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

# Caenorhabditis angaria
#	Submitted (15-OCT-2010) Division of Biology, California Institute
#	of Technology, 1200 E. California Blvd., Pasadena, CA 91125, USA 

#	Division of Biology, California Institute of Technology(PS1010) ps10rel4 (GCA_000165025.1)
#
#	http://www.ncbi.nlm.nih.gov/Traces/wgs/?val=AEHI01

###########################################################################
## Download sequence (DONE - 2011-05-31 - Hiram)
    mkdir /hive/data/genomes/caeAng1
    cd /hive/data/genomes/caeAng1
    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_PS1010/ps1010rel4/
    faSize unplaced_scaffolds/FASTA/unplaced.scaf.fa.gz
# 79761545 bases (4502764 N's 75258781 real 75258781 upper 0 lower)
#	in 33559 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, "<localID2acc") or die "can not read localID2acc";
while (my $line = <FH>) {
    chomp $line;
    my ($scaf, $glName) = split('\s+', $line);
    $scaf =~ s/ps1010rel4_//;	# remove redundant name info
    die "ERROR: duplicate glName: $glName" if (exists($scafName{$glName}));
    $scafName{$glName} = $scaf;
}
close (FH);

open (AG, "|gzip -c > caeAng1.scaf.agp.gz") or die "can not write to gzip -c > caeAng1.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/^#/) {
	printf AG "%s", $line;
    } else {
	chomp $line;
	my ($glName, $rest) = split('\s+', $line, 2);
	printf AG "%s\t%s\n", $scafName{$glName}, $rest;
    }
}
close (FH);
close (AG);

open (FA, "|gzip -c > caeAng1.scaf.fa.gz") or die "can not write to gzip -c > caeAng1.scaf.fa.gz";
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/>gi.[0-9]+.gb.//;
	$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    0m22.682s


    faSize caeAng1.scaf.fa.gz 
# 79761545 bases (4502764 N's 75258781 real 75258781 upper 0 lower)
#	in 33559 sequences in 1 files

    checkAgpAndFa  caeAng1.scaf.agp.gz caeAng1.scaf.fa.gz 2>&1 | tail -1
    #	All AGP and FASTA entries agree - both files are valid

###########################################################################
## Initial sequence (DONE - 2011-05-31 - Hiram)
    cd /hive/data/genomes/caeAng1
    cat << '_EOF_' > caeAng1.config.ra
# Config parameters for makeGenomeDb.pl:
db caeAng1
clade worm
genomeCladePriority 70
scientificName Caenorhabditis angaria
commonName C. angaria
assemblyDate Oct. 2010
assemblyShortLabel WS225
assemblyLabel Division of Biology, California Institute of Technology(PS1010) ps10rel4 (GCA_000165025.1)
orderKey 838
mitoAcc none
fastaFiles /hive/data/genomes/caeAng1/genbank/caeAng1.scaf.fa.gz
agpFiles /hive/data/genomes/caeAng1/genbank/caeAng1.scaf.agp.gz
# qualFiles none
dbDbSpeciesDir worm
taxId 96668
'_EOF_'
    # << happy emacs

    mkdir jkStuff
    #	run just to AGP to make sure things are sane first
    time nice -n +19 makeGenomeDb.pl caeAng1.config.ra -stop=agp \
      > jkStuff/makeGenomeDb.agp.log 2>&1
    #	real    0m22.767s

    #	check that log to verify it has no errors
    #	now, continuing to make the Db and all
    time nice -n +19 makeGenomeDb.pl caeAng1.config.ra -continue=db \
      > jkStuff/makeGenomeDb.db.log 2>&1
    #	real    1m19.007s
    #	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 - 2011-05-31 - Hiram)
    mkdir /hive/data/genomes/caeAng1/bed/repeatMasker
    cd /hive/data/genomes/caeAng1/bed/repeatMasker
    time nice -n +19 doRepeatMasker.pl -noSplit -bigClusterHub=swarm \
	-species="caenorhabditis sp. ps1010" -buildDir=`pwd` caeAng1 \
	> do.log 2>&1 &
    #	real    108m37.276s

    #	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
# 79761545 bases (4502764 N's 75258781 real 74350029 upper 908752 lower)
#	in 33559 sequences in 1 files
# %1.14 masked total, %1.21 masked real

###########################################################################
## Simple Repeats (DONE - 2011-05-31 - Hiram)
    mkdir /cluster/data/caeAng1/bed/simpleRepeat
    cd /cluster/data/caeAng1/bed/simpleRepeat
    time nice -n +19 doSimpleRepeat.pl -smallClusterHub=memk \
	-workhorse=hgwdev -buildDir=`pwd` caeAng1 > do.log 2>&1 &
    #	real    19m27.079s
    cat fb.simpleRepeat 
    #	3868038 bases of 75258781 (5.140%) in intersection

###########################################################################
## WindowMasker (DONE - 2011-05-31 - Hiram)
    ssh hgwdev
    mkdir /hive/data/genomes/caeAng1/bed/windowMasker
    cd /hive/data/genomes/caeAng1/bed/windowMasker
    time nice -n +19 doWindowMasker.pl -verbose=2 -buildDir=`pwd` \
	-workhorse=hgwdev caeAng1 > do.log 2>&1 &
    #	real    2m38.301s

    twoBitToFa caeAng1.wmsk.sdust.2bit stdout | faSize stdin
# 79761545 bases (4502764 N's 75258781 real 46477651 upper 28781130 lower)
#	in 33559 sequences in 1 files
# %36.08 masked total, %38.24 masked real

    #	load this initial data to get ready to clean it
    cd /hive/data/genomes/caeAng1/bed/windowMasker
    hgLoadBed caeAng1 windowmaskerSdust windowmasker.sdust.bed.gz
    #	Loaded 790580 elements of size 3
    featureBits -countGaps caeAng1 windowmaskerSdust
    #	33265794 bases of 79761545 (41.707%) in intersection

    #	eliminate the gaps from the masking
    featureBits caeAng1 -not gap -bed=notGap.bed
    #	75258781 bases of 75258781 (100.000%) in intersection
    time nice -n +19 featureBits caeAng1 windowmaskerSdust notGap.bed \
	-bed=stdout | gzip -c > cleanWMask.bed.gz
    #	28781130 bases of 75258781 (38.243%) in intersection
    #	real    10m6.750s

    #	reload track to get it clean
    hgLoadBed caeAng1 windowmaskerSdust cleanWMask.bed.gz
    #	Loaded 790135 elements of size 4
    featureBits -countGaps caeAng1 windowmaskerSdust
    #	28781130 bases of 79761545 (36.084%) in intersection

    #	mask the sequence with this clean mask
    zcat cleanWMask.bed.gz \
	| twoBitMask ../../caeAng1.unmasked.2bit stdin \
	    -type=.bed caeAng1.cleanWMSdust.2bit
    twoBitToFa caeAng1.cleanWMSdust.2bit stdout | faSize stdin \
        > caeAng1.cleanWMSdust.faSize.txt
    cat caeAng1.cleanWMSdust.faSize.txt
# 79761545 bases (4502764 N's 75258781 real 46477651 upper 28781130 lower)
#	in 33559 sequences in 1 files
# %36.08 masked total, %38.24 masked real

########################################################################
# MASK SEQUENCE WITH WM+TRF (DONE - 2011-05-31 - Hiram)
    cd /hive/data/genomes/caeAng1
    twoBitMask -add bed/windowMasker/caeAng1.cleanWMSdust.2bit \
	bed/simpleRepeat/trfMask.bed caeAng1.2bit
    #	safe to ignore the warnings about BED file with >=13 fields
    twoBitToFa caeAng1.2bit stdout | faSize stdin > faSize.caeAng1.txt
    cat faSize.caeAng1.txt
# 79761545 bases (4502764 N's 75258781 real 46424184 upper 28834597 lower)
#	in 33559 sequences in 1 files
# %36.15 masked total, %38.31 masked real

    #	create symlink to gbdb
    ssh hgwdev
    rm /gbdb/caeAng1/caeAng1.2bit
    ln -s `pwd`/caeAng1.2bit /gbdb/caeAng1/caeAng1.2bit

#########################################################################
# MAKE 11.OOC FILE FOR BLAT (DONE - 2011-05-31 - Hiram)
    # numerator is caeAng1 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 \( 75258781  / 2897310462 \) \* 1024
    #	( 75258781 / 2897310462 ) * 1024 = 26.598804

    # Round up to use -repMatch=100 since 60 would result in too many
    cd /hive/data/genomes/caeAng1
    blat caeAng1.2bit /dev/null /dev/null -tileSize=11 \
      -makeOoc=jkStuff/caeAng1.11.ooc -repMatch=100
    #	Wrote 5510 overused 11-mers to jkStuff/caeAng1.11.ooc
    # there are no non-bridged gaps here to make a lift file from
    # cd jkStuff
    # gapToLift -verbose=2 caeAng1 caeAng1.nonBridged.lift -bedFile=caeAng1.nonBridged.bed

    mkdir /hive/data/staging/data/caeAng1
    cp -p chrom.sizes caeAng1.2bit jkStuff/caeAng1.11.ooc \
	/hive/data/staging/data/caeAng1

#########################################################################
# GENBANK AUTO UPDATE (DONE - 2011-05-26 - Hiram)
    # align with latest genbank process.
    ssh hgwdev
    cd ~/kent/src/hg/makeDb/genbank
    git pull
    # edit etc/genbank.conf to add caeAng1 just before caeRem3

# caeAng1 (C. angaria)
caeAng1.serverGenome = /hive/data/genomes/caeAng1/caeAng1.2bit
caeAng1.clusterGenome = /scratch/data/caeAng1/caeAng1.2bit
caeAng1.ooc = /scratch/data/caeAng1/caeAng1.11.ooc
caeAng1.lift = no
caeAng1.refseq.mrna.native.pslCDnaFilter  = ${lowCover.refseq.mrna.native.pslCDnaFilter}
caeAng1.refseq.mrna.xeno.pslCDnaFilter    = ${lowCover.refseq.mrna.xeno.pslCDnaFilter}
caeAng1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter}
caeAng1.genbank.mrna.xeno.pslCDnaFilter   = ${lowCover.genbank.mrna.xeno.pslCDnaFilter}
caeAng1.genbank.est.native.pslCDnaFilter  = ${lowCover.genbank.est.native.pslCDnaFilter}
caeAng1.refseq.mrna.native.load = no
caeAng1.refseq.mrna.xeno.load  = yes
caeAng1.refseq.mrna.xeno.loadDesc = yes
caeAng1.genbank.mrna.xeno.load = yes
caeAng1.genbank.est.native.load = yes
caeAng1.genbank.est.native.loadDesc = no
caeAng1.downloadDir = caeAng1
caeAng1.perChromTables = no

    git commit -m "Added caeAng1 C. angaria 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 caeAng1 &
    #	logFile:  var/build/logs/2011.05.26-09:19:08.caeAng1.initalign.log
    #	real    291m13.960s

    # load database when finished
    ssh hgwdev
    cd /cluster/data/genbank
    time nice -n +19 ./bin/gbDbLoadStep -drop -initialLoad caeAng1
    #	logFile: var/dbload/hgwdev/logs/2011.05.25-15:46:59.dbload.log
    #	real    22m27.349s

    # enable daily alignment and update of hgwdev
    cd ~/kent/src/hg/makeDb/genbank
    git pull
    # add caeAng1 to:
        etc/align.dbs
        etc/hgwdev.dbs
    git push
    make etc-update

#########################################################################
# lastz swap ce10 to caeAng1 (DONE - 2011-06-08 - Hiram)
    # original alignment on ce10
    cd /hive/data/genomes/ce10/bed/lastzCaeAng1.2011-06-08
    cat fb.ce10.chainCaeAng1Link.txt 
    #	17675040 bases of 100286070 (17.625%) in intersection

    mkdir /hive/data/genomes/caeAng1/bed/blastz.ce10.swap
    cd /hive/data/genomes/caeAng1/bed/blastz.ce10.swap
    time nice -n +19 doBlastzChainNet.pl -verbose=2 \
	/hive/data/genomes/ce10/bed/lastzCaeAng1.2011-06-08/DEF \
	-syntenicNet -workhorse=hgwdev -bigClusterHub=swarm \
	-smallClusterHub=encodek -swap > swap.log 2>&1 &
    #	real    2m29.548s

    cat fb.caeAng1.chainCe10Link.txt 
    #	17607671 bases of 75258781 (23.396%) in intersection

#########################################################################
# Constructing Downloads (DONE - 2011-06-10 - Hiram)
    cd /hive/data/genomes/caeAng1
    time makeDownloads.pl -dbHost=hgwdev -workhorse=hgwdev -verbose=2 caeAng1 \
	 > downloads.log 2>&1
    #	real    0m40.587s
    # 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

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