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

# Caenorhabditis sp9. JU1422
#	Washington University School of Medicine GSC
#
#	http://www.ncbi.nlm.nih.gov/Traces/wgs/?val=AENM01

###########################################################################
## Download sequence (DONE - 2011-05-27 - Hiram)
    mkdir /hive/data/genomes/caeSp91
    cd /hive/data/genomes/caeSp91
    mkdir genbank
    cd genbank
    wget --no-parent --timestamping -m -nH --cut-dirs=7 \
	ftp://ftp.ncbi.nlm.nih.gov/genbank/genomes/Eukaryotes/invertebrates/Caenorhabditis_sp_9_MAF_2010/Caenorhabditis_sp9_JU1422-3.0.1/

    faSize unplaced_scaffolds/FASTA/unplaced.scaf.fa.gz
# 204396809 bases (17856539 N's 186540270 real 186540270 upper 0 lower)
# in 7636 sequences in 1 files

    # change the names from GL numbers to scaffold numbers
    cat << '_EOF_' > scafNames.pl
#!/bin/env perl

use strict;
use warnings;

my $argc = scalar(@ARGV);

if ($argc != 1) {
    printf STDERR "usage: scafNames.pl makeItSo\n";
    printf STDERR "via the scaffold_localID2acc file translate names\n";
    printf STDERR "in the AGP and FASTA files to construct UCSC versions.\n";
}

my %scafName;   # index is GL name, value is scaffold name

open (FH, "<scaffold_localID2acc") or die "can not read scaffold_localID2acc";
while (my $line = <FH>) {
    chomp $line;
    my ($scaf, $glName) = split('\s+', $line);
    die "ERROR: duplicate glName: $glName" if (exists($scafName{$glName}));
    $scafName{$glName} = $scaf;
}
close (FH);

open (FA, "|gzip -c > caeSp91.scaf.agp.gz") or die "can not write to gzip -c >
caeSp91.scaf.agp.gz";
open (FH, "zcat unplaced_scaffolds/AGP/unplaced.scaf.agp.gz|") or
    die "can not read unplaced_scaffolds/AGP/unplaced.scaf.agp.gz";
while (my $line = <FH>) {
    if ($line =~ m/^GL/) {
        chomp $line;
        my ($glName, $rest) = split('\s+', $line, 2);
        printf FA "%s\t%s\n", $scafName{$glName}, $rest;
    } else {
        printf FA "%s", $line;
    }
}
close (FH);
close (FA);

open (FA, "|gzip -c > caeSp91.scaf.fa.gz") or die "can not write to gzip -c >
caeSp91.scaf.fa.gz";
# unplaced genomic scaffold Scaffold0, whole genome shotgun sequence
open (FH, "zcat unplaced_scaffolds/FASTA/unplaced.scaf.fa.gz|") or
        die "can not read unplaced_scaffolds/FASTA/unplaced.scaf.fa.gz";
while (my $line = <FH>) {
    if ($line =~ m/^>/) {
        chomp $line;
        $line =~ s/.*gb.GL/GL/;
        $line =~ s/. Caeno.*//;
        printf FA ">%s\n", $scafName{$line};
        
    } else {
        printf FA "%s", $line;
    }
}
close (FH);
close (FA);
'_EOF_'
    # << happy emacs
    chmod +x ./scafNames.pl
    time ./scafNames.pl makeItSo
    #	real    0m53.606s
    faSize caeSp91.scaf.fa.gz
# 204396809 bases (17856539 N's 186540270 real 186540270 upper 0 lower)
# in 7636 sequences in 1 files

    checkAgpAndFa  caeSp91.scaf.agp.gz caeSp91.scaf.fa.gz 2>&1 | tail -1
    #	All AGP and FASTA entries agree - both files are valid

###########################################################################
## Initial sequence (DONE - 2011-05-27 - Hiram)
    cd /hive/data/genomes/caeSp91
    cat << '_EOF_' > caeSp91.config.ra
# Config parameters for makeGenomeDb.pl:
db caeSp91
clade worm
genomeCladePriority 68
scientificName Caenorhabditis sp9. JU1422
commonName C. sp. 9 JU1422
assemblyDate Nov. 2010
assemblyShortLabel WUSTL 3.0.1
assemblyLabel Washington University School of Medicine GSC Caenorhabditis sp. 9 JU1422 MAF-2010 3.0.1 (GCA_000186805.1)
orderKey 880
mitoAcc none
fastaFiles /hive/data/genomes/caeSp91/genbank/caeSp91.scaf.fa.gz
agpFiles /hive/data/genomes/caeSp91/genbank/caeSp91.scaf.agp.gz
# qualFiles none
dbDbSpeciesDir worm
taxId 870437
'_EOF_'
    # << happy emacs

    mkdir jkStuff
    #	run just to AGP to make sure things are sane first
    time nice -n +19 makeGenomeDb.pl caeSp91.config.ra -stop=agp \
      > jkStuff/makeGenomeDb.agp.log 2>&1
    #	real    0m33.321s
    #	check that log to verify it has no errors
    #	now, continuing to make the Db and all
    time nice -n +19 makeGenomeDb.pl caeSp91.config.ra -continue=db \
      > jkStuff/makeGenomeDb.db.log 2>&1
    #	real    1m44.286s
    #	check that log to verify it has no errors

    #	take the trackDb business there and check it into the source tree
    #	fixup the description, gap and gold html page descriptions

###########################################################################
## RepeatMasker (DONE - 2011-05-27 - Hiram)
    mkdir /hive/data/genomes/caeSp91/bed/repeatMasker
    cd /hive/data/genomes/caeSp91/bed/repeatMasker
    # need the -species option since RM doesn't recognize this one
    time nice -n +19 doRepeatMasker.pl -noSplit -bigClusterHub=swarm \
	-species "caenorhabditis" -buildDir=`pwd` caeSp91 > do.log 2>&1 &
    #	real    49m43.035s

    #	from the do.log:
# RepeatMasker version development-$Id: RepeatMasker,v
#	1.25 2010/09/08 21:32:26 angie Exp $
#	CC   RELEASE 20090604; 

    cat faSize.rmsk.txt
# 204396809 bases (17856539 N's 186540270 real 161867053 upper 24673217 lower)
#	in 7636 sequences in 1 files
# %12.07 masked total, %13.23 masked real

###########################################################################
## Simple Repeats (DONE - 2011-05-27 - Hiram)
    mkdir /cluster/data/caeSp91/bed/simpleRepeat
    cd /cluster/data/caeSp91/bed/simpleRepeat
    time nice -n +19 doSimpleRepeat.pl -smallClusterHub=memk \
	-workhorse=hgwdev -buildDir=`pwd` caeSp91 > do.log 2>&1 &
    #	real	19m36.815s
    cat fb.simpleRepeat 
    #	6927541 bases of 186540270 (3.714%) in intersection

###########################################################################
## WindowMasker (DONE - 2011-05-27 - Hiram)
    ssh hgwdev
    mkdir /hive/data/genomes/caeSp91/bed/windowMasker
    cd /hive/data/genomes/caeSp91/bed/windowMasker
    time nice -n +19 doWindowMasker.pl -verbose=2 -buildDir=`pwd` \
	-workhorse=hgwdev caeSp91 > do.log 2>&1 &
    #	real    9m4.717s

    twoBitToFa caeSp91.wmsk.sdust.2bit stdout | faSize stdin
# 204396809 bases (17856539 N's 186540270 real 127610843 upper 58929427 lower)
# in 7636 sequences in 1 files

    #	load this initial data to get ready to clean it
    cd /hive/data/genomes/caeSp91/bed/windowMasker
    hgLoadBed caeSp91 windowmaskerSdust windowmasker.sdust.bed.gz
    #	Loaded 1421722 elements of size 3
    featureBits -countGaps caeSp91 windowmaskerSdust
    #	76785966 bases of 204396809 (37.567%) in intersection

    #	eliminate the gaps from the masking
    featureBits caeSp91 -not gap -bed=notGap.bed
    #	186540270 bases of 186540270 (100.000%) in intersection
    time nice -n +19 featureBits caeSp91 windowmaskerSdust notGap.bed \
	-bed=stdout | gzip -c > cleanWMask.bed.gz
    #	58929427 bases of 186540270 (31.591%) in intersection
    #	real    0m28.912s

    #	reload track to get it clean
    hgLoadBed caeSp91 windowmaskerSdust cleanWMask.bed.gz
    #	Loaded 1422910 elements of size 4
    featureBits -countGaps caeSp91 windowmaskerSdust
    #	58929427 bases of 204396809 (28.831%) in intersection

    #	mask the sequence with this clean mask
    zcat cleanWMask.bed.gz \
	| twoBitMask ../../caeSp91.unmasked.2bit stdin \
	    -type=.bed caeSp91.cleanWMSdust.2bit
    twoBitToFa caeSp91.cleanWMSdust.2bit stdout | faSize stdin \
        > caeSp91.cleanWMSdust.faSize.txt
    cat caeSp91.cleanWMSdust.faSize.txt
# 204396809 bases (17856539 N's 186540270 real 127610843 upper 58929427 lower)
#	in 7636 sequences in 1 files
# %28.83 masked total, %31.59 masked real

########################################################################
# MASK SEQUENCE WITH WM+TRF (DONE - 2011-05-31 - Hiram)
    cd /hive/data/genomes/caeSp91
    twoBitMask -add bed/windowMasker/caeSp91.cleanWMSdust.2bit \
	bed/simpleRepeat/trfMask.bed caeSp91.2bit
    #	safe to ignore the warnings about BED file with >=13 fields
    twoBitToFa caeSp91.2bit stdout | faSize stdin > faSize.caeSp91.txt
    cat faSize.caeSp91.txt
# 204396809 bases (17856539 N's 186540270 real 127471397 upper 59068873 lower)
#	in 7636 sequences in 1 files
# %28.90 masked total, %31.67 masked real

    #	create symlink to gbdb
    ssh hgwdev
    rm /gbdb/caeSp91/caeSp91.2bit
    ln -s `pwd`/caeSp91.2bit /gbdb/caeSp91/caeSp91.2bit

#########################################################################
# MAKE 11.OOC FILE FOR BLAT (DONE - 2011-05-31 - Hiram)
    # numerator is caeSp91 gapless bases "real" as reported by faSize 
    # denominator is hg19 gapless bases "real" as reported by faSize
    # 1024 is threshold used for human -repMatch:
    calc \( 186540270  / 2897310462 \) \* 1024
    #	( 186540270 / 2897310462 ) * 1024 = 65.929157

    # Round up to use -repMatch=100 since 60 would result in too many
    cd /hive/data/genomes/caeSp91
    blat caeSp91.2bit /dev/null /dev/null -tileSize=11 \
      -makeOoc=jkStuff/caeSp91.11.ooc -repMatch=100
    #	Wrote 15514 overused 11-mers to jkStuff/caeSp91.11.ooc
    # there are no non-bridged gaps here to make a lift file from
    # cd jkStuff
    # gapToLift -verbose=2 caeSp91 caeSp91.nonBridged.lift -bedFile=caeSp91.nonBridged.bed

    mkdir /hive/data/staging/data/caeSp91
    cp -p chrom.sizes caeSp91.2bit jkStuff/caeSp91.11.ooc \
	/hive/data/staging/data/caeSp91

#########################################################################
# GENBANK AUTO UPDATE (DONE - 2011-05-27 - Hiram)
    # align with latest genbank process.
    ssh hgwdev
    cd ~/kent/src/hg/makeDb/genbank
    git pull
    # edit etc/genbank.conf to add caeSp91 just before caePb2

# caeSp91 (C. brenneri)
caeSp91.serverGenome = /hive/data/genomes/caeSp91/caeSp91.2bit
caeSp91.clusterGenome = /scratch/data/caeSp91/caeSp91.2bit
caeSp91.ooc = /scratch/data/caeSp91/caeSp91.11.ooc
caeSp91.lift = no
caeSp91.refseq.mrna.native.pslCDnaFilter  = ${lowCover.refseq.mrna.native.pslCDnaFilter}
caeSp91.refseq.mrna.xeno.pslCDnaFilter    = ${lowCover.refseq.mrna.xeno.pslCDnaFilter}
caeSp91.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter}
caeSp91.genbank.mrna.xeno.pslCDnaFilter   = ${lowCover.genbank.mrna.xeno.pslCDnaFilter}
caeSp91.genbank.est.native.pslCDnaFilter  = ${lowCover.genbank.est.native.pslCDnaFilter}
caeSp91.refseq.mrna.native.load = no
caeSp91.refseq.mrna.xeno.load  = yes
caeSp91.refseq.mrna.xeno.loadDesc = yes
caeSp91.genbank.mrna.xeno.load = yes
caeSp91.genbank.est.native.load = yes
caeSp91.genbank.est.native.loadDesc = no
caeSp91.downloadDir = caeSp91
caeSp91.perChromTables = no


    git commit -m "Added caeSp91 C. brenneri WS220" etc/genbank.conf
    git push
    # update /cluster/data/genbank/:
    make etc-update

    screen		#	use a screen to manage this job
    cd /cluster/data/genbank
    time nice -n +19 bin/gbAlignStep -initial caeSp91 &
    #	logFile:  var/build/logs/2011.05.26-16:08:08.caeSp91.initalign.log
    #	real    642m20.841s

    # load database when finished
    ssh hgwdev
    cd /cluster/data/genbank
    time nice -n +19 ./bin/gbDbLoadStep -drop -initialLoad caeSp91
    #	logFile: var/dbload/hgwdev/logs/2011.05.27-09:45:02.dbload.log
    #	real    23m5.504s

    # enable daily alignment and update of hgwdev
    cd ~/kent/src/hg/makeDb/genbank
    git pull
    # add caeSp91 to:
        etc/align.dbs
        etc/hgwdev.dbs
    git commit -m "adding caeSp91 C. brenneri WS220" etc/align.dbs etc/hgwdev.dbs

    git push
    make etc-update

#########################################################################
# lastz ce10 to caeSp91 swap (DONE - 2011-06-07 - Hiram)
    #	original alignment on ce10
    cd /hive/data/genomes/ce10/bed/lastzCaeSp91.2011-06-07
    cat fb.ce10.chainCaeSp91Link.txt 
    #	42289932 bases of 100286070 (42.169%) in intersection

    mkdir /hive/data/genomes/caeSp91/bed/blastz.ce10.swap
    cd /hive/data/genomes/caeSp91/bed/blastz.ce10.swap
    time nice -n +19 doBlastzChainNet.pl -verbose=2 \
	/hive/data/genomes/ce10/bed/lastzCaeSp91.2011-06-07/DEF \
	-syntenicNet -workhorse=hgwdev -bigClusterHub=swarm \
	-smallClusterHub=encodek -swap > swap.log 2>&1 &
    #	real    6m27.559s

    cat fb.caeSp91.chainCe10Link.txt
    #	67679550 bases of 186540270 (36.281%) in intersection

############################################################################
# Constructing Downloads (DONE - 2011-06-10 - Hiram)
    cd /hive/data/genomes/caeSp91
    time makeDownloads.pl -dbHost=hgwdev -workhorse=hgwdev -verbose=2 caeSp91 \
	 > downloads.log 2>&1
    #	real    1m40.329s
    # fixup the README files constructed in goldenPath/*/README.txt

    # add window masker bed file:
    cp -p bed/windowMasker/cleanWMask.bed.gz \
	goldenPath/bigZips/chromWMSdust.bed.gz

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