#############################################################################
## 3-Way Multiz (DONE - 2018-06-14 - Hiram)
    ssh hgwdev
    mkdir /hive/data/genomes/micMur3/bed/multiz3way
    cd /hive/data/genomes/micMur3/bed/multiz3way

    # from the 219.nh in the source tree, select out the 3 used here:
    /cluster/bin/phast/tree_doctor \
        --prune-all-but hg38,otoGar3,micMur3 \
        /cluster/home/hiram/kent/src/hg/utils/phyloTrees/219.nh \
          > micMur3.3way.nh.0
    cat micMur3.3way.nh.0
    # (hg38:0.130414,(micMur3:0.085600,otoGar3:0.119400):0.020520);

    # using TreeGraph2 tree editor on the Mac, rearrange to get micMur3
    # at the top:
    # ((micMur3:0.0856,otoGar3:0.1194):0.02052,hg38:0.130414);

    #	what that looks like:
 ~/kent/src/hg/utils/phyloTrees/asciiTree.pl micMur3.3way.nh | sed -e 's/^/# /;'
# ((micMur3:0.0856,
#  otoGar3:0.1194):0.02052,
# hg38:0.130414);

    # extract species list from that .nh file
    sed 's/[a-z][a-z]*_//g; s/:[0-9\.][0-9\.]*//g; s/;//; /^ *$/d' \
        micMur3.3way.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`" micMur3.3way.nh | sed -e 's/00*)/)/g; s/00*,/,/g' \
       | $HOME/kent/src/hg/utils/phyloTrees/asciiTree.pl /dev/stdin \
         > micMur3.3way.commonNames.nh
    cat micMur3.3way.commonNames.nh | sed -e 's/^/# /;'
# ((Mouse_lemur:0.0856,
#  Bushbaby:0.1194):0.02052,
# Human:0.130414);

#	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/micMur3_3way.png

    ~/kent/src/hg/utils/phyloTrees/asciiTree.pl micMur3.3way.nh > t.nh
    ~/kent/src/hg/utils/phyloTrees/scientificNames.sh t.nh \
       | $HOME/kent/src/hg/utils/phyloTrees/asciiTree.pl /dev/stdin \
          > micMur3.3way.scientificNames.nh
    rm -f t.nh
    cat micMur3.3way.scientificNames.nh | sed -e 's/^/# /;'
# ((Microcebus_murinus:0.0856,
#  Otolemur_garnettii:0.1194):0.02052,
# Homo_sapiens:0.130414);

    /cluster/bin/phast/all_dists micMur3.3way.nh | grep micMur3 \
        | sed -e "s/micMur3.//" | sort -k2n > 3way.distances.txt
    #	Use this output to create the table below
    cat 3way.distances.txt | sed -e 's/^/# /;'
# otoGar3       0.205000
# hg38  0.236534

    printf '#!/usr/bin/env perl

use strict;
use warnings;

open (FH, "<3way.distances.txt") or
        die "can not read 3way.distances.txt";

my $count = 0;
while (my $line = <FH>) {
    chomp $line;
    my ($D, $dist) = split('"'"'\\s+'"'"', $line);
    my $chain = "chain" . ucfirst($D);
    my $B="/hive/data/genomes/micMur3/bed/lastz.$D/fb.micMur3." .
        $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.micMur3/fb.${D}.chainMicMur3Link.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 micMur3  on other     other species
# 01  0.2050 (% 70.702) (% 69.178) - Bushbaby otoGar3
# 02  0.2365 (% 36.904) (% 29.728) - Human hg38

# 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' \
	micMur3.3way.nh | xargs echo | sed 's/ //g; s/,/ /g' > tree.nh

    sed 's/[()]//g; s/,/ /g' tree.nh > species.list
    # micMur3 otoGar3 hg38

    # survey N50 for each
    for db in `cat species.list`
do
n50.pl /hive/data/genomes/$db/chrom.sizes
done
#       reading: /hive/data/genomes/micMur3/chrom.sizes
#       contig count: 7678, total size: 2487409138, one half size: 1243704569
# cumulative    N50 count       contig  contig size
1144871449      9       chr11   108226025
1243704569 one half size
1253043427      10      chr7    108171978
#       reading: /hive/data/genomes/otoGar3/chrom.sizes
#       contig count: 7793, total size: 2519724550, one half size: 1259862275
# cumulative    N50 count       contig  contig size
1254578701      46      GL873565        13992998
1259862275 one half size
1268431362      47      GL873566        13852661
#       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

    #	bash shell syntax here ...
    cd /hive/data/genomes/micMur3/bed/multiz3way
    export H=/hive/data/genomes/micMur3/bed
    mkdir mafLinks
    # good assemblies can use syntenic net:
    #  otoGar3 hg38
    for G in otoGar3 hg38
    do
      mkdir mafLinks/$G
      echo ln -s ${H}/lastz.$G/axtChain/micMur3.${G}.synNet.maf.gz ./mafLinks/$G
      ln -s ${H}/lastz.$G/axtChain/micMur3.${G}.synNet.maf.gz ./mafLinks/$G
    done

    # verify the symLinks are good:
    ls -ogrtL mafLinks/*/* | sed -e 's/^/# /; s/-rw-rw-r-- 1//;'
#   597399601 Mar  4  2017 mafLinks/hg38/micMur3.hg38.synNet.maf.gz
#  1071310562 Feb  1 04:33 mafLinks/otoGar3/micMur3.otoGar3.synNet.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/micMur3/bed/multiz3way/mafSplit
    cd /hive/data/genomes/micMur3/bed/multiz3way/mafSplit
    time for D in `sed -e "s/micMur3 //" ../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    1m39.690s

    # 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
    # 92
    find . -type f | grep ".maf$" | xargs -L 1 basename | sort -u > maf.list
    wc -l maf.list
    # 58 maf.list

    mkdir /hive/data/genomes/micMur3/bed/multiz3way/splitRun
    cd /hive/data/genomes/micMur3/bed/multiz3way/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 = micMur3
set c = $1
set result = $2
set run = `/bin/pwd`
set tmp = /dev/shm/$db/multiz.$c
set pairs = /hive/data/genomes/micMur3/bed/multiz3way/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 $(file1) {check out line+ /hive/data/genomes/micMur3/bed/multiz3way/splitRun/maf/$(root1).maf}
#ENDLOOP
' > template

    ln -s ../../mafSplit/maf.list maf.list
    ssh ku
    cd /hive/data/genomes/micMur3/bed/multiz3way/splitRun/run
    gensub2 maf.list single template jobList
    para create jobList
    para try ... check ... push ... etc...
# Completed: 58 of 58 jobs
# CPU time in finished jobs:      10360s     172.66m     2.88h    0.12d  0.000 y
# IO & Wait Time:                   166s       2.77m     0.05h    0.00d  0.000 y
# Average job time:                 181s       3.02m     0.05h    0.00d
# Longest finished job:             760s      12.67m     0.21h    0.01d
# Submission to last job:           946s      15.77m     0.26h    0.01d

    # combine into one file  (the 1>&2 redirect sends the echo to stderr)
    cd /hive/data/genomes/micMur3/bed/multiz3way
    head -1 splitRun/maf/018.maf > multiz3way.maf
    time for F in splitRun/maf/*.maf
do
    echo "${F}" 1>&2
    egrep -v "^#" ${F}
done >> multiz3way.maf
    # real    0m17.602s

    tail -1 splitRun/maf/018.maf >> multiz3way.maf
# -rw-rw-r-- 1 5286978730 Jun 14 16:43 multiz3way.maf

    # Load into database
    ssh hgwdev
    cd /hive/data/genomes/micMur3/bed/multiz3way
    mkdir /gbdb/micMur3/multiz3way
    ln -s `pwd`/multiz3way.maf /gbdb/micMur3/multiz3way
    cd /dev/shm
    time hgLoadMaf micMur3 multiz3way
# Loaded 6611020 mafs in 1 files from /gbdb/micMur3/multiz3way
# real    1m33.848s

    time hgLoadMafSummary -verbose=2 -minSize=30000 \
	-mergeGap=1500 -maxSize=200000 micMur3 multiz3waySummary \
	/gbdb/micMur3/multiz3way/multiz3way.maf
# Created 334687 summary blocks from 9361072 components and 6611020 mafs from /gbdb/micMur3/multiz3way/multiz3way.maf
# real    1m42.093s

# -rw-rw-r-- 1   328445960 Jun 14 16:45 multiz3way.tab
# -rw-rw-r-- 1    15044382 Jun 14 16:48 multiz3waySummary.tab

    wc -l multiz3way*.tab
#   6611020 multiz3way.tab
#    334687 multiz3waySummary.tab

    rm multiz3way*.tab

##############################################################################
# GAP ANNOTATE MULTIZ7WAY MAF AND LOAD TABLES (DONE - 2018-06-14 - 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/micMur3/bed/multiz3way/anno/mafSplit
    cd /hive/data/genomes/micMur3/bed/multiz3way/anno/mafSplit

    time mafSplit -outDirDepth=2 -byTarget -useFullSequenceName \
        /dev/null . ../../multiz3way.maf
    #   real    1m30.590s

    find . -type f | wc -l
    #   69

    # check for N.bed files everywhere:
    cd /hive/data/genomes/micMur3/bed/multiz3way/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/micMur3/bed/multiz3way/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/micMur3/bed/multiz3way/anno
    mkdir result
    find ./mafSplit -type d | sed -e '/^.\/mafSplit$/d; s#./mafSplit/##' | while read D
do
    echo mkdir -p result/${D}
    mkdir -p result/${D}
done
    printf '#LOOP
mafAddIRows -nBeds=nBeds mafSplit/$(path1) /hive/data/genomes/micMur3/micMur3.2bit {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 -ram=32g create jobList
    para try ... check ... push ...
# Completed: 69 of 69 jobs
# CPU time in finished jobs:        574s       9.57m     0.16h    0.01d  0.000 y
# IO & Wait Time:                   251s       4.18m     0.07h    0.00d  0.000 y
# Average job time:                  12s       0.20m     0.00h    0.00d
# Longest finished job:              49s       0.82m     0.01h    0.00d
# Submission to last job:           439s       7.32m     0.12h    0.01d

    # 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/5/7/chrM.maf > micMur3.3way.maf
    time find ./result -type f | while read F
do
    echo "${F}" 1>&2
    grep -h -v "^#" ${F}
done >> micMur3.3way.maf
    # real    0m22.043s

    #	these maf files do not have the end marker, this does nothing:
    #	tail -q -n 1 result/5/7/chrM.maf >> micMur3.3way.maf
    # How about an official end marker:
    echo "##eof maf" >> micMur3.3way.maf
    ls -og
# -rw-rw-r-- 1 6567442730 Jun 14 17:08 micMur3.3way.maf

    du -hsc micMur3.3way.maf
    # 6.2G    micMur3.3way.maf

    # construct symlinks to get the individual maf files into gbdb:
    rm /gbdb/micMur3/multiz3way/multiz3way.maf   # remove previous results
    ln -s `pwd`/micMur3.3way.maf /gbdb/micMur3/multiz3way/multiz3way.maf

    # Load into database
    cd /dev/shm
    time hgLoadMaf -pathPrefix=/gbdb/micMur3/multiz3way micMur3 multiz3way
    # Loaded 7625882 mafs in 1 files from /gbdb/micMur3/multiz3way
    # real    2m3.113s

    time hgLoadMafSummary -verbose=2 -minSize=30000 \
	-mergeGap=1500 -maxSize=200000 micMur3 multiz3waySummary \
        /gbdb/micMur3/multiz3way/multiz3way.maf
    # Created 334687 summary blocks from 9361072 components and 7625882 mafs from /gbdb/micMur3/multiz3way/multiz3way.maf
    # real    1m56.219s

    # -rw-rw-r-- 1   379246576 Jun 14 17:10 multiz3way.tab
    # -rw-rw-r-- 1    15713756 Jun 14 17:14 multiz3waySummary.tab

    rm multiz3way*.tab

######################################################################
# MULTIZ7WAY MAF FRAMES (DONE - 2018-06-14 - Hiram)
    ssh hgwdev
    mkdir /hive/data/genomes/micMur3/bed/multiz3way/frames
    cd /hive/data/genomes/micMur3/bed/multiz3way/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 hgFixed -N -e \
            "select id from organism where name='"'"'$orgName'"'"'"`
    if ($orgId == "") then
        echo "Mrnas: 0"
    else
        set count = `hgsql hgFixed -N -e "select count(*) from gbCdnaInfo where organism='"'"'$orgId'"'"'"`
        echo "Mrnas: ${count}"
    endif
end
' > showGenes.csh

    chmod +x ./showGenes.csh
    time ./showGenes.csh
# micMur3: ensGene: 45162, xenoRefGene: 229116, Mrnas: 262
# otoGar3: ensGene: 28565, xenoRefGene: 479738, Mrnas: 195
# hg38: ensGene: 208239, knownGene: 196838, mgcGenes: 35329, ncbiRefSeq: 159322, refGene: 75554, xenoRefGene: 190035, Mrnas: 11529081
    # about 1m 30s

    # from that summary, use these gene sets:
    # knownGene - hg38
    # ensGene - micMur3 otoGar3
 
    mkdir genes
    #   1. knownGene: hg38
    for DB in hg38
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: 21554 failed: 0

    #   2. ensGene: micMur3 otoGar3
    for DB in micMur3 otoGar3
do
    hgsql -N -e "select name,chrom,strand,txStart,txEnd,cdsStart,cdsEnd,exonCount,exonStarts,exonEnds from ensGene" ${DB} \
      | genePredSingleCover stdin stdout | gzip -2c \
        > /dev/shm/${DB}.tmp.gz
    mv /dev/shm/${DB}.tmp.gz genes/$DB.gp.gz
    printf "# ${DB}: "
    genePredCheck -db=${DB} genes/${DB}.gp.gz
done
# micMur3: checked: 18028 failed: 0
# otoGar3: checked: 19472 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/hg38.gp.gz: 21554
# genes/micMur3.gp.gz: 18028
# genes/otoGar3.gp.gz: 19472

    time (cat ../anno/micMur3.3way.maf \
	| genePredToMafFrames micMur3 stdin stdout \
          `cat ../species.list.txt | xargs echo \
            | sed -e "s#\([a-zA-Z0-9]*\)#\1 genes/\1.gp.gz#g;"` \
		| gzip > multiz3wayFrames.bed.gz)
    # real    1m22.628s

    # verify there are frames on everything, should be 4 species:
    zcat multiz3wayFrames.bed.gz | awk '{print $4}' | sort | uniq -c \
       | sed -e 's/^/# /;'
#  205931 hg38
#  180126 micMur3
#  253766 otoGar3

    #   load the resulting file
    ssh hgwdev
    cd /hive/data/genomes/micMur3/bed/multiz3way/frames
    time hgLoadMafFrames micMur3 multiz3wayFrames multiz3wayFrames.bed.gz
    #   real    0m7.686s

    time featureBits -countGaps micMur3 multiz3wayFrames
# 36430773 bases of 2487409138 (1.465%) in intersection
# real    0m7.052s

    #   enable the trackDb entries:
# frames multiz3wayFrames
# irows on
    #   appears to work OK

#########################################################################
# Phylogenetic tree from 3-way (DONE - 2018-06-14 - Hiram)
    mkdir /hive/data/genomes/micMur3/bed/multiz3way/4d
    cd /hive/data/genomes/micMur3/bed/multiz3way/4d

    # using the ensGene
    hgsql -N -e "select name,chrom,strand,txStart,txEnd,cdsStart,cdsEnd,exonCount,exonStarts,exonEnds from ensGene" micMur3 \
      | genePredSingleCover stdin stdout > micMur3.ensGeneNR.gp
    genePredCheck -db=micMur3 micMur3.ensGeneNR.gp
    # checked: 18028 failed: 0

    # the annotated maf is:
    og ../anno/micMur3.3way.maf
# -rw-rw-r-- 1 6567442730 Jun 14 17:08 ../anno/micMur3.3way.maf

    mkdir annoSplit
    cd annoSplit
    time mafSplit -verbose=2 -outDirDepth=2 -byTarget -useFullSequenceName \
	/dev/null . ../../anno/micMur3.3way.maf
    # real    2m1.807s

    find . -type f | wc -l
    #  69

    ssh ku
    mkdir /hive/data/genomes/micMur3/bed/multiz3way/4d/run
    cd /hive/data/genomes/micMur3/bed/multiz3way/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 = micMur3.ensGeneNR.gp
set r = "/hive/data/genomes/micMur3/bed/multiz3way"
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$c\\t/\\tmicMur3.$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
# 69 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 create jobList
    para try ... check
    para time
# Completed: 65 of 69 jobs
# Crashed: 4 jobs
# CPU time in finished jobs:        457s       7.62m     0.13h    0.01d  0.000 y
# IO & Wait Time:                   161s       2.68m     0.04h    0.00d  0.000 y
# Average job time:                  10s       0.16m     0.00h    0.00d
# Longest finished job:              34s       0.57m     0.01h    0.00d
# Submission to last job:           101s       1.68m     0.03h    0.00d

    # 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/micMur3/bed/multiz3way/4d
    # remove the broken empty files, size 0 and size 1:
    find ./mfa -type f -size 0 | xargs rm -f
    # this does not work, don't know why
    ### find ./mfa -type f -size 1 | xargs rm -f
    # use this empty list procedure instead:
    find ./mfa -type f | xargs ls -og | awk '$3 < 2' | awk '{print $NF}' \
        > empty.list
    # can be verified with:
    cat empty.list | xargs ls -og | sort -k3n | less
    cat empty.list | xargs rm -f
    # see what is left:
    ls -ogrt mfa/*/*/*.mfa | sort -k3nr | wc
    #    41     287    2238

    # 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    0m1.168s

    # check they are all in there:
    grep "^>" 4d.all.mfa | wc -l
    # 3
    grep "^>" 4d.all.mfa | sed -e 's/^/# /;'
# >micMur3
# >otoGar3
# >hg38

    sed 's/[a-z][a-z]*_//g; s/:[0-9\.][0-9\.]*//g; s/;//; /^ *$/d' \
	../micMur3.3way.nh | xargs echo | sed -e 's/ //g' > tree_commas.nh
    # tree_commas.nh looks like:
    # ((micMur3,otoGar3),hg38)

    # 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    0m0.654s

    mv phyloFit.mod all.mod

    grep TREE all.mod
# TREE: ((micMur3:0.0904485,otoGar3:0.133383):0.0669468,hg38:0.0669468);

    # compare these calculated lengths to the tree extracted from 191way:
    cat ../micMur3.3way.nh
#       ((micMur3:0.0856,otoGar3:0.1194):0.02052,hg38:0.130414);

    grep TREE all.mod | sed -e 's/TREE: //' \
       | /cluster/bin/phast/all_dists /dev/stdin | grep micMur3 \
          | sed -e "s/micMur3.//;"  | sort > new.dists
    /cluster/bin/phast/all_dists ../micMur3.3way.nh | grep micMur3 \
        | sed -e "s/micMur3.//;" | 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
#       otoGar3 0.223832        0.205000        0.018832        9.186341
#       hg38    0.224342        0.236534        -0.012192       -5.154439

     # doesn't work so well with such different trees

#########################################################################
# phastCons 3-way (DONE - 2018-06-14 - Hiram)
    # split 3way mafs into 10M chunks and generate sufficient statistics
    # files for # phastCons
    ssh ku
    mkdir -p /hive/data/genomes/micMur3/bed/multiz3way/cons/SS
    cd /hive/data/genomes/micMur3/bed/multiz3way/cons/SS
    mkdir result done

    printf '#!/bin/csh -ef
set d = $1
set c = $2
set doneDir = done/$d
set MAF = /hive/data/genomes/micMur3/bed/multiz3way/anno/result/$d/$c.maf
set WINDOWS = /hive/data/genomes/micMur3/bed/multiz3way/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
# 69 maf.list

    ssh ku
    cd /hive/data/genomes/micMur3/bed/multiz3way/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=64 push
# Completed: 69 of 69 jobs
# CPU time in finished jobs:        746s      12.43m     0.21h    0.01d  0.000 y
# IO & Wait Time:                   202s       3.37m     0.06h    0.00d  0.000 y
# Average job time:                  14s       0.23m     0.00h    0.00d
# Longest finished job:              52s       0.87m     0.01h    0.00d
# Submission to last job:           103s       1.72m     0.03h    0.00d

    find ./result -type f | wc -l
    # 294

    # 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/micMur3/bed/multiz3way/cons/run.cons
    cd /hive/data/genomes/micMur3/bed/multiz3way/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/micMur3/bed/multiz3way/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
    #	294 ss.list

    # Create parasol batch and run it
    # run for all species
    cd /hive/data/genomes/micMur3/bed/multiz3way/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 create jobList
    para try ... check ...
    para -maxJob=64 push
# Completed: 294 of 294 jobs
# CPU time in finished jobs:       5033s      83.89m     1.40h    0.06d  0.000 y
# IO & Wait Time:                  1922s      32.03m     0.53h    0.02d  0.000 y
# Average job time:                  24s       0.39m     0.01h    0.00d
# Longest finished job:              33s       0.55m     0.01h    0.00d
# Submission to last job:           184s       3.07m     0.05h    0.00d

    # create Most Conserved track
    cd /hive/data/genomes/micMur3/bed/multiz3way/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    0m48.658s

    time /cluster/bin/scripts/lodToBedScore tmpMostConserved.bed \
         > mostConserved.bed
    # real    0m5.673s

    # -rw-rw-r-- 1 22298268 Jun 14 18:08 mostConserved.bed

    # load into database
    ssh hgwdev
    cd /hive/data/genomes/micMur3/bed/multiz3way/cons/all
    time hgLoadBed micMur3 phastConsElements3way mostConserved.bed
    # Read 645869 elements of size 5 from mostConserved.bed
    # real    0m5.559s

    # 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 micMur3 -enrichment ensGene:cds phastConsElements3way
# ensGene:cds 1.303%, phastConsElements3way 5.817%, both 0.830%, cover 63.67%, enrich 10.95x
# real    0m11.726s

    # Create merged posterier probability file and wiggle track data files
    cd /hive/data/genomes/micMur3/bed/multiz3way/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/phastCons3way.wigFix.gz)
    #   real    23m48.045s
# -rw-rw-r-- 1 2417131021 Jun 14 18:34 phastCons3way.wigFix.gz

    # check integrity of data with wigToBigWig
    time (zcat downloads/phastCons3way.wigFix.gz \
	| wigToBigWig -verbose=2 stdin /hive/data/genomes/micMur3/chrom.sizes \
	    phastCons3way.bw) > bigWig.log 2>&1
    egrep "real|VmPeak" bigWig.log
    # pid=23258: VmPeak:    19028104 kB
    # real    25m38.455s

    bigWigInfo phastCons3way.bw | sed -e 's/^/# /;'
# version: 4
# isCompressed: yes
# isSwapped: 0
# primaryDataSize: 3,801,574,234
# primaryIndexSize: 74,859,628
# zoomLevels: 10
# chromCount: 69
# basesCovered: 1,732,608,342
# mean: 0.199336
# min: 0.000000
# max: 0.997000
# std: 0.269823

    #	encode those files into wiggle data
    time (zcat downloads/phastCons3way.wigFix.gz \
	| wigEncode stdin phastCons3way.wig phastCons3way.wib)
    # Converted stdin, upper limit 1.00, lower limit 0.00
    # real    9m45.235s

    du -hsc *.wi?
    #	1.7G    phastCons3way.wib
    #   226M    phastCons3way.wig

    # Load gbdb and database with wiggle.
    ln -s `pwd`/phastCons3way.wib /gbdb/micMur3/multiz3way/phastCons3way.wib
    time hgLoadWiggle -pathPrefix=/gbdb/micMur3/multiz3way \
	micMur3 phastCons3way phastCons3way.wig
    #   real    0m26.607s

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

    wigTableStats.sh micMur3 phastCons3way
    # micMur3.phastCons3way    0 0.997 0.199336 1732608342 3.45371e+08
    # db.table              min max mean count sumData stdDev viewLimits
#     stdDev  viewLimits
    # 0.269823 viewLimits=0:0.997

    #  Create histogram to get an overview of all the data
    time hgWiggle -doHistogram -db=micMur3 \
	-hBinSize=0.001 -hBinCount=1000 -hMinVal=0.0 -verbose=2 \
	    phastCons3way > histogram.data 2>&1
    #	real    1m40.570s

    #	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 " Mouse lemur Microcebus murinus micMur3 Histogram phastCons3way track"
set xlabel " phastCons3way 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 3-way (DONE - 2018-06-15 - Hiram)
    # run phyloP with score=LRT
    ssh ku
    mkdir /cluster/data/micMur3/bed/multiz3way/consPhyloP
    cd /cluster/data/micMur3/bed/multiz3way/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}'
    #	0.569
    /cluster/bin/phast.build/cornellCVS/phast.2010-12-30/bin/modFreqs \
	../../4d/all.mod 0.569 > all.mod
    # verify, the BACKGROUND should now be paired up:
    grep BACK all.mod
    #   BACKGROUND: 0.215500 0.284500 0.284500 0.215500 

    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/micMur3/bed/multiz3way/consPhyloP
set tmp = $cons/tmp/$grp/$f
/bin/rm -fr $tmp
/bin/mkdir -p $tmp
set ssSrc = "/hive/data/genomes/micMur3/bed/multiz3way/cons/SS/result/$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
    #	294 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/micMur3/bed/multiz3way/consPhyloP/all
    cd /hive/data/genomes/micMur3/bed/multiz3way/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=64 push
    para time > run.time
# Completed: 294 of 294 jobs
# CPU time in finished jobs:       1024s      17.07m     0.28h    0.01d  0.000 y
# IO & Wait Time:                  2589s      43.14m     0.72h    0.03d  0.000 y
# Average job time:                  12s       0.20m     0.00h    0.00d
# Longest finished job:              17s       0.28m     0.00h    0.00d
# Submission to last job:           262s       4.37m     0.07h    0.00d

    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/phyloP3way.wigFix.gz)
    #   real    13m57.387s

    # check integrity of data with wigToBigWig
    time (zcat downloads/phyloP3way.wigFix.gz \
	| wigToBigWig -verbose=2 stdin /hive/data/genomes/micMur3/chrom.sizes \
	phyloP3way.bw) > bigWig.log 2>&1
    egrep "real|VmPeak" bigWig.log
    # pid=43080: VmPeak:    19028104 kB
    # real    25m52.899s

    bigWigInfo phyloP3way.bw | sed -e 's/^/# /;'
# version: 4
# isCompressed: yes
# isSwapped: 0
# primaryDataSize: 1,687,583,334
# primaryIndexSize: 74,859,628
# zoomLevels: 10
# chromCount: 69
# basesCovered: 1,732,608,342
# mean: 0.073093
# min: -1.989000
# max: 0.434000
# std: 0.511784

    #	encode those files into wiggle data
    time (zcat downloads/phyloP3way.wigFix.gz \
	| wigEncode stdin phyloP3way.wig phyloP3way.wib)
    # Converted stdin, upper limit 0.43, lower limit -1.99
    # real    9m52.929s

    du -hsc *.wi?
    # 1.7G    phyloP3way.wib
    # 224M    phyloP3way.wig

    # Load gbdb and database with wiggle.
    ln -s `pwd`/phyloP3way.wib /gbdb/micMur3/multiz3way/phyloP3way.wib
    time hgLoadWiggle -pathPrefix=/gbdb/micMur3/multiz3way micMur3 \
	phyloP3way phyloP3way.wig
    # real    0m25.308s

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

    wigTableStats.sh micMur3 phyloP3way
# db.table      min max mean count sumData
# micMur3.phyloP3way -1.989 0.434 0.0730935 1732608342 1.26642e+08
#       stdDev viewLimits
#     0.511784 viewLimits=-1.989:0.434

    #	that range is: 0.434+1.989 = 2.423 for hBinSize=0.002423

    #  Create histogram to get an overview of all the data
    time hgWiggle -doHistogram \
	-hBinSize=0.002423 -hBinCount=1000 -hMinVal=-1.989 -verbose=2 \
	    -db=micMur3 phyloP3way > histogram.data 2>&1
    # real    1m39.574s

    # 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 0.000051
# median 0.000240
# Q3 0.001269
# average 0.003040
# min 0.000000
# max 0.104443
# count 329
# total 1.000009
# standard deviation 0.010154

    # find the X range for the 2:5 graph
    grep "^[0-9]" histogram.data | ave -col=2 stdin \
      | sed -e 's/^/# /;'
# Q1 -1.194260
# median -0.891381
# Q3 -0.617582
# average -0.858939
# min -1.989000
# max 0.431577
# count 329
# total -282.590953
# standard deviation 0.633148

    #	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 " Mouse lemur Microcebus murinus micMur3 Histogram phyloP3way track"
set xlabel " phyloP3way score"
set ylabel " Relative Frequency"
set y2label " Cumulative Relative Frequency (CRF)"
set y2range [0:1]
set y2tics
set xtics
set xrange [-2:0.5]
set yrange [0:0.15]

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 &
    # this is a very choppy graph compared the the larger N-way alignments
    # has various holes in the data

#############################################################################
# hgPal downloads (DONE - 2018-06-15 - Hiram)
#   FASTA from 3-way for ensGene

    ssh hgwdev
    screen -S micMur3HgPal
    mkdir /hive/data/genomes/micMur3/bed/multiz3way/pal
    cd /hive/data/genomes/micMur3/bed/multiz3way/pal
    cat ../species.list | tr '[ ]' '[\n]' > order.list

    # BEWARE: high count contig assemblies can take hours to run this simple
    # preparation script
    export mz=multiz3way
    export gp=ensGene
    export db=micMur3
    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    1m32.374s

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

    chmod +x ensGene.jobs 

    time (./$gp.jobs) > $gp.jobs.log 2>&1 &
    # real    14m50.750s

    export mz=multiz3way
    export gp=ensGene
    time find ./exonAA -type f | grep exonAA.fa.gz | xargs zcat \
     | gzip -c > $gp.$mz.exonAA.fa.gz
    #  real    0m12.859s

    time find ./exonNuc -type f | grep exonNuc.fa.gz | xargs zcat \
     | gzip -c > $gp.$mz.exonNuc.fa.gz
    #  real    0m32.792s

  # -rw-rw-r--  1 26057469 Jun 15 16:41 ensGene.multiz3way.exonAA.fa.gz
  # -rw-rw-r--  1 38863651 Jun 15 16:42 ensGene.multiz3way.exonNuc.fa.gz

    export mz=multiz3way
    export gp=ensGene
    export db=micMur3
    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

    # verify the /multiz3way/README.txt file mentions these alignments
    # add it if not there

#############################################################################
# construct download files for 3-way (DONE - 2018-06-15 - Hiram)
    mkdir /usr/local/apache/htdocs-hgdownload/goldenPath/micMur3/multiz3way
    mkdir /usr/local/apache/htdocs-hgdownload/goldenPath/micMur3/phastCons3way
    mkdir /usr/local/apache/htdocs-hgdownload/goldenPath/micMur3/phyloP3way
    mkdir /hive/data/genomes/micMur3/bed/multiz3way/downloads
    cd /hive/data/genomes/micMur3/bed/multiz3way/downloads
    mkdir multiz3way phastCons3way phyloP3way
    cd multiz3way
    time cp -p ../../anno/micMur3.3way.maf .
    #   real    0m10.690s

    # -rw-rw-r-- 1 6567442730 Jun 14 17:08 micMur3.3way.maf

    du -hsc *
    #  6.2G    micMur3.3way.maf

    time gzip *.maf
    # real    23m23.610s

    # -rw-rw-r-- 1 1789293002 Jun 14 17:08 micMur3.3way.maf.gz

    du -hsc *.maf.gz
    #  1.7G    micMur3.3way.maf.gz

    grep TREE ../../4d/all.mod | awk '{print $NF}' \
      | ~/kent/src/hg/utils/phyloTrees/asciiTree.pl /dev/stdin \
         > micMur3.3way.nh
    ~/kent/src/hg/utils/phyloTrees/commonNames.sh micMur3.3way.nh \
      | ~/kent/src/hg/utils/phyloTrees/asciiTree.pl /dev/stdin \
         > micMur3.3way.commonNames.nh
    ~/kent/src/hg/utils/phyloTrees/scientificNames.sh micMur3.3way.nh \
	| $HOME/kent/src/hg/utils/phyloTrees/asciiTree.pl /dev/stdin \
	    > micMur3.3way.scientificNames.nh
    time md5sum *.nh *.maf.gz > md5sum.txt
    #   real    0m6.058s

    ln -s `pwd`/* \
        /usr/local/apache/htdocs-hgdownload/goldenPath/micMur3/multiz3way

    du -hsc *.maf.gz ../../anno/micMur3.3way.maf
    #  1.7G    micMur3.3way.maf.gz
    #  6.2G    ../../anno/micMur3.3way.maf

    # obtain the README.txt from otoGar3/multiz3way and update for this
    #   situation

    #####################################################################
    cd /hive/data/genomes/micMur3/bed/multiz3way/downloads/phastCons3way

    ln -s ../../cons/all/downloads/phastCons3way.wigFix.gz \
        ./micMur3.phastCons3way.wigFix.gz
    ln -s ../../cons/all/phastCons3way.bw ./micMur3.phastCons3way.bw
    ln -s ../../cons/all/all.mod ./micMur3.phastCons3way.mod
    time md5sum *.gz *.mod *.bw > md5sum.txt
    #   real    0m24.680s

    # obtain the README.txt from otoGar3/phastCons3way and update for this
    #   situation
    ln -s `pwd`/* \
      /usr/local/apache/htdocs-hgdownload/goldenPath/micMur3/phastCons3way

    #####################################################################
    cd /hive/data/genomes/micMur3/bed/multiz3way/downloads/phyloP3way

    ln -s ../../consPhyloP/all/downloads/phyloP3way.wigFix.gz \
        ./micMur3.phyloP3way.wigFix.gz
    ln -s ../../consPhyloP/run.phyloP/all.mod micMur3.phyloP3way.mod
    ln -s ../../consPhyloP/all/phyloP3way.bw micMur3.phyloP3way.bw

    time md5sum *.mod *.bw *.gz > md5sum.txt
    #   real    0m13.555s

    # obtain the README.txt from otoGar3/phyloP3way and update for this
    #   situation
    ln -s `pwd`/* \
      /usr/local/apache/htdocs-hgdownload/goldenPath/micMur3/phyloP3way

    ###########################################################################
    ## create upstream refGene maf files
    cd /hive/data/genomes/micMur3/bed/multiz3way/downloads/multiz3way
    # bash script
#!/bin/sh
export geneTbl="ensGene"
for S in 1000 2000 5000
do
    echo "making upstream${S}.maf"
    featureBits micMur3 ${geneTbl}:upstream:${S} -fa=/dev/null -bed=stdout \
        | perl -wpe 's/_up[^\t]+/\t0/' | sort -k1,1 -k2,2n \
        | /cluster/bin/$MACHTYPE/mafFrags micMur3 multiz3way \
                stdin stdout \
                -orgs=/hive/data/genomes/micMur3/bed/multiz3way/species.list \
        | gzip -c > upstream${S}.${geneTbl}.maf.gz
    echo "done upstream${S}.${geneTbl}.maf.gz"
done
    #   real    6m0.388s

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

    # some other symlinks were already made above
    # verify the README.txt has note about upstream files, add if not there
    ln -s `pwd`/upstream*.gz `pwd`/README.txt \
        /usr/local/apache/htdocs-hgdownload/goldenPath/micMur3/multiz3way

#############################################################################
# wiki page for 3-way (DONE - 2018-06-15 - Hiram)
    mkdir /hive/users/hiram/bigWays/micMur3.3way
    cd /hive/users/hiram/bigWays
    echo "micMur3" > micMur3.3way/ordered.list
    awk '{print $1}' /hive/data/genomes/micMur3/bed/multiz3way/3way.distances.txt \
       >> micMur3.3way/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 micMur3.3way/ordered.list
    # dbDb.sh constructs micMur3.3way/MicMur3_3-way_conservation_alignment.html
    # may need to add new assembly references to srcReference.list and
    # urlReference.list
    ./dbDb.sh micMur3 3way
    # sizeStats.pl constructs micMur3.3way/MicMur3_3-way_Genome_size_statistics.html
    # this requires entries in coverage.list for new sequences
    ./sizeStats.pl micMur3 3way

    # defCheck.pl constructs MicMur3_3-way_conservation_lastz_parameters.html
    ./defCheck.pl micMur3 3way

    # this constructs the html pages in micMur3.3way/:
# -rw-rw-r-- 1 2325 Jun 15 15:38 MicMur3_3-way_conservation_alignment.html
# -rw-rw-r-- 1 3644 Jun 15 15:38 MicMur3_3-way_Genome_size_statistics.html
# -rw-rw-r-- 1 2716 Jun 15 15:38 MicMur3_3-way_conservation_lastz_parameters.html
    # add those pages to the genomewiki.  Their page names are the
    # names of the .html files without the .html:
#  MicMur3_3-way_conservation_alignment
#  MicMur3_3-way_Genome_size_statistics
#  MicMur3_3-way_conservation_lastz_parameters

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

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