#############################################################################
## 12way Multiz (DONE - 2020-02-26 - Hiram)
    ssh hgwdev
    mkdir /hive/data/genomes/danRer10/bed/multiz12way
    cd /hive/data/genomes/danRer10/bed/multiz12way

    # from the 218-way in the source tree, select out the 12 used here:
    /cluster/bin/phast/tree_doctor \
        --prune-all-but hg38,mm10,galGal5,xenTro9,latCha1,lepOcu1,calMil1,tetNig2,fr3,gasAcu1,oryLat2,danRer10 \
        /cluster/home/hiram/kent/src/hg/utils/phyloTrees/218way.nh \
           | sed -e 's/galGal5/galGal6/;' > danRer10.12way.nh.0
     ~/kent/src/hg/utils/phyloTrees/asciiTree.pl danRer10.12way.nh.0 \
       | sed -e 's/^/# /;
# ((((((hg38:0.145908,
#      mm10:0.356483):0.460153,
#     galGal6:0.559442):0.05,
#    xenTro9:0.347944):0.1,
#   latCha1:0.977944):0.111354,
#  (((((tetNig2:0.124159,
#      fr3:0.203847):0.19518,
#     oryLat2:0.48197):0.015,
#    gasAcu1:0.246413):0.27064,
#   danRer10:0.730752):0.143632,
#  lepOcu1:0.400000):0.326688):0.100000,
# calMil1:0.75);


    # using TreeGraph2 tree editor on the Mac, rearrange to get danRer10
    # at the top:

    #	what that looks like:
~/kent/src/hg/utils/phyloTrees/asciiTree.pl danRer10.12way.nh | sed -e 's/^/# /;'
# ((((danRer10:0.730752,
#    (gasAcu1:0.246413,
#    (oryLat2:0.48197,
#    (tetNig2:0.124159,
#    fr3:0.203847):0.19518):0.015):0.27064):0.143632,
#   lepOcu1:0.4):0.326688,
#  ((((hg38:0.145908,
#     mm10:0.356483):0.460153,
#    galGal6:0.559442):0.05,
#   xenTro9:0.347944):0.1,
#  latCha1:0.977944):0.111354):0.1,
# calMil1:0.75);

    # extract species list from that .nh file
    sed 's/[a-z][a-z]*_//g; s/:[0-9\.][0-9\.]*//g; s/;//; /^ *$/d' \
        danRer10.12way.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`" danRer10.12way.nh | sed -e 's/00*)/)/g; s/00*,/,/g' \
       | $HOME/kent/src/hg/utils/phyloTrees/asciiTree.pl /dev/stdin \
         | sed -e 's/__/_/g;' > danRer10.12way.commonNames.nh
    cat danRer10.12way.commonNames.nh | sed -e 's/^/# /;'
# ((((Zebrafish:0.730752,
#    (Stickleback:0.246413,
#    (Medaka:0.48197,
#    (Tetraodon:0.124159,
#    Fugu:0.203847):0.19518):0.015):0.27064):0.143632,
#   Spotted_gar:0.4):0.326688,
#  ((((Human:0.145908,
#     Mouse:0.356483):0.460153,
#    Chicken:0.559442):0.05,
#   X_tropicalis:0.347944):0.1,
#  Coelacanth:0.977944):0.111354):0.1,
# Elephant_shark:0.75);

#	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/danRer10_12way.png

    ~/kent/src/hg/utils/phyloTrees/asciiTree.pl danRer10.12way.nh > t.nh
    ~/kent/src/hg/utils/phyloTrees/scientificNames.sh t.nh \
       | $HOME/kent/src/hg/utils/phyloTrees/asciiTree.pl /dev/stdin \
          > danRer10.12way.scientificNames.nh
    cat danRer10.12way.scientificNames.nh | sed -e 's/^/# /;'
# ((((Danio_rerio:0.730752,
#    (Gasterosteus_aculeatus:0.246413,
#    (Oryzias_latipes:0.48197,
#    (Tetraodon_nigroviridis:0.124159,
#    Takifugu_rubripes:0.203847):0.19518):0.015):0.27064):0.143632,
#   Lepisosteus_oculatus:0.4):0.326688,
#  ((((Homo_sapiens:0.145908,
#     Mus_musculus:0.356483):0.460153,
#    Gallus_gallus:0.559442):0.05,
#   Xenopus_tropicalis:0.347944):0.1,
#  Latimeria_chalumnae:0.977944):0.111354):0.1,
# Callorhinchus_milii:0.75);

    /cluster/bin/phast/all_dists danRer10.12way.nh | grep danRer10 \
        | sed -e "s/danRer10.//" | sort -k2n > 12way.distances.txt
    #	Use this output to create the table below
    cat 12way.distances.txt | sed -e 's/^/# /;'
# gasAcu1       1.247805
# lepOcu1       1.274384
# tetNig2       1.335731
# fr3   1.415419
# oryLat2       1.498362
# xenTro9       1.760370
# galGal6       2.021868
# calMil1       2.051072
# hg38  2.068487
# mm10  2.279062
# latCha1       2.290370

    printf '#!/usr/bin/env perl

use strict;
use warnings;

open (FH, "<12way.distances.txt") or
        die "can not read 12way.distances.txt";

my $count = 0;
while (my $line = <FH>) {
    chomp $line;
    my ($D, $dist) = split('"'"'\\s+'"'"', $line);
    my $chain = "chain" . ucfirst($D);
    my $B="/hive/data/genomes/danRer10/bed/lastz.$D/fb.danRer10." .
        $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.danRer10/fb.${D}.chainDanRer10Link.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 (%%%% %%05.3f) (%%%% %%05.3f) - %%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

### type of chain: 'chain'
#       featureBits chainLink measures
#               chainLink
#  N distance  on danRer10  on other     other species
# 01  1.2478 (% 9.814) (% 27.557) - Stickleback gasAcu1
# 02  1.2744 (% 8.409) (% 11.294) - Spotted gar lepOcu1
# 03  1.3357 (% 6.063) (% 23.344) - Tetraodon tetNig2
# 04  1.4154 (% 7.080) (% 22.699) - Fugu fr3
# 05  1.4984 (% 9.640) (% 17.684) - Medaka oryLat2
# 06  1.7604 (% 6.731) (% 7.029) - X. tropicalis xenTro9
# 07  2.0219 (% 5.871) (% 6.171) - Chicken galGal6
# 08  2.0511 (% 5.599) (% 7.088) - Elephant shark calMil1
# 09  2.0685 (% 7.110) (% 3.357) - Human hg38
# 10  2.2791 (% 5.228) (% 2.769) - Mouse mm10
# 11  2.2904 (% 6.319) (% 4.504) - Coelacanth latCha1

# 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' \
	danRer10.12way.nh | xargs echo | sed 's/ //g; s/,/ /g' > tree.nh

    sed 's/[()]//g; s/,/ /g' tree.nh > species.list
    # danRer10 gasAcu1 oryLat2 tetNig2 fr3 lepOcu1 hg38 mm10 galGal6 xenTro9 latCha1 calMil1

    # survey N50 for each
    for db in `cat species.list`
do
n50.pl /hive/data/genomes/$db/chrom.sizes 2>&1 | head -4 | grep -v N50 
done
#       reading: /hive/data/genomes/danRer10/chrom.sizes
#       contig count: 1061, total size: 1371719383, one half size: 685859691
685335267       11      chr8    54191831
#       reading: /hive/data/genomes/gasAcu1/chrom.sizes
#       contig count: 23, total size: 463354448, one half size: 231677224
215092307       7       chrXIX  20240660
#       reading: /hive/data/genomes/oryLat2/chrom.sizes
#       contig count: 7189, total size: 869000216, one half size: 434500108
430162296       13      chr15   30000224
#       reading: /hive/data/genomes/tetNig2/chrom.sizes
#       contig count: 27, total size: 358618246, one half size: 179309123
167871265       4       chr3    15489435
#       reading: /hive/data/genomes/fr3/chrom.sizes
#       contig count: 6835, total size: 391484715, one half size: 195742357
188661948       13      chr22   11609757
#       reading: /hive/data/genomes/lepOcu1/chrom.sizes
#       contig count: 1925, total size: 945874548, one half size: 472937274
423108882       7       chrLG7  50812227
#       reading: /hive/data/genomes/hg38/chrom.sizes
#       contig count: 595, total size: 3257347282, one half size: 1628673641
1547391171      8       chrX    156040895
#       reading: /hive/data/genomes/mm10/chrom.sizes
#       contig count: 66, total size: 2730871774, one half size: 1365435887
1312176979      8       chr7    145441459
#       reading: /hive/data/genomes/galGal6/chrom.sizes
#       contig count: 464, total size: 1065365425, one half size: 532682712
458128853       3       chr3    110838418
#       reading: /hive/data/genomes/xenTro9/chrom.sizes
#       contig count: 6822, total size: 1440398454, one half size: 720199227
648724361       4       chr3    137218701
#       reading: /hive/data/genomes/latCha1/chrom.sizes
#       contig count: 22819, total size: 2860591921, one half size: 1430295960
1429463522      829     JH127390        925337
#       reading: /hive/data/genomes/calMil1/chrom.sizes
#       contig count: 21204, total size: 974498586, one half size: 487249293
484739066       59      KI635913        4564766

    #	bash shell syntax here ...
    cd /hive/data/genomes/danRer10/bed/multiz12way
    export H=/hive/data/genomes/danRer10/bed
    mkdir mafLinks
    # these are all distant assemblies, can use ordinary net:
    for G in gasAcu1 oryLat2 tetNig2 fr3 lepOcu1 hg38 mm10 galGal6 \
	xenTro9 latCha1 calMil1
    do
      mkdir mafLinks/$G
      echo ln -s ${H}/lastz.$G/mafNet/danRer10.${G}.net.maf.gz ./mafLinks/$G
      ln -s ${H}/lastz.$G/mafNet/danRer10.${G}.net.maf.gz ./mafLinks/$G
    done

    # verify the symLinks are good:
    ls -ogrtL mafLinks/*/* | sed -e 's/^/# /; s/-rw-rw-r-- 1//;'
#  66991086 Feb  9  2015 mafLinks/hg38/danRer10.hg38.net.maf.gz
#  50189830 Sep 18  2015 mafLinks/mm10/danRer10.mm10.net.maf.gz
#  60631047 Feb  9  2017 mafLinks/tetNig2/danRer10.tetNig2.net.maf.gz
#  70106431 Feb  9  2017 mafLinks/fr3/danRer10.fr3.net.maf.gz
#  95760363 Feb  9  2017 mafLinks/oryLat2/danRer10.oryLat2.net.maf.gz
#  95378303 Feb 10  2017 mafLinks/gasAcu1/danRer10.gasAcu1.net.maf.gz
#  87196632 Feb 25 11:25 mafLinks/lepOcu1/danRer10.lepOcu1.net.maf.gz
#  63376503 Feb 25 12:15 mafLinks/latCha1/danRer10.latCha1.net.maf.gz
#  59790355 Feb 25 16:31 mafLinks/galGal6/danRer10.galGal6.net.maf.gz
#  63181229 Feb 25 16:37 mafLinks/xenTro9/danRer10.xenTro9.net.maf.gz
#  55318165 Feb 25 17:21 mafLinks/calMil1/danRer10.calMil1.net.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/danRer10/bed/multiz12way/mafSplit
    cd /hive/data/genomes/danRer10/bed/multiz12way/mafSplit
    time for D in `sed -e "s/danRer10 //" ../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    0m35.938s

    # 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
    # 2791
    find . -type f | grep ".maf$" | xargs -L 1 basename | sort -u > maf.list
    wc -l maf.list
    # 256maf.list

    mkdir /hive/data/genomes/danRer10/bed/multiz12way/splitRun
    cd /hive/data/genomes/danRer10/bed/multiz12way/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 = danRer10
set c = $1
set result = $2
set run = `/bin/pwd`
set tmp = /dev/shm/$db/multiz.$c
set pairs = /hive/data/genomes/danRer10/bed/multiz12way/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 $(file1) {check out line+ /hive/data/genomes/danRer10/bed/multiz12way/splitRun/maf/$(root1).maf}
#ENDLOOP
' > template

    ln -s ../../mafSplit/maf.list maf.list
    ssh ku
    cd /hive/data/genomes/danRer10/bed/multiz12way/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:      27124s     452.06m     7.53h    0.31d  0.001 y
# IO & Wait Time:                   701s      11.69m     0.19h    0.01d  0.000 y
# Average job time:                 109s       1.81m     0.03h    0.00d
# Longest finished job:            2174s      36.23m     0.60h    0.03d
# Submission to last job:          2267s      37.78m     0.63h    0.03d

    # combine into one file  (the 1>&2 redirect sends the echo to stderr)
    cd /hive/data/genomes/danRer10/bed/multiz12way
    head -1 splitRun/maf/217.maf > multiz12way.maf
    time for F in splitRun/maf/*.maf
do
    echo "${F}" 1>&2
    egrep -v "^#" ${F}
done >> multiz12way.maf
    # real    1m12.634s

    tail -1 splitRun/maf/217.maf >> multiz12way.maf
# -rw-rw-r--  1 2931187404 Mar  9 11:57 multiz12way.maf

    # Load into database
    ssh hgwdev
    cd /hive/data/genomes/danRer10/bed/multiz12way
    mkdir /gbdb/danRer10/multiz12way
    ln -s `pwd`/multiz12way.maf /gbdb/danRer10/multiz12way
    cd /dev/shm
    time hgLoadMaf danRer10 multiz12way
# Loaded 4609310 mafs in 1 files from /gbdb/danRer10/multiz12way
# real    0m44.124s

    time hgLoadMafSummary -verbose=2 -minSize=30000 \
	-mergeGap=1500 -maxSize=200000 danRer10 multiz12waySummary \
	/gbdb/danRer10/multiz12way/multiz12way.maf
# Created 1343139 summary blocks from 20786747 components and 4609310 mafs from /gbdb/danRer10/multiz12way/multiz12way.maf
# real    0m50.372s

# -rw-rw-r--   1  225415432 Mar  9 11:58 multiz12way.tab
# -rw-rw-r--   1   60694329 Mar  9 12:01 multiz12waySummary.tab

    wc -l multiz12way*.tab
#  4609310 multiz12way.tab
#  1343139 multiz12waySummary.tab

    rm multiz12way*.tab

##############################################################################
# GAP ANNOTATE multiz12way MAF AND LOAD TABLES (DONE - 2020-03-09 - 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/danRer10/bed/multiz12way/anno/mafSplit
    cd /hive/data/genomes/danRer10/bed/multiz12way/anno/mafSplit

    time mafSplit -outDirDepth=2 -byTarget -useFullSequenceName \
        /dev/null . ../../multiz12way.maf
    #   real    0m43.493s

    find . -type f | wc -l
    #   1012

    # check for N.bed files everywhere:
    cd /hive/data/genomes/danRer10/bed/multiz12way/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/danRer10/bed/multiz12way/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/danRer10/bed/multiz12way/anno
    mkdir result
    # there was a stray 'result/mafSplit' directory ending up in this, avoid
    # it via the grep -v mafSplit
    find ./mafSplit -type d | sed -e 's#./mafSplit/##' | grep -v mafSplit \
       | while read D
do
    echo mkdir -p result/${D}
    mkdir -p result/${D}
done
    printf '#LOOP
mafAddIRows -nBeds=nBeds mafSplit/$(path1) /hive/data/genomes/danRer10/danRer10.2bit {check out exists+ result/$(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: 1012 of 1012 jobs
# CPU time in finished jobs:        427s       7.12m     0.12h    0.00d  0.000 y
# IO & Wait Time:                  2676s      44.59m     0.74h    0.03d  0.000 y
# Average job time:                   3s       0.05m     0.00h    0.00d
# Longest finished job:              14s       0.23m     0.00h    0.00d
# Submission to last job:           112s       1.87m     0.03h    0.00d

    # 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/0/2/chrUn_KN149893v1.maf > danRer10.12way.maf
    time find ./result -type f | while read F
do
    echo "${F}" 1>&2
    grep -h -v "^#" ${F}
done >> danRer10.12way.maf
    # real    1m22.625s

    #	these maf files do not have the end marker, this does nothing:
    #	tail -q -n 1 result/0/2/chrUn_KN149893v1.maf >> danRer10.12way.maf
    # How about an official end marker:
    echo "##eof maf" >> danRer10.12way.maf
    ls -og
# -rw-rw-r--  1 5791972643 Mar  9 12:13 danRer10.12way.maf

    du -hsc danRer10.12way.maf ../*.maf
    # 5.4G    danRer10.12way.maf
    # 2.8G    ../multiz12way.maf

    # construct symlinks to get the individual maf files into gbdb:
    rm /gbdb/danRer10/multiz12way/multiz12way.maf   # remove previous results
    ln -s `pwd`/danRer10.12way.maf /gbdb/danRer10/multiz12way/multiz12way.maf

    # Load into database
    cd /dev/shm
    time hgLoadMaf -pathPrefix=/gbdb/danRer10/multiz12way danRer10 multiz12way
    # Loaded 4981463 mafs in 1 files from /gbdb/danRer10/multiz12way
    # real    1m4.890s

    time hgLoadMafSummary -verbose=2 -minSize=30000 \
	-mergeGap=1500 -maxSize=200000 danRer10 multiz12waySummary \
        /gbdb/danRer10/multiz12way/multiz12way.maf
# Created 1343139 summary blocks from 20786747 components and 4981463 mafs from /gbdb/danRer10/multiz12way/multiz12way.maf
# real    0m59.393s

# -rw-rw-r--   1  244520097 Mar  9 12:14 multiz12way.tab
# -rw-rw-r--   1   63380607 Mar  9 12:18 multiz12waySummary.tab

    rm multiz12way*.tab

######################################################################
# multiz12way MAF FRAMES (DONE - 2020-03-09 - Hiram)
    ssh hgwdev
    mkdir /hive/data/genomes/danRer10/bed/multiz12way/frames
    cd /hive/data/genomes/danRer10/bed/multiz12way/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
# danRer10: ensGene: 62895, mgcGenes: 16938, ncbiRefSeq: 56101, refGene: 16812, xenoRefGene: 136995, Mrnas: 1535827
# gasAcu1: ensGene: 29245, refGene: 65, xenoRefGene: 291425, Mrnas: 280208
# oryLat2: ensGene: 25434, refGene: 903, xenoRefGene: 262904, Mrnas: 669014
# tetNig2: ensGene: 24078, xenoRefGene: 252452, Mrnas: 100127
# fr3: ensGene: 29241, ncbiRefSeq: 33131, refGene: 655, Mrnas: 335149
# lepOcu1: ensGene: 27887, Mrnas: 87
# hg38: ensGene: 208239, knownGene: 247541, mgcGenes: 36638, ncbiRefSeq: 166923, refGene: 85561, xenoRefGene: 198240, Mrnas: 11716560
# mm10: ensGene: 103734, knownGene: 142446, mgcGenes: 27606, ncbiRefSeq: 106520, refGene: 44703, xenoRefGene: 190199, Mrnas: 5493887
# galGal6: ensGene: 39288, ncbiRefSeq: 62183, refGene: 7482, xenoRefGene: 149238, Mrnas: 639553
# xenTro9: ensGene: 56323, ncbiRefSeq: 43724, refGene: 8806, xenoRefGene: 161423, Mrnas: 1298807
# latCha1: ensGene: 26660, ncbiRefSeq: 40763, xenoRefGene: 427419, Mrnas: 86
# calMil1: ensGene: 49990, ncbiRefSeq: 30682, xenoRefGene: 401231, Mrnas: 146276

real    1m57.753s

    # use knownGene for hg38 and mm10
    # everything else use ensGene
 
    mkdir genes

    #   1. knownGene: hg38 and 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: 22100 failed: 0
#  mm10: checked: 22026 failed: 0

    #   2. ensGene: danRer10 gasAcu1 oryLat2 tetNig2 fr3 lepOcu1
    #               galGal6 xenTro9 latCha1 calMil1
    for DB in danRer10 gasAcu1 oryLat2 tetNig2 fr3 lepOcu1 galGal6 xenTro9 latCha1 calMil1
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
# danRer10: checked: 25259 failed: 0
# gasAcu1: checked: 20631 failed: 0
# oryLat2: checked: 19586 failed: 0
# tetNig2: checked: 19539 failed: 0
# fr3: checked: 20017 failed: 0
# lepOcu1: checked: 18252 failed: 0
# galGal6: checked: 16651 failed: 0
# xenTro9: checked: 19819 failed: 0
# latCha1: checked: 19539 failed: 0
# calMil1: checked: 19188 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/calMil1.gp.gz: 19188
# genes/danRer10.gp.gz: 25259
# genes/fr3.gp.gz: 20017
# genes/galGal6.gp.gz: 16651
# genes/gasAcu1.gp.gz: 20631
# genes/hg38.gp.gz: 22082
# genes/latCha1.gp.gz: 19539
# genes/lepOcu1.gp.gz: 18252
# genes/mm10.gp.gz: 22026
# genes/oryLat2.gp.gz: 19586
# genes/tetNig2.gp.gz: 19539
# genes/xenTro9.gp.gz: 19819

    time (cat ../anno/danRer10.12way.maf \
	| genePredToMafFrames danRer10 stdin stdout \
          `cat ../species.list.txt | xargs echo \
            | sed -e "s#\([a-zA-Z0-9]*\)#\1 genes/\1.gp.gz#g;"` \
		| gzip > multiz12wayFrames.bed.gz)
    # real    1m29.321s

    # verify there are frames on everything, should be 4 species:
    zcat multiz12wayFrames.bed.gz | awk '{print $4}' | sort | uniq -c \
       | sed -e 's/^/# /;'
#  421479 calMil1
#  235622 danRer10
#  413788 fr3
#  451258 galGal6
#  420945 gasAcu1
#  415541 hg38
#  432488 latCha1
#  460409 lepOcu1
#  426202 mm10
#  401711 oryLat2
#  383412 tetNig2
#  433380 xenTro9

    #   load the resulting file
    ssh hgwdev
    cd /hive/data/genomes/danRer10/bed/multiz12way/frames
    time hgLoadMafFrames danRer10 multiz12wayFrames multiz12wayFrames.bed.gz
    #   real    0m10.853s

    time featureBits -countGaps danRer10 multiz12wayFrames
    # 54994220 bases of 1371719383 (4.009%) in intersection
    # real    0m23.424s

    #   enable the trackDb entries:
# frames multiz12wayFrames
# irows on
    #   appears to work OK

#########################################################################
# Phylogenetic tree from 12way (DONE - 2020-03-09 - Hiram)
    mkdir /hive/data/genomes/danRer10/bed/multiz12way/4d
    cd /hive/data/genomes/danRer10/bed/multiz12way/4d

    # using the ensGene
    hgsql -N -e "select name,chrom,strand,txStart,txEnd,cdsStart,cdsEnd,exonCount,exonStarts,exonEnds from refGene" danRer10 \
      | genePredSingleCover stdin stdout > danRer10.ensGeneNR.gp
    genePredCheck -db=danRer10 danRer10.ensGeneNR.gp
    # checked: 14875 failed: 0

    # the annotated maf is:
    og ../anno/danRer10.12way.maf
# -rw-rw-r-- 1 5791972643 Mar  9 12:13 ../anno/danRer10.12way.maf

    mkdir annoSplit
    cd annoSplit
    time mafSplit -verbose=2 -outDirDepth=2 -byTarget -useFullSequenceName \
	/dev/null . ../../anno/danRer10.12way.maf
    # real    1m30.335s

    find . -type f | wc -l
    #   1012
    ssh ku
    mkdir /hive/data/genomes/danRer10/bed/multiz12way/4d/run
    cd /hive/data/genomes/danRer10/bed/multiz12way/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
    cat << '_EOF_' > 4d.csh
#!/bin/csh -fex
set PHASTBIN = /cluster/bin/phast.build/cornellCVS/phast.2010-12-30/bin
set GP = danRer10.ensGeneNR.gp

set r = "/hive/data/genomes/danRer10/bed/multiz12way"
set c = $1
set infile = $r/4d/$2
set outDir = $r/4d/$3
set outfile = $r/4d/run/$4
/bin/mkdir -p $outDir
cd /dev/shm
/bin/awk -v C=$c '$2 == C {print}' $r/4d/$GP | sed -e "s/\t$c\t/\tdanRer10.$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
_EOF_
#########################################
    chmod +x 4d.csh

    find ../annoSplit -type f | sed -e "s#../annoSplit/##" > maf.list
    wc -l maf.list
# 1012 maf.list

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

    mkdir ../mfa
    gensub2 maf.list single template jobList
    para create jobList
    para try ... check
    para time
# Completed: 1012 of 1012 jobs
# CPU time in finished jobs:        406s       6.77m     0.11h    0.00d  0.000 y
# IO & Wait Time:                  2465s      41.08m     0.68h    0.03d  0.000 y
# Average job time:                   3s       0.05m     0.00h    0.00d
# Longest finished job:              21s       0.35m     0.01h    0.00d
# Submission to last job:           107s       1.78m     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/danRer10/bed/multiz12way/4d
    # remove the broken empty files, size 0 and size 1:
    find ./mfa -type f -size 0 | xargs rm -f
    # sometimes this doesn't work, don't know why, it isn't safe, it
    # outputs files that are larger than size 1:
    ### XXX 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
    #             140     980    8396

    # 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    0m1.369s

    # check they are all in there:
    grep "^>" 4d.all.mfa | sed -e 's/^/# /;'
# >danRer10
# >gasAcu1
# >oryLat2
# >tetNig2
# >fr3
# >lepOcu1
# >hg38
# >mm10
# >galGal6
# >xenTro9
# >latCha1
# >calMil1

    sed 's/[a-z][a-z]*_//g; s/:[0-9\.][0-9\.]*//g; s/;//; /^ *$/d' \
	../danRer10.12way.nh | xargs echo | sed -e 's/ //g' > tree_commas.nh
    # tree_commas.nh looks like:
    # ((((danRer10,(gasAcu1,(oryLat2,(tetNig2,fr3)))),lepOcu1),((((hg38,mm10),galGal6),xenTro9),latCha1)),calMil1)


    # 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    7m11.213s

    mv phyloFit.mod all.mod

    grep TREE all.mod
# TREE: ((((danRer10:0.611884,(gasAcu1:0.328166,(oryLat2:0.456031,
# (tetNig2:0.205925,fr3:0.188605):0.228366):0.00373574):0.355398):0.157683,
# lepOcu1:0.563099):0.19044,((((hg38:0.183526,mm10:0.265304):0.337095,
# galGal6:0.450474):0.106427,xenTro9:0.776415):0.0616915,
# latCha1:0.561233):0.0520656):0.328637,calMil1:0.328637);


    # compare these calculated lengths to the tree extracted from 191way:
    grep TREE all.mod | sed -e 's/TREE: //' \
       | /cluster/bin/phast/all_dists /dev/stdin | grep danRer10 \
          | sed -e "s/danRer10.//;"  | sort > new.dists
    /cluster/bin/phast/all_dists ../danRer10.12way.nh | grep danRer10 \
        | sed -e "s/danRer10.//;" | sort > old.dists
     # printing out the 'new', the 'old' the 'difference' and percent difference
    join new.dists old.dists | awk '{
  printf "#\t%s\t%8.5f\t%8.5f\t%8.5f\t%8.5f\n", $1, $2, $3, $2-$3, 100*($2-$3)/$3 }' \
      | sort -k3n
#       gasAcu1  1.29545         1.24781         0.04764         3.81814
#       lepOcu1  1.33267         1.27438         0.05828         4.57335
#       fr3      1.38799         1.41542        -0.02743        -1.93794
#       tetNig2  1.40531         1.33573         0.06958         5.20898
#       oryLat2  1.42705         1.49836        -0.07131        -4.75940
#       latCha1  1.57331         2.29037        -0.71706        -31.30778
#       calMil1  1.61728         2.05107        -0.43379        -21.14948
#       galGal6  1.63067         2.02187        -0.39120        -19.34859
#       hg38     1.70081         2.06849        -0.36768        -17.77507
#       mm10     1.78259         2.27906        -0.49647        -21.78405
#       xenTro9  1.85018         1.76037         0.08981         5.10171

#########################################################################
# phastCons 12way (DONE - 2020-03-09 - Hiram)
    # split 12way mafs into 10M chunks and generate sufficient statistics
    # files for # phastCons
    ssh ku
    mkdir -p /hive/data/genomes/danRer10/bed/multiz12way/cons/SS
    cd /hive/data/genomes/danRer10/bed/multiz12way/cons/SS
    mkdir result done

    printf '#!/bin/csh -ef
set d = $1
set c = $2
set doneDir = done/$d
set MAF = /hive/data/genomes/danRer10/bed/multiz12way/anno/result/$d/$c.maf
set WINDOWS = /hive/data/genomes/danRer10/bed/multiz12way/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
# 1012 maf.list

    ssh ku
    cd /hive/data/genomes/danRer10/bed/multiz12way/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: 1012 of 1012 jobs
# CPU time in finished jobs:        752s      12.53m     0.21h    0.01d  0.000 y
# IO & Wait Time:                  2558s      42.64m     0.71h    0.03d  0.000 y
# Average job time:                   3s       0.05m     0.00h    0.00d
# Longest finished job:              50s       0.83m     0.01h    0.00d
# Submission to last job:            78s       1.30m     0.02h    0.00d

    find ./result -type f | wc -l
    # 988

    # 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/danRer10/bed/multiz12way/cons/run.cons
    cd /hive/data/genomes/danRer10/bed/multiz12way/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/danRer10/bed/multiz12way/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
    #	988 ss.list

    # Create parasol batch and run it
    # run for all species
    mkdir /hive/data/genomes/danRer10/bed/multiz12way/cons/all
    cd /hive/data/genomes/danRer10/bed/multiz12way/cons/all
    #	Using the .mod tree
    cp -p ../../4d/all.mod ./all.mod

    gensub2 ../run.cons/ss.list single ../run.cons/template jobList
    para -ram=32g create jobList
    para try ... check ...
    para push
# Completed: 988 of 988 jobs
# CPU time in finished jobs:       2515s      41.91m     0.70h    0.03d  0.000 y
# IO & Wait Time:                  6393s     106.56m     1.78h    0.07d  0.000 y
# Average job time:                   9s       0.15m     0.00h    0.00d
# Longest finished job:              30s       0.50m     0.01h    0.00d
# Submission to last job:            51s       0.85m     0.01h    0.00d

    # create Most Conserved track
    cd /hive/data/genomes/danRer10/bed/multiz12way/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    0m32.669s

    time /cluster/bin/scripts/lodToBedScore tmpMostConserved.bed \
         > mostConserved.bed
    # real    0m8.310s

    # -rw-rw-r--  1 51368105 Mar  9 15:30 mostConserved.bed

    # load into database
    ssh hgwdev
    cd /hive/data/genomes/danRer10/bed/multiz12way/cons/all
    time hgLoadBed danRer10 phastConsElements12way mostConserved.bed
    # Read 1488448 elements of size 5 from mostConserved.bed
    # real    0m8.385s

    # on human we often try for 6% 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 46 --target-coverage 0.3
    time featureBits danRer10 -enrichment refGene:cds phastConsElements12way
# refGene:cds 1.564%, phastConsElements12way 17.638%, both 1.288%,
#      cover 82.38%, enrich 4.67x
#  real    0m9.863s

    # Create merged posterier probability file and wiggle track data files
    cd /hive/data/genomes/danRer10/bed/multiz12way/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/phastCons12way.wigFix.gz)
    # real    3m10.237s

# -rw-rw-r-- 1 449679749 Mar  9 15:35 phastCons12way.wigFix.gz


    # check integrity of data with wigToBigWig
    time (zcat downloads/phastCons12way.wigFix.gz \
	| wigToBigWig -verbose=2 stdin /hive/data/genomes/danRer10/chrom.sizes \
	    phastCons12way.bw) > bigWig.log 2>&1
    egrep "real|VmPeak" bigWig.log
# pid=62255: VmPeak:     3407948 kB
# real    2m59.768s

    bigWigInfo phastCons12way.bw | sed -e 's/^/# /;'
# version: 4
# isCompressed: yes
# isSwapped: 0
# primaryDataSize: 721,160,862
# primaryIndexSize: 17,722,396
# zoomLevels: 10
# chromCount: 867
# basesCovered: 311,564,898
# mean: 0.714476
# min: 0.000000
# max: 1.000000
# std: 0.348523

    #	encode those files into wiggle data
    time (zcat downloads/phastCons12way.wigFix.gz \
	| wigEncode stdin phastCons12way.wig phastCons12way.wib)
    # Converted stdin, upper limit 1.00, lower limit 0.00
    #  real    1m16.871s


    du -hsc *.wi?
    # 298M    phastCons12way.wib
    #  53M     phastCons12way.wig

    # Load gbdb and database with wiggle.
    ln -s `pwd`/phastCons12way.wib /gbdb/danRer10/multiz12way/phastCons12way.wib
    time hgLoadWiggle -pathPrefix=/gbdb/danRer10/multiz12way \
	danRer10 phastCons12way phastCons12way.wig
    #   real    0m3.628s

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

    wigTableStats.sh danRer10 phastCons12way
# db.table               min max mean       count sumData
# danRer10.phastCons12way 0 1 0.714476 311564898 2.22606e+08
#     stdDev  viewLimits
#    0.348523 viewLimits=0:1

    #  Create histogram to get an overview of all the data
    #  Do not mix stderr with the output, it gets confused
    time hgWiggle -doHistogram -db=danRer10 \
	-hBinSize=0.001 -hBinCount=1000 -hMinVal=0.0 -verbose=2 \
	    phastCons12way > danRer10.phastCons12way.histogram.data 2> t.err
    #	real    0m16.475s

    # the Y axis range:
    grep -v "^#" danRer10.phastCons12way.histogram.data \
      | awk '{print $5}'  | ave stdin | sed -e 's/^/# /;'
# Q1 0.000172
# median 0.000255
# Q3 0.000602
# average 0.001000
# min 0.000007
# max 0.093661
# count 1000
# total 1.000006
# standard deviation 0.004616

    #	create plot of histogram:

    # updated for new gnuplot on hgwdev 2018-11-26 (can't get font to change)
    printf 'set terminal pngcairo size 1000,600 background "#000000" font "/usr/share/fonts/default/Type1/n022004l.pfb"
set output "danRer10.phastCons12way.histo.png"
set size 1.0, 1.0
set style line 1 lt 2 lc rgb "#ff88ff" lw 2
set style line 2 lt 2 lc rgb "#66ff66" lw 2
set style line 3 lt 2 lc rgb "#ffff00" lw 2
set style line 4 lt 2 lc rgb "#ffffff" lw 2
set border lc rgb "#ffff00"
set key left box ls 3
set key tc variable
set grid noxtics
set y2tics
set grid ytics ls 4
set title " Rat/danRer10 Histogram phastCons12way track" \
    tc rgb "#ffffff"
set xlabel " phastCons12way score" tc rgb "#ffffff"
set ylabel " Relative Frequency" tc rgb "#ff88ff"
set y2label " Cumulative Relative Frequency (CRF)" tc rgb "#66ff66"
set y2range [0:1]
set yrange [0:0.1]

plot "danRer10.phastCons12way.histogram.data" using 2:5 title " RelFreq" with impulses ls 1, \
        "danRer10.phastCons12way.histogram.data" using 2:7 axes x1y2 title " CRF" with lines ls 2
' | gnuplot

    display danRer10.phastCons12way.histo.png &

#########################################################################
# phyloP for 12way (DONE - 2020-03-18 - Hiram)
    # run phyloP with score=LRT
    ssh ku
    mkdir /cluster/data/danRer10/bed/multiz12way/consPhyloP
    cd /cluster/data/danRer10/bed/multiz12way/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}'
    #	0.557
    /cluster/bin/phast.build/cornellCVS/phast.2010-12-30/bin/modFreqs \
	../../4d/all.mod 0.557 > all.mod
    # verify, the BACKGROUND should now be paired up:
    grep BACK all.mod
    #   BACKGROUND: 0.208000 0.292000 0.292000 0.208000 

    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/danRer10/bed/multiz12way/consPhyloP
set tmp = $cons/tmp/$grp/$f
/bin/rm -fr $tmp
/bin/mkdir -p $tmp
set ssSrc = "/hive/data/genomes/danRer10/bed/multiz12way/cons/SS/result/$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
    #	988 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/danRer10/bed/multiz12way/consPhyloP/all
    cd /hive/data/genomes/danRer10/bed/multiz12way/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=63 push
    para time > run.time
# Completed: 988 of 988 jobs
# CPU time in finished jobs:      18582s     309.71m     5.16h    0.22d  0.001 y
# IO & Wait Time:                  6554s     109.23m     1.82h    0.08d  0.000 y
# Average job time:                  25s       0.42m     0.01h    0.00d
# Longest finished job:             254s       4.23m     0.07h    0.00d
# Submission to last job:           486s       8.10m     0.14h    0.01d

    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/phyloP12way.wigFix.gz)
    #   real    3m22.175s

    # check integrity of data with wigToBigWig
    time (zcat downloads/phyloP12way.wigFix.gz \
	| wigToBigWig -verbose=2 stdin /hive/data/genomes/danRer10/chrom.sizes \
	phyloP12way.bw) > bigWig.log 2>&1
    egrep "real|VmPeak" bigWig.log
# pid=162963: VmPeak:    3407948 kB
# real    2m54.795s

    bigWigInfo phyloP12way.bw | sed -e 's/^/# /;'
# version: 4
# isCompressed: yes
# isSwapped: 0
# primaryDataSize: 580,443,197
# primaryIndexSize: 17,722,396
# zoomLevels: 10
# chromCount: 867
# basesCovered: 311,564,898
# mean: 0.549000
# min: -2.566000
# max: 3.744000
# std: 0.881331

    #	encode those files into wiggle data
    time (zcat downloads/phyloP12way.wigFix.gz \
	| wigEncode stdin phyloP12way.wig phyloP12way.wib)
# Converted stdin, upper limit 3.74, lower limit -2.57
# real    1m19.223s

    du -hsc *.wi?
    # 298M    phyloP12way.wib
    # 53M     phyloP12way.wig

    # Load gbdb and database with wiggle.
    ln -s `pwd`/phyloP12way.wib /gbdb/danRer10/multiz12way/phyloP12way.wib
    time hgLoadWiggle -pathPrefix=/gbdb/danRer10/multiz12way danRer10 \
	phyloP12way phyloP12way.wig
    # real    0m3.914s

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

    wigTableStats.sh danRer10 phyloP12way
# db.table              min max mean count sumData
# danRer10.phyloP12way     -2.566 3.744 0.549 311564898 1.71049e+08
#       stdDev viewLimits
#     0.881332 viewLimits=-2.566:3.744

    #	that range is: 2.566+3.744 = 6.310 for hBinSize=0.00631

    #  Create histogram to get an overview of all the data
    #  do NOT mix up stderr with the output, it interferes with the output
    time (hgWiggle -doHistogram \
	-hBinSize=0.00631 -hBinCount=1000 -hMinVal=-2.566 -verbose=2 \
	    -db=danRer10 phyloP12way) > danRer10.phyloP12way.histogram.data \
               2> t.err
    # real    0m14.661s

    # find the Y range for the 2:6 graph
    grep "^[0-9]" danRer10.phyloP12way.histogram.data | ave -col=5 stdin \
      | sed -e 's/^/# /;'
# Q1 0.000046
# median 0.000237
# Q3 0.001022
# average 0.001013
# min 0.000000
# max 0.023355
# count 987
# total 0.999989
# standard deviation 0.002159

    # find the X range for the 2:6 graph
    grep "^[0-9]" danRer10.phyloP12way.histogram.data | ave -col=2 stdin \
      | sed -e 's/^/# /;'
# Q1 -0.985345
# median 0.570070
# Q3 2.125485
# average 0.570096
# min -2.566000
# max 3.744000
# count 987
# total 562.684331
# standard deviation 1.798949

    #	create plot of histogram:
    # updated for new gnuplot on hgwdev 2018-11-26 (can't get font to change)
    printf 'set terminal pngcairo size 1000,600 background "#000000" font "/usr/share/fonts/default/Type1/n022004l.pfb"
set output "danRer10.phyloP12way.histo.png"
set size 1.0, 1.0
set style line 1 lt 2 lc rgb "#ff88ff" lw 2
set style line 2 lt 2 lc rgb "#66ff66" lw 2
set style line 3 lt 2 lc rgb "#ffff00" lw 2
set style line 4 lt 2 lc rgb "#ffffff" lw 2
set border lc rgb "#ffff00"
set key left box ls 3
set key tc variable
set grid noxtics
set y2tics
set grid ytics ls 4
set title " Rat/danRer10 Histogram phyloP12way track" \
    tc rgb "#ffffff"
set xlabel " phyloP12way score" tc rgb "#ffffff"
set ylabel " Relative Frequency" tc rgb "#ff88ff"
set y2label " Cumulative Relative Frequency (CRF)" tc rgb "#66ff66"
set y2range [0:1]
set xrange [-2.6:3.8]
set yrange [0:0.03]

plot "danRer10.phyloP12way.histogram.data" using 2:5 title " RelFreq" with impulses ls 1, \
        "danRer10.phyloP12way.histogram.data" using 2:7 axes x1y2 title " CRF" with lines ls 2
' | gnuplot

# set xrange [-4.4:0.97]

    display danRer10.phyloP12way.histo.png &

    # appears to have an odd hole in the data near X=0 ?

#############################################################################
# hgPal downloads (DONE - 2020-03-18 - Hiram)
#   FASTA from 12way for refGene

    ssh hgwdev
    screen -S danRer10HgPal
    mkdir /hive/data/genomes/danRer10/bed/multiz12way/pal
    cd /hive/data/genomes/danRer10/bed/multiz12way/pal
    cat ../species.list | tr '[ ]' '[\n]' > order.list

    # this for loop takes about 2.6 hours on this large count contig assembly
    export mz=multiz12way
    export gp=ensGene
    export db=danRer10
    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    0m0.680s

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

    chmod +x  $gp.jobs 

    time (./$gp.jobs) > $gp.jobs.log 2>&1 &
    # real    8m29.976s

    export mz=multiz12way
    export gp=ensGene
    time find ./exonAA -type f | grep exonAA.fa.gz | xargs zcat \
     | gzip -c > $gp.$mz.exonAA.fa.gz
    #  real    0m20.579s

    time find ./exonNuc -type f | grep exonNuc.fa.gz | xargs zcat \
     | gzip -c > $gp.$mz.exonNuc.fa.gz
    #  real    1m53.293s

# -rw-rw-r-- 1 123892644 Mar 18 15:03 ensGene.multiz12way.exonAA.fa.gz
# -rw-rw-r-- 1 234280591 Mar 18 15:06 ensGene.multiz12way.exonNuc.fa.gz

    export mz=multiz12way
    export gp=ensGene
    export db=danRer10
    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 12way (DONE - 2020-03-19 - Hiram)
    mkdir /usr/local/apache/htdocs-hgdownload/goldenPath/danRer10/multiz12way
    mkdir /usr/local/apache/htdocs-hgdownload/goldenPath/danRer10/phastCons12way
    mkdir /usr/local/apache/htdocs-hgdownload/goldenPath/danRer10/phyloP12way
    mkdir /hive/data/genomes/danRer10/bed/multiz12way/downloads
    cd /hive/data/genomes/danRer10/bed/multiz12way/downloads
    mkdir multiz12way phastCons12way phyloP12way
    cd multiz12way
    time cp -p ../../anno/danRer10.12way.maf .
    #   real    0m9.852s

    # -rw-rw-r-- 1 5791972643 Mar  9 12:13 danRer10.12way.maf

    du -hsc *
    #  5.4G    danRer10.12way.maf

    time gzip *.maf
    #   10 to 20 minutes

    # -rw-rw-r-- 1 1185287804 Mar  9 12:13 danRer10.12way.maf.gz

    du -hsc *.maf.gz ../../anno/*.maf
# 1.2G    danRer10.12way.maf.gz
# 5.4G    ../../anno/danRer10.12way.maf

    grep TREE ../../4d/all.mod | awk '{print $NF}' \
      | ~/kent/src/hg/utils/phyloTrees/asciiTree.pl /dev/stdin \
         > danRer10.12way.nh
    ln -s ../../danRer10.12way.commonNames.nh .
    ln -s ../../danRer10.12way.scientificNames.nh .
    time md5sum *.nh *.maf.gz > md5sum.txt
    #   real    0m3.346s

    ln -s `pwd`/* \
        /usr/local/apache/htdocs-hgdownload/goldenPath/danRer10/multiz12way

    # obtain the README.txt from galGal6/multiz77way and update for this
    #   situation

    # to get the species table list for the README:
    for F in `cat ../../species.list`
do
      hgsql -N -e "select organism,scientificName,description from dbDb where name=\"$F\";" hgcentraltest
done | cat

Zebrafish       Danio rerio     Sep. 2014 (GRCz10/danRer10) (reference)

Stickleback     Gasterosteus aculeatus  Feb. 2006 (Broad/gasAcu1)
Medaka  Oryzias latipes Oct. 2005 (NIG/UT MEDAKA1/oryLat2)
Tetraodon       Tetraodon nigroviridis  Mar. 2007 (Genoscope 8.0/tetNig2)
Fugu    Takifugu rubripes       Oct. 2011 (FUGU5/fr3)
Spotted gar     Lepisosteus oculatus    Dec 2011 (LepOcu1/lepOcu1)
Human   Homo sapiens    Dec. 2013 (GRCh38/hg38)
Mouse   Mus musculus    Dec. 2011 (GRCm38/mm10)
Chicken Gallus gallus   Mar. 2018 (GRCg6a/galGal6)
X. tropicalis   Xenopus tropicalis      Jul. 2016 (Xenopus_tropicalis_v9.1/xenTro9)
Coelacanth      Latimeria chalumnae     Aug. 2011 (Broad/latCha1)
Elephant shark  Callorhinchus milii     Dec. 2013 (Callorhinchus_milii-6.1.3/calMil1)

    #####################################################################
    cd /hive/data/genomes/danRer10/bed/multiz12way/downloads/phastCons12way

    ln -s ../../cons/all/downloads/phastCons12way.wigFix.gz \
        ./danRer10.phastCons12way.wigFix.gz
    ln -s ../../cons/all/phastCons12way.bw ./danRer10.phastCons12way.bw
    ln -s ../../cons/all/all.mod ./danRer10.phastCons12way.mod
    time md5sum *.gz *.mod *.bw > md5sum.txt
    #   real    0m3.635s

    # obtain the README.txt from galGal6/phastCons77way and update for this

    #   situation
    ln -s `pwd`/* \
      /usr/local/apache/htdocs-hgdownload/goldenPath/danRer10/phastCons12way

    #####################################################################
    cd /hive/data/genomes/danRer10/bed/multiz12way/downloads/phyloP12way

    ln -s ../../consPhyloP/all/downloads/phyloP12way.wigFix.gz \
        ./danRer10.phyloP12way.wigFix.gz
    ln -s ../../consPhyloP/run.phyloP/all.mod danRer10.phyloP12way.mod
    ln -s ../../consPhyloP/all/phyloP12way.bw danRer10.phyloP12way.bw

    time md5sum *.mod *.bw *.gz > md5sum.txt
    #   real    0m3.417s

    # obtain the README.txt from galGal6/phyloP77way and update for this
    #   situation
    ln -s `pwd`/* \
      /usr/local/apache/htdocs-hgdownload/goldenPath/danRer10/phyloP12way

    ###########################################################################
    ## create upstream refGene maf files
    cd /hive/data/genomes/danRer10/bed/multiz12way/downloads/multiz12way
    # bash script
#!/bin/sh
export geneTbl="refGene"
for S in 1000 2000 5000
do
    echo "making upstream${S}.maf"
    featureBits danRer10 ${geneTbl}:upstream:${S} -fa=/dev/null -bed=stdout \
        | perl -wpe 's/_up[^\t]+/\t0/' | sort -k1,1 -k2,2n \
        | /cluster/bin/$MACHTYPE/mafFrags danRer10 multiz12way \
                stdin stdout \
                -orgs=/hive/data/genomes/danRer10/bed/multiz12way/species.list \
        | gzip -c > upstream${S}.${geneTbl}.maf.gz &
    echo "done upstream${S}.${geneTbl}.maf.gz"
done
wait
    #   real    3m40.415s

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

    # some other symlinks were already made above
    # obtain the README.txt from cavPor3/multiz12way and update for this
    #   situation
    ln -s `pwd`/upstream*.gz `pwd`/README.txt \
        /usr/local/apache/htdocs-hgdownload/goldenPath/danRer10/multiz12way

#############################################################################
# wiki page for 12way (DONE - 2020-03-18 - Hiram)
    mkdir /hive/users/hiram/bigWays/danRer10.12way
    cd /hive/users/hiram/bigWays
    echo "danRer10" > danRer10.12way/ordered.list
    awk '{print $1}' /hive/data/genomes/danRer10/bed/multiz12way/12way.distances.txt \
       >> danRer10.12way/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 danRer10.12way/ordered.list
    # dbDb.sh constructs danRer10.12way/GalVar1_12way_conservation_alignment.html
    # may need to add new assembly references to srcReference.list and
    # urlReference.list

    ./dbDb.sh danRer10 12way
    # sizeStats.pl constructs danRer10.12way/GalVar1_12way_Genome_size_statistics.html
    # this requires entries in coverage.list for new sequences
    ./sizeStats.pl danRer10 12way

    # defCheck.pl constructs GalVar1_12way_conservation_lastz_parameters.html
    ./defCheck.pl danRer10 12way

    # this constructs the html pages in danRer10.12way/:
# -rw-rw-r-- 1 6821 Mar 18 16:07 DanRer10_12-way_conservation_alignment.html
# -rw-rw-r-- 1 8990 Mar 18 16:07 DanRer10_12-way_Genome_size_statistics.html
# -rw-rw-r-- 1 5347 Mar 18 16:07 DanRer10_12-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_12way_conservation_alignment
#  GalVar1_6way_Genome_size_statistics
#  GalVar1_6way_conservation_lastz_parameters

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

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