 0

    #   2. xenoRefGene: tupChi1
    for DB in tupChi1
do
hgsql -N -e "select name,chrom,strand,txStart,txEnd,cdsStart,cdsEnd,exonCount,exonStarts,exonEnds
from xenoRefGene" ${DB} \
      | genePredSingleCover stdin stdout | gzip -2c \
        > /dev/shm/${DB}.tmp.gz
    mv /dev/shm/${DB}.tmp.gz genes/$DB.gp.gz
    printf "# ${DB}: "
    genePredCheck -db=${DB} genes/${DB}.gp.gz
done
# tupChi1: checked: 30481 failed: 0

    #   3. ncbiRefSeq for galVar1
    for DB in galVar1
do
hgsql -N -e "select * from ncbiRefSeq" ${DB} | cut -f2- \
      | genePredSingleCover stdin stdout | gzip -2c \
        > /dev/shm/${DB}.tmp.gz
    mv /dev/shm/${DB}.tmp.gz genes/$DB.gp.gz
    echo -n "# ${DB}: "
    genePredCheck -db=${DB} genes/${DB}.gp.gz
done
# galVar1: checked: 23389 failed: 0


    # verify counts for genes are reasonable:
    for T in genes/*.gz
do
    echo -n "# $T: "
    zcat $T | cut -f1 | sort | uniq -c | wc -l
done
# genes/galVar1.gp.gz: 23054
# genes/hg38.gp.gz: 21375
# genes/mm10.gp.gz: 21100
# genes/tupChi1.gp.gz: 25028

    time (cat ../anno/galVar1.4way.maf \
	| genePredToMafFrames galVar1 stdin stdout \
          `cat ../species.list.txt | xargs echo \
            | sed -e "s#\([a-zA-Z0-9]*\)#\1 genes/\1.gp.gz#g;"` \
		| gzip > multiz4wayFrames.bed.gz)
    # real    1m59.500s

    # verify there are frames on everything, should be 5 species:
    zcat multiz4wayFrames.bed.gz | awk '{print $4}' | sort | uniq -c \
       | sed -e 's/^/# /;'
#  192705 galVar1
#  222812 hg38
#  218601 mm10
#  230893 tupChi1

    #   load the resulting file
    ssh hgwdev
    cd /hive/data/genomes/galVar1/bed/multiz4way/frames
    time hgLoadMafFrames galVar1 multiz4wayFrames multiz4wayFrames.bed.gz
    #   real    0m10.869s

    time featureBits -countGaps galVar1 multiz4wayFrames
    # 38399505 bases of 3187660572 (1.205%) in intersection
    #  real    0m52.029s

    #   enable the trackDb entries:
# frames multiz4wayFrames
# irows on
    #   appears to work OK

#########################################################################
# Phylogenetic tree from 5-way (DONE - 2017-04-20 - Hiram)
    mkdir /hive/data/genomes/galVar1/bed/multiz4way/4d
    cd /hive/data/genomes/galVar1/bed/multiz4way/4d

    # using the ncbiRefSeq
    hgsql -N -e "select * from ncbiRefSeq;" galVar1 \
      | cut -f2- | genePredSingleCover stdin stdout > /dev/shm/galVar1.tmp.gp
    mv /dev/shm/galVar1.tmp.gp galVar1.ncbiRefSeq.gp
    genePredCheck -db=galVar1 galVar1.ncbiRefSeq.gp
    # checked: 23389 failed: 0

    genePredSingleCover galVar1.ncbiRefSeq.gp stdout \
       | sort > galVar1.ncbiRefSeqNR.gp
    genePredCheck -db=galVar1 galVar1.ncbiRefSeqNR.gp
    # checked: 23389 failed: 0

    # the annotated maf is:
    og ../anno/galVar1.4way.maf
# -rw-rw-r-- 1 10018032961 Apr 20 15:22 ../anno/galVar1.4way.maf

    mkdir annoSplit
    cd annoSplit
    time mafSplit -verbose=2 -outDirDepth=2 -byTarget -useFullSequenceName \
	/dev/null . ../../anno/galVar1.4way.maf
    # real    3m42.384s

    find . -type f | wc -l
    #   81881
    ssh ku
    mkdir /hive/data/genomes/galVar1/bed/multiz4way/4d/run
    cd /hive/data/genomes/galVar1/bed/multiz4way/4d/run
    mkdir ../mfa

    # newer versions of msa_view have a slightly different operation
    # the sed of the gp file inserts the reference species in the chr name
    printf '#!/bin/csh -fe
set PHASTBIN = /cluster/bin/phast.build/cornellCVS/phast.2010-12-30/bin
set GP = galVar1.ncbiRefSeqNR.gp
set r = "/hive/data/genomes/galVar1/bed/multiz4way"
set c = $1:r
set infile = $r/4d/annoSplit/$2
set outDir = $r/4d/mfa/$3:h
set outfile = $r/4d/mfa/$3
/bin/mkdir -p $outDir
cd /dev/shm
/bin/awk -v C=$c '"'"'$2 == C {print}'"'"' $r/4d/$GP | sed -e "s/\\t$c\\t/\\tgalVar1.$c\\t/" > $c.gp
set NL=`wc -l $c.gp| gawk '"'"'{print $1}'"'"'`
echo $NL
if ("$NL" != "0") then
    $PHASTBIN/msa_view --4d --features $c.gp -i MAF $infile -o SS > $c.ss
    $PHASTBIN/msa_view -i SS --tuple-size 1 $c.ss > $outfile
else
    echo "" > $outfile
endif
/bin/rm -f /dev/shm/$c.gp /dev/shm/$c.ss
' > 4d.csh

    chmod +x 4d.csh

    find ../annoSplit -type f | sed -e "s#../annoSplit/##" > maf.list
    wc -l maf.list
# 81881 maf.list

    printf '#LOOP
4d.csh $(file1) $(path1) {check out line+ ../mfa/$(dir1)/$(dir2)$(root1).mfa}
#ENDLOOP
' > template

    gensub2 maf.list single template jobList
    para -maxJob=200 create jobList
    para try ... check
    para time
# Completed: 81602 of 81881 jobs
# Crashed: 64 jobs
# Other count: 215 jobs
# CPU time in finished jobs:       2681s      44.68m     0.74h    0.03d  0.000 y
# IO & Wait Time:                207874s    3464.57m    57.74h    2.41d  0.007 y
# Average job time:                   3s       0.04m     0.00h    0.00d
# Longest finished job:               6s       0.10m     0.00h    0.00d
# Submission to last job:          1596s      26.60m     0.44h    0.02d

    # Not all results have contents, or finish successfully, that is OK
    # it is because not all contigs have genes, only gene sequences are measured

    # combine mfa files
    ssh hgwdev
    cd /hive/data/genomes/galVar1/bed/multiz4way/4d
    # remove the broken empty files, size 0 and size 1:
    find ./mfa -type f -size 0 | xargs rm -f
    # almost always, this does not work, don't know why
    find ./mfa -type f -size 1 | xargs rm -f
    # when it doesn't, use this empty list procedure
    find ./mfa -type f | xargs ls -og | awk '$3 < 2' | awk '{print $NF}' \
        > empty.list
    cat empty.list | xargs rm -f
    # see what is left:
    ls -ogrt mfa/*/*/*.mfa | sort -k3nr | wc
    #     8111   56777  478539

    # want comma-less species.list
    time /cluster/bin/phast.build/cornellCVS/phast.2010-12-30/bin/msa_view \
	--aggregate "`cat ../species.list`" mfa/*/*/*.mfa | sed s/"> "/">"/ \
	    > 4d.all.mfa
    # real    1m0.044s
# -rw-rw-r--  1 15349974 Apr 20 16:30 4d.all.mfa

    # check they are all in there:
    grep "^>" 4d.all.mfa | wc -l
    # 4
    grep "^>" 4d.all.mfa | sed -e 's/^/# /;'
# >galVar1
# >tupChi1
# >hg38
# >mm10

    sed 's/[a-z][a-z]*_//g; s/:[0-9\.][0-9\.]*//g; s/;//; /^ *$/d' \
	../galVar1.4way.nh | xargs echo | sed -e 's/ //g' > tree_commas.nh
    # tree_commas.nh looks like:
    # (((galVar1,tupChi1),hg38),mm10)

    # use phyloFit to create tree model (output is phyloFit.mod)
    time /cluster/bin/phast.build/cornellCVS/phast.2010-12-30/bin/phyloFit \
	    --EM --precision MED --msa-format FASTA --subst-mod REV \
		--tree tree_commas.nh 4d.all.mfa
    #  real    0m0.790s

    mv phyloFit.mod all.mod

    grep TREE all.mod
# TREE:
# (((galVar1:0.102671,tupChi1:0.18244):0.012114,hg38:0.111278):0.163537,
#	mm10:0.163537);

    # compare these calculated lengths to the tree extracted from 213way:
    grep TREE all.mod | sed -e 's/TREE: //' \
       | /cluster/bin/phast/all_dists /dev/stdin | grep galVar1 \
          | sed -e "s/galVar1.//;"  | sort > new.dists
    /cluster/bin/phast/all_dists ../galVar1.4way.nh | grep galVar1 \
        | sed -e "s/galVar1.//;" | sort > old.dists
     # printing out the 'new', the 'old' the 'difference' and percent difference
    join new.dists old.dists | awk '{
  printf "#\t%s\t%8.6f\t%8.6f\t%8.6f\t%8.6f\n", $1, $2, $3, $2-$3, 100*($2-$3)/$3 }' \
      | sort -k3n
#       hg38    0.226063        0.278845        -0.052782       -18.928796
#       tupChi1 0.285111        0.200000        0.085111        42.555500
#       mm10    0.441859        0.493420        -0.051561       -10.449718


     # compare this tree with the one generated from the cavPor3 5-way
    grep TREE all.mod | sed -e 's/TREE: //' \
     | /cluster/bin/phast/all_dists /dev/stdin | grep cavPor3 \
        | sed -e "s/cavPor3.//" | sort > galVar1.cavPor3.dists
    grep TREE /hive/data/genomes/cavPor3/bed/multiz4way/4d/all.mod \
       | sed -e 's/TREE: //' \
       | /cluster/bin/phast/all_dists /dev/stdin | grep cavPor3 \
          | sed -e "s/cavPor3.//;"  | sort > cavPor3.cavPor3.dists
    # appears to be systematically shorter branch lengths with this galVar1
    # reference, all by a similar percentage:
    # table headings:
#       species  galVar1        cavPor3        galVar1-cavPor3     percent
#                dist est.     dist est.         difference      difference
    join galVar1.cavPor3.dists cavPor3.cavPor3.dists | awk '{
  printf "#\t%s\t%8.6f\t%8.6f\t%8.6f\t%8.6f\n", $1, $2, $3, $2-$3, 100*($2-$3)/$3 }' \
      | sort -k3n
#       galVar1 0.370042        0.383228        -0.013186       -3.440772
#       hg38    0.376549        0.390633        -0.014084       -3.605430
#       tupBel1 0.448642        0.464419        -0.015777       -3.397148
#       mm10    0.490751        0.509725        -0.018974       -3.722399

#########################################################################
# phastCons 5-way (DONE - 2017-04-21 - Hiram)
    # split 4way mafs into 10M chunks and generate sufficient statistics
    # files for # phastCons
    ssh ku
    mkdir -p /hive/data/genomes/galVar1/bed/multiz4way/cons/SS
    cd /hive/data/genomes/galVar1/bed/multiz4way/cons/SS
    mkdir result done

    printf '#!/bin/csh -ef
set d = $1
set c = $2
set doneDir = done/$d
set MAF = /hive/data/genomes/galVar1/bed/multiz4way/anno/result/$d/$c.maf
set WINDOWS = /hive/data/genomes/galVar1/bed/multiz4way/cons/SS/result/$d/$c
set WC = `cat $MAF | wc -l`
set NL = `grep "^#" $MAF | wc -l`
if ( -s $3 ) then
    exit 0
endif
if ( -s $3.running ) then
    exit 0
endif

/bin/mkdir -p $doneDir
/bin/date >> $3.running

/bin/rm -fr $WINDOWS
/bin/mkdir -p $WINDOWS
pushd $WINDOWS > /dev/null
if ( $WC != $NL ) then
/cluster/bin/phast.build/cornellCVS/phast.2010-12-30/bin/msa_split \\
    $MAF -i MAF -o SS -r $WINDOWS/$c -w 10000000,0 -I 1000 -B 5000
endif
popd > /dev/null
/bin/date >> $3
/bin/rm -f $3.running
' > mkSS.csh

    chmod +x mkSS.csh

    printf '#LOOP
mkSS.csh $(dir1) $(root1) {check out line+ done/$(dir1)/$(root1)}
#ENDLOOP
' > template

    find ../../anno/result -type f | sed -e "s#../../anno/result/##" > maf.list
    wc -l maf.list
# 81881 maf.list

    ssh ku
    cd /hive/data/genomes/galVar1/bed/multiz4way/cons/SS

    gensub2 maf.list single template jobList
    # beware overwhelming the cluster with these quick high I/O jobs
    para create jobList
    para try ... check ... etc
    para -maxJob=200 push
# Completed: 81881 of 81881 jobs
# CPU time in finished jobs:       3080s      51.33m     0.86h    0.04d  0.000 y
# IO & Wait Time:                274569s    4576.16m    76.27h    3.18d  0.009 y
# Average job time:                   3s       0.06m     0.00h    0.00d
# Longest finished job:               9s       0.15m     0.00h    0.00d
# Submission to last job:          1525s      25.42m     0.42h    0.02d


    find ./result -type f | wc -l
    # 26294

    # Run phastCons
    #	This job is I/O intensive in its output files, beware where this
    #	takes place or do not run too many at once.
    ssh ku
    mkdir -p /hive/data/genomes/galVar1/bed/multiz4way/cons/run.cons
    cd /hive/data/genomes/galVar1/bed/multiz4way/cons/run.cons

    #	This is setup for multiple runs based on subsets, but only running
    #   the 'all' subset here.
    #   It triggers off of the current working directory
    #	$cwd:t which is the "grp" in this script.  Running:
    #	all and vertebrates

    printf '#!/bin/csh -fe
set PHASTBIN = /cluster/bin/phast.build/cornellCVS/phast.2010-12-30/bin
set c = $1
set d = $2
set f = $3
set len = $4
set cov = $5
set rho = $6
set grp = $cwd:t
set cons = /hive/data/genomes/galVar1/bed/multiz4way/cons
set tmp = $cons/tmp/${d}_${c}
mkdir -p $tmp
set ssSrc = $cons/SS/result
set useGrp = "$grp.mod"
if (-s $cons/$grp/$grp.non-inf) then
  ln -s $cons/$grp/$grp.mod $tmp
  ln -s $cons/$grp/$grp.non-inf $tmp
  ln -s $ssSrc/$d/$f $tmp
else
  ln -s $ssSrc/$d/$f $tmp
  ln -s $cons/$grp/$grp.mod $tmp
endif
pushd $tmp > /dev/null
if (-s $grp.non-inf) then
  $PHASTBIN/phastCons $f $useGrp \
    --rho $rho --expected-length $len --target-coverage $cov --quiet \\
    --not-informative `cat $grp.non-inf` \\
    --seqname $c --idpref $c --most-conserved $c.bed --score > $c.pp
else
  $PHASTBIN/phastCons $f $useGrp \\
    --rho $rho --expected-length $len --target-coverage $cov --quiet \\
    --seqname $c --idpref $c --most-conserved $c.bed --score > $c.pp
endif
popd > /dev/null
mkdir -p pp/$d bed/$d
sleep 4
touch pp/$d bed/$d
rm -f pp/$d/$c.pp
rm -f bed/$d/$c.bed
mv $tmp/$c.pp pp/$d
mv $tmp/$c.bed bed/$d
rm -fr $tmp
rmdir --ignore-fail-on-non-empty $cons/tmp/$d:h
' > doPhast.csh

    chmod +x doPhast.csh

    #	this template will serve for all runs
    #	root1 == chrom name, file1 == ss file name without .ss suffix
    printf '#LOOP
../run.cons/doPhast.csh $(root1) $(dir1) $(file1) 45 0.3 0.3 {check out line+ pp/$(dir1)/$(root1).pp}
#ENDLOOP
' > template

    find ../SS/result -type f | sed -e "s#../SS/result/##" > ss.list
    wc -l ss.list
    #	26294 ss.list

    # Create parasol batch and run it
    # run for all species
    cd /hive/data/genomes/galVar1/bed/multiz4way/cons
    mkdir -p all
    cd all
    #	Using the .mod tree
    cp -p ../../4d/all.mod ./all.mod

    gensub2 ../run.cons/ss.list single ../run.cons/template jobList
    para -maxJob=200 create jobList
    para try ... check ...
    para push
# Completed: 26294 of 26294 jobs
# CPU time in finished jobs:       6934s     115.57m     1.93h    0.08d  0.000 y
# IO & Wait Time:                178641s    2977.34m    49.62h    2.07d  0.006 y
# Average job time:                   7s       0.12m     0.00h    0.00d
# Longest finished job:              14s       0.23m     0.00h    0.00d
# Submission to last job:          3070s      51.17m     0.85h    0.04d

    # create Most Conserved track
    cd /hive/data/genomes/galVar1/bed/multiz4way/cons/all
    time cut -f1 ../../../../chrom.sizes | while read C
do
    ls -d bed/?/?/${C} 2> /dev/null | while read D
    do
        echo ${D}/${C}*.bed 1>&2
        cat ${D}/${C}*.bed
    done | sort -k1,1 -k2,2n \
    | awk '{printf "%s\t%d\t%d\tlod=%d\t%s\n", "'${C}'", $2, $3, $5, $5;}'
done > tmpMostConserved.bed
    # real    25m32.069s

# -rw-rw-r--  1 30417050 Apr 20 21:43 tmpMostConserved.bed

    time /cluster/bin/scripts/lodToBedScore tmpMostConserved.bed \
         > mostConserved.bed
    # real    0m6.665s
    # -rw-rw-r--  1 31147994 Apr 20 21:59 mostConserved.bed


    # load into database
    ssh hgwdev
    cd /hive/data/genomes/galVar1/bed/multiz4way/cons/all
    time hgLoadBed galVar1 phastConsElements4way mostConserved.bed
    # Read 793456 elements of size 5 from mostConserved.bed
    # real    0m7.744s

    # on human we often try for 5% overall cov, and 70% CDS cov
    # most bets are off here for that goal, these alignments are too few
    #	and too far between
    #	--rho 0.3 --expected-length 45 --target-coverage 0.3
    time featureBits galVar1 -enrichment ncbiRefSeq:cds phastConsElements4way
# ncbiRefSeq:cds 1.217%, phastConsElements4way 4.014%, both 0.821%,
#    cover 67.47%, enrich 16.81x
# real    1m41.299s

    # Create merged posterier probability file and wiggle track data files
    cd /hive/data/genomes/galVar1/bed/multiz4way/cons/all
    mkdir downloads

    # the third sed fixes the chrom names, removing the partition extensions
    time (find ./pp -type f | sed -e "s#^./##; s#\.# d #g; s#-# m #;" \
	| sort -k1,1 -k3,3n | sed -e "s# d #.#g; s# m #-#g;" | xargs cat \
	| sed -e 's/\.[0-9][0-9]*-[0-9][0-9]* start/ start/' \
        | gzip -c > downloads/phastCons4way.wigFix.gz)
    #   real    27m11.145s

# -rw-rw-r-- 1 2272116515 Apr 20 22:34 phastCons4way.wigFix.gz

    # check integrity of data with wigToBigWig
    time (zcat downloads/phastCons4way.wigFix.gz \
	| wigToBigWig -verbose=2 stdin /hive/data/genomes/galVar1/chrom.sizes \
	    phastCons4way.bw) > bigWig.log 2>&1
    egrep "real|VmPeak" bigWig.log
    # pid=79741: VmPeak:    20741124 kB
    # real    28m12.795s

    bigWigInfo phastCons4way.bw | sed -e 's/^/# /;'
# version: 4
# isCompressed: yes
# isSwapped: 0
# primaryDataSize: 3,494,009,543
# primaryIndexSize: 84,462,776
# zoomLevels: 10
# chromCount: 26294
# basesCovered: 1,893,718,304
# mean: 0.126530
# min: 0.000000
# max: 1.000000
# std: 0.239909

    #	encode those files into wiggle data
    time (zcat downloads/phastCons4way.wigFix.gz \
	| wigEncode stdin phastCons4way.wig phastCons4way.wib)
    # Converted stdin, upper limit 1.00, lower limit 0.00
    #  real    10m13.030s


    du -hsc *.wi?
    #  1.8G    phastCons4way.wib
    #  283M    phastCons4way.wig

    # Load gbdb and database with wiggle.
    ln -s `pwd`/phastCons4way.wib /gbdb/galVar1/multiz4way/phastCons4way.wib
    time hgLoadWiggle -pathPrefix=/gbdb/galVar1/multiz4way \
	galVar1 phastCons4way phastCons4way.wig
    #   real    0m30.859s

    # use to set trackDb.ra entries for wiggle min and max
    # and verify table is loaded correctly

    wigTableStats.sh galVar1 phastCons4way
# db.table             min max mean       count sumData
# galVar1.phastCons4way   0 1 0.12653 1893718304 2.39611e+08
#     stdDev  viewLimits
#    0.239909 viewLimits=0:1

    #  Create histogram to get an overview of all the data
    time hgWiggle -doHistogram -db=galVar1 \
	-hBinSize=0.001 -hBinCount=1000 -hMinVal=0.0 -verbose=2 \
	    phastCons4way > histogram.data 2>&1
    #	real    3m43.665s

    #	create plot of histogram:

    printf 'set terminal png small x000000 xffffff xc000ff x66ff66 xffff00 x00ffff font \
"/usr/share/fonts/default/Type1/n022004l.pfb"
set size 1.4, 0.8
set key left box
set grid noxtics
set grid ytics
set title " Malayan flying lemur galVar1 Histogram phastCons4way track"
set xlabel " phastCons4way score"
set ylabel " Relative Frequency"
set y2label " Cumulative Relative Frequency (CRF)"
set y2range [0:1]
set y2tics
set yrange [0:0.02]

plot "histogram.data" using 2:5 title " RelFreq" with impulses, \\
        "histogram.data" using 2:7 axes x1y2 title " CRF" with lines
' | gnuplot > histo.png

    display histo.png &

#########################################################################
# phyloP for 5-way (DONE - 2017-04-21 - Hiram)
    # run phyloP with score=LRT
    ssh ku
    mkdir /cluster/data/galVar1/bed/multiz4way/consPhyloP
    cd /cluster/data/galVar1/bed/multiz4way/consPhyloP

    mkdir run.phyloP
    cd run.phyloP
    # Adjust model file base composition background and rate matrix to be
    # representative of the chromosomes in play
    grep BACKGROUND ../../4d/all.mod | awk '{printf "%0.3f\n", $3 + $4}'
    #	0.564
    /cluster/bin/phast.build/cornellCVS/phast.2010-12-30/bin/modFreqs \
	../../4d/all.mod 0.564 > all.mod
    # verify, the BACKGROUND should now be paired up:
    grep BACK all.mod
    #   BACKGROUND: 0.218000 0.282000 0.282000 0.218000 

    printf '#!/bin/csh -fe
set PHASTBIN = /cluster/bin/phast.build/cornellCVS/phast.2010-12-30/bin
set f = $1
set d = $f:h
set file1 = $f:t
set out = $2
set cName = $f:t:r
set grp = $cwd:t
set cons = /hive/data/genomes/galVar1/bed/multiz4way/consPhyloP
set tmp = $cons/tmp/$grp/$f
/bin/rm -fr $tmp
/bin/mkdir -p $tmp
set ssSrc = "/hive/data/genomes/galVar1/bed/multiz4way/cons/SS/result/$f"
set useGrp = "$grp.mod"
/bin/ln -s $cons/run.phyloP/$grp.mod $tmp
pushd $tmp > /dev/null
$PHASTBIN/phyloP --method LRT --mode CONACC --wig-scores --chrom $cName \\
    -i SS $useGrp $ssSrc.ss > $file1.wigFix
popd > /dev/null
/bin/mkdir -p $out:h
sleep 4
/bin/touch $out:h
/bin/mv $tmp/$file1.wigFix $out
/bin/rm -fr $tmp
/bin/rmdir --ignore-fail-on-non-empty $cons/tmp/$grp/$d
/bin/rmdir --ignore-fail-on-non-empty $cons/tmp/$grp/$d:h
/bin/rmdir --ignore-fail-on-non-empty $cons/tmp/$grp
/bin/rmdir --ignore-fail-on-non-empty $cons/tmp
' > doPhyloP.csh

    chmod +x doPhyloP.csh

    # Create list of chunks
    find ../../cons/SS/result -type f | grep ".ss$" \
	| sed -e "s/.ss$//; s#^../../cons/SS/result/##" > ss.list
    # make sure the list looks good
    wc -l ss.list
    #	26294 ss.list

    # Create template file
    #	file1 == $chr/$chunk/file name without .ss suffix
    printf '#LOOP
../run.phyloP/doPhyloP.csh $(path1) {check out line+ wigFix/$(dir1)/$(file1).wigFix}
#ENDLOOP
' > template

    ######################   Running all species  #######################
    # setup run for all species
    mkdir /hive/data/genomes/galVar1/bed/multiz4way/consPhyloP/all
    cd /hive/data/genomes/galVar1/bed/multiz4way/consPhyloP/all
    rm -fr wigFix
    mkdir wigFix

    gensub2 ../run.phyloP/ss.list single ../run.phyloP/template jobList
    #	beware overwhelming the cluster with these fast running high I/O jobs
    para create jobList
    para try ... check ... push ... etc ...
    para -maxJob=53 push
    para time > run.time
# Completed: 26294 of 26294 jobs
# CPU time in finished jobs:       3456s      57.61m     0.96h    0.04d  0.000 y
# IO & Wait Time:                294665s    4911.08m    81.85h    3.41d  0.009 y
# Average job time:                  11s       0.19m     0.00h    0.00d
# Longest finished job:              23s       0.38m     0.01h    0.00d
# Submission to last job:          5010s      83.50m     1.39h    0.06d

    mkdir downloads

    time (find ./wigFix -type f | sed -e "s#^./##; s#\.# d #g; s#-# m #;" \
	| sort -k1,1 -k3,3n | sed -e "s# d #.#g; s# m #-#g;" | xargs cat \
	| gzip -c > downloads/phyloP4way.wigFix.gz)
    #   real    26m3.262s

    # check integrity of data with wigToBigWig
    time (zcat downloads/phyloP4way.wigFix.gz \
	| wigToBigWig -verbose=2 stdin /hive/data/genomes/galVar1/chrom.sizes \
	phyloP4way.bw) > bigWig.log 2>&1
    egrep "real|VmPeak" bigWig.log
    # pid=61850: VmPeak:    20741120 kB
    # real    28m31.224s

    bigWigInfo phyloP4way.bw | sed -e 's/^/# /;'
# version: 4
# isCompressed: yes
# isSwapped: 0
# primaryDataSize: 2,594,155,567
# primaryIndexSize: 84,462,776
# zoomLevels: 10
# chromCount: 26294
# basesCovered: 1,893,718,304
# mean: 0.058438
# min: -2.340000
# max: 0.694000
# std: 0.585564

    #	encode those files into wiggle data
    time (zcat downloads/phyloP4way.wigFix.gz \
	| wigEncode stdin phyloP4way.wig phyloP4way.wib)
    # Converted stdin, upper limit 0.69, lower limit -2.34
    # real    11m6.632s

    du -hsc *.wi?
    # 1.8G    phyloP4way.wib
    # 287M    phyloP4way.wig

    # Load gbdb and database with wiggle.
    ln -s `pwd`/phyloP4way.wib /gbdb/galVar1/multiz4way/phyloP4way.wib
    time hgLoadWiggle -pathPrefix=/gbdb/galVar1/multiz4way galVar1 \
	phyloP4way phyloP4way.wig
    # real    0m31.240s

    # use to set trackDb.ra entries for wiggle min and max
    # and verify table is loaded correctly

    wigTableStats.sh galVar1 phyloP4way
# db.table             min   max   mean      count     sumData
# galVar1.phyloP4way -2.34 0.694 0.0584383 1893718304 1.10666e+08
#       stdDev viewLimits
#	0.585564 viewLimits=-2.34:0.694

    #	that range is: 0.694+2.34 = 3.034 for hBinSize=0.003034

    #  Create histogram to get an overview of all the data
    time hgWiggle -doHistogram \
	-hBinSize=0.003034 -hBinCount=1000 -hMinVal=-2.34 -verbose=2 \
	    -db=galVar1 phyloP4way > histogram.data 2>&1
    # real    3m13.589s


    # find the Y range for the 2:5 graph
    grep -v chrom histogram.data | grep "^[0-9]" | ave -col=5 stdin \
      | sed -e 's/^/# /;'
# Q1 0.000076
# median 0.000252
# Q3 0.000978
# average 0.001223
# min 0.000000
# max 0.055976
# count 818
# total 1.000013
# standard deviation 0.003612

    # find the X range for the 2:5 graph
    grep "^[0-9]" histogram.data | ave -col=2 stdin \
      | sed -e 's/^/# /;'
# Q1 -1.551160
# median -0.930707
# Q3 -0.307220
# average -0.885657
# min -2.340000
# max 0.690966
# count 818
# total -724.467365
# standard deviation 0.820016

    #	create plot of histogram:
    printf 'set terminal png small x000000 xffffff xc000ff x66ff66 xffff00 x00ffff font \
"/usr/share/fonts/default/Type1/n022004l.pfb"
set size 1.4, 0.8
set key left box
set grid noxtics
set grid ytics
set title " Malayan flying lemur galVar1 Histogram phyloP4way track"
set xlabel " phyloP4way score"
set ylabel " Relative Frequency"
set y2label " Cumulative Relative Frequency (CRF)"
set y2range [0:1]
set y2tics
set xtics
set xrange [-2.6:0.85]
set yrange [0:0.033]

plot "histogram.data" using 2:5 title " RelFreq" with impulses, \
        "histogram.data" using 2:7 axes x1y2 title " CRF" with lines
' | gnuplot > histo.png

    display histo.png &
    # appears to have an odd hole in the data just above X=0 ?

#############################################################################
# hgPal downloads (DONE - 2017-04-21 - Hiram)
#   FASTA from 5-way for knownGene, refGene and knownCanonical

    ssh hgwdev
    screen -S galVar1HgPal
    mkdir /hive/data/genomes/galVar1/bed/multiz4way/pal
    cd /hive/data/genomes/galVar1/bed/multiz4way/pal
    cat ../species.list | tr '[ ]' '[\n]' > order.list

    # this for loop takes about 2.5 hours on this large count contig assembly
    export mz=multiz4way
    export gp=ncbiRefSeq
    export db=galVar1
    export I=0
    export D=0
    mkdir exonAA exonNuc
    printf '#!/bin/sh\n' > $gp.jobs

    time for C in `sort -nk2 ../../../chrom.sizes | cut -f1`
    do
        I=`echo $I | awk '{print $1+1}'`
        D=`echo $D | awk '{print $1+1}'`
        dNum=`echo $D | awk '{printf "%03d", int($1/1000)}'`
        mkdir -p exonNuc/${dNum} > /dev/null
        mkdir -p exonAA/${dNum} > /dev/null
	echo "mafGene -chrom=$C -exons -noTrans $db $mz $gp order.list stdout | gzip -c > exonNuc/${dNum}/$C.exonNuc.fa.gz &"
	echo "mafGene -chrom=$C -exons $db $mz $gp order.list stdout | gzip -c > exonAA/${dNum}/$C.exonAA.fa.gz &"
        if [ $I -gt 16 ]; then
            echo "date"
            echo "wait"
            I=0
        fi
    done >> $gp.jobs
    # real    55m30.266s

    echo "date" >> $gp.jobs
    echo "wait" >> $gp.jobs

    chmod +x $gp.jobs 

    time (./$gp.jobs) > $gp.jobs.log 2>&1 &
    # real    15m0.312s

    export mz=multiz4way
    export gp=ncbiRefSeq
    time find ./exonAA -type f | grep exonAA.fa.gz | xargs zcat \
     | gzip -c > $gp.$mz.exonAA.fa.gz
    #  real    3m47.095s

    time find ./exonNuc -type f | grep exonNuc.fa.gz | xargs zcat \
     | gzip -c > $gp.$mz.exonNuc.fa.gz
    #   real    4m14.836s

    # -rw-rw-r--   1 30254637 Apr 21 18:51 ncbiRefSeq.multiz4way.exonAA.fa.gz
    # -rw-rw-r--   1 48823595 Apr 21 21:53 ncbiRefSeq.multiz4way.exonNuc.fa.gz

    export mz=multiz4way
    export gp=ncbiRefSeq
    export db=galVar1
    export pd=/usr/local/apache/htdocs-hgdownload/goldenPath/$db/$mz/alignments
    mkdir -p $pd
    md5sum *.fa.gz > md5sum.txt
    ln -s `pwd`/$gp.$mz.exonAA.fa.gz $pd/$gp.exonAA.fa.gz
    ln -s `pwd`/$gp.$mz.exonNuc.fa.gz $pd/$gp.exonNuc.fa.gz
    ln -s `pwd`/md5sum.txt $pd/

    rm -rf exonAA exonNuc

#############################################################################
# construct download files for 5-way (DONE - 2017-04-21 - Hiram)
    mkdir /usr/local/apache/htdocs-hgdownload/goldenPath/galVar1/multiz4way
    mkdir /usr/local/apache/htdocs-hgdownload/goldenPath/galVar1/phastCons4way
    mkdir /usr/local/apache/htdocs-hgdownload/goldenPath/galVar1/phyloP4way
    mkdir /hive/data/genomes/galVar1/bed/multiz4way/downloads
    cd /hive/data/genomes/galVar1/bed/multiz4way/downloads
    mkdir multiz4way phastCons4way phyloP4way
    cd multiz4way
    time cp -p ../../anno/galVar1.4way.maf .
    #   real    0m21.540s

    # -rw-rw-r-- 1 10018032961 Apr 20 15:22 galVar1.4way.maf

    du -hsc *
    #  9.4G     galVar1.4way.maf

    time gzip *.maf
    #   real    40m20.076s
 
    # -rw-rw-r-- 1 2624441450 Apr 20 15:22 galVar1.4way.maf.gz

    du -hsc *.maf.gz
    #  2.5G    galVar1.4way.maf.gz

    ###########################################################################
    ## create upstream refGene maf files
    cd /hive/data/genomes/galVar1/bed/multiz4way/downloads/multiz4way
    # bash script
#!/bin/sh
export geneTbl="ncbiRefSeq"
for S in 1000 2000 5000
do
    echo "making upstream${S}.maf"
    featureBits galVar1 ${geneTbl}:upstream:${S} -fa=/dev/null -bed=stdout \
        | perl -wpe 's/_up[^\t]+/\t0/' | sort -k1,1 -k2,2n \
        | /cluster/bin/$MACHTYPE/mafFrags galVar1 multiz4way \
                stdin stdout \
                -orgs=/hive/data/genomes/galVar1/bed/multiz4way/species.list \
        | gzip -c > upstream${S}.${geneTbl}.maf.gz
    echo "done upstream${S}.${geneTbl}.maf.gz"
done
    #   real    11m13.365s

    md5sum *.maf.gz *.nh upstream*.gz README.txt >> md5sum.txt

    # some other symlinks were already made above
    # obtain the README.txt from cavPor3/multiz4way and update for this
    #   situation
    ln -s `pwd`/upstream*.gz `pwd`/README.txt \
        /usr/local/apache/htdocs-hgdownload/goldenPath/galVar1/multiz4way

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

    grep TREE ../../4d/all.mod | awk '{print $NF}' \
      | ~/kent/src/hg/utils/phyloTrees/asciiTree.pl /dev/stdin \
         > galVar1.4way.nh
    ~/kent/src/hg/utils/phyloTrees/commonNames.sh galVar1.4way.nh \
      | ~/kent/src/hg/utils/phyloTrees/asciiTree.pl /dev/stdin \
         > galVar1.4way.commonNames.nh
    ~/kent/src/hg/utils/phyloTrees/scientificNames.sh galVar1.4way.nh \
	| $HOME/kent/src/hg/utils/phyloTrees/asciiTree.pl /dev/stdin \
	    > galVar1.4way.scientificNames.nh
    time md5sum *.nh *.maf.gz > md5sum.txt
    #   real    0m35.144s

    ln -s `pwd`/* \
        /usr/local/apache/htdocs-hgdownload/goldenPath/galVar1/multiz4way

    du -hsc *.maf.gz ../../anno/galVar1.4way.maf
    #  2.5G     galVar1.4way.maf.gz
    #  9.4G     ../../anno/galVar1.4way.maf

    # obtain the README.txt from tupChi1/multiz4way and update for this
    #   situation

    #####################################################################
    cd /hive/data/genomes/galVar1/bed/multiz4way/downloads/phastCons4way

    ln -s ../../cons/all/downloads/phastCons4way.wigFix.gz \
        ./galVar1.phastCons4way.wigFix.gz
    ln -s ../../cons/all/phastCons4way.bw ./galVar1.phastCons4way.bw
    ln -s ../../cons/all/all.mod ./galVar1.phastCons4way.mod
    time md5sum *.gz *.mod *.bw > md5sum.txt
    #   real    0m20.354s

    # obtain the README.txt from tupChi1/phastCons4way and update for this
    #   situation
    ln -s `pwd`/* \
      /usr/local/apache/htdocs-hgdownload/goldenPath/galVar1/phastCons4way

    #####################################################################
    cd /hive/data/genomes/galVar1/bed/multiz4way/downloads/phyloP4way

    ln -s ../../consPhyloP/all/downloads/phyloP4way.wigFix.gz \
        ./galVar1.phyloP4way.wigFix.gz
    ln -s ../../consPhyloP/run.phyloP/all.mod galVar1.phyloP4way.mod
    ln -s ../../consPhyloP/all/phyloP4way.bw galVar1.phyloP4way.bw

    time md5sum *.mod *.bw *.gz > md5sum.txt
    #   real    0m29.662s

    # obtain the README.txt from galVar1/phyloP4way and update for this
    #   situation
    ln -s `pwd`/* \
      /usr/local/apache/htdocs-hgdownload/goldenPath/galVar1/phyloP4way

#############################################################################
# wiki page for 5-way (DONE - 2017-04-21 - Hiram)
    mkdir /hive/users/hiram/bigWays/galVar1.4way
    cd /hive/users/hiram/bigWays
    echo "galVar1" > galVar1.4way/ordered.list
    awk '{print $1}' /hive/data/genomes/galVar1/bed/multiz4way/4way.distances.txt \
       >> galVar1.4way/ordered.list

    # sizeStats.sh catches up the cached measurements required for data
    # in the tables.  They are usually already mostly done, only new
    # assemblies will have updates.
    ./sizeStats.sh galVar1.4way/ordered.list
    # dbDb.sh constructs galVar1.4way/GalVar1_5-way_conservation_alignment.html
    # may need to add new assembly references to srcReference.list and
    # urlReference.list
    ./dbDb.sh galVar1 4way
    # sizeStats.pl constructs galVar1.4way/GalVar1_5-way_Genome_size_statistics.html
    # this requires entries in coverage.list for new sequences
    ./sizeStats.pl galVar1 4way

    # defCheck.pl constructs GalVar1_5-way_conservation_lastz_parameters.html
    ./defCheck.pl galVar1 4way

    # this constructs the html pages in galVar1.4way/:
# -rw-rw-r-- 1 2862 Apr 21 22:25 GalVar1_4-way_conservation_alignment.html
# -rw-rw-r-- 1 4252 Apr 21 22:25 GalVar1_4-way_Genome_size_statistics.html
#-rw-rw-r-- 1 3022 Apr 21 22:25 GalVar1_4-way_conservation_lastz_parameters.html

    # add those pages to the genomewiki.  Their page names are the
    # names of the .html files without the .html:
#  GalVar1_4-way_conservation_alignment
#  GalVar1_4-way_Genome_size_statistics
#  GalVar1_4-way_conservation_lastz_parameters

    # when you view the first one you enter, it will have links to the
    # missing two.

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