#!/usr/bin/env perl

use strict;
use warnings;
use File::Basename;

my %betterName;	# key is asmId, value is common name

my $home = $ENV{'HOME'};
my $srcDir = "$home/kent/src/hg/makeDb/doc/VGP";

open (FH, "<$srcDir/commonNames.txt") or die "can not read $srcDir/commonNames.txt";
while (my $line = <FH>) {
  chomp $line;
  my ($asmId, $name) = split('\t', $line);
  $betterName{$asmId} = $name;
}
close (FH);

my @orderList;	# asmId of the assemblies in order from the *.list files
# the order to read the different .list files:
my $assemblyCount = 0;

open (FH, "<commonNameOrder.list") or die "can not read commonNameOrder.list";
while (my $line = <FH>) {
  chomp $line;
  my ($commonName, $asmId) = split('\t', $line);
  push @orderList, $asmId;
  ++$assemblyCount;
}
close (FH);

my $orderKey = 1;
foreach my $asmId (@orderList) {
  my $asmReport="$asmId/download/${asmId}_assembly_report.txt";
  my $descr=`grep -i "organism name:" $asmReport | head -1 | sed -e 's#.*organism name: *##i; s# (.*\$##;'`;
  chomp $descr;
  my $orgName=`grep -i "organism name:" $asmReport | head -1 | sed -e 's#.* name: .* (##; s#).*##;'`;
  chomp $orgName;
  $orgName = $betterName{$asmId} if (exists($betterName{$asmId}));

  printf "genome %s\n", $asmId;
  printf "trackDb genomes/%s/%s.trackDb.txt\n", $asmId, $asmId;
  printf "groups groups.txt\n";
  printf "description %s\n", $orgName;
  printf "twoBitPath genomes/%s/%s.2bit\n", $asmId, $asmId;
  printf "organism %s\n", $descr;
  my $chrName=`head -1 $asmId/$asmId.chrom.sizes | awk '{print \$1}'`;
  chomp $chrName;
  my $bigChrom=`head -1 $asmId/$asmId.chrom.sizes | awk '{print \$NF}'`;
  chomp $bigChrom;
  my $oneThird = int($bigChrom/3);
  my $tenK = $oneThird + 10000;
  $tenK = $bigChrom if ($tenK > $bigChrom);
  my $defPos="${chrName}:${oneThird}-${tenK}";
  if ( -s "$asmId/defaultPos.txt" ) {
    $defPos=`cat "$asmId/defaultPos.txt"`;
    chomp $defPos;
  }
  printf "defaultPos %s\n", $defPos;
  printf "orderKey %d\n", $orderKey++;
  printf "scientificName %s\n", $descr;
  printf "htmlPath genomes/%s/html/%s.description.html\n", $asmId, $asmId;
  printf "\n";
  my $localGenomesFile = "$asmId/${asmId}.genomes.txt";
  open (GF, ">$localGenomesFile") or die "can not write to $localGenomesFile";
  printf GF "genome %s\n", $asmId;
  printf GF "trackDb %s/%s.trackDb.txt\n", $asmId, $asmId;
  printf GF "groups groups.txt\n";
  printf GF "description %s\n", $orgName;
  printf GF "twoBitPath %s/%s.2bit\n", $asmId, $asmId;
  printf GF "organism %s\n", $descr;
  printf GF "defaultPos %s\n", $defPos;
  printf GF "orderKey %d\n", $orderKey++;
  printf GF "scientificName %s\n", $descr;
  printf GF "htmlPath %s/html/%s.description.html\n", $asmId, $asmId;
  close (GF);
}

__END__


description Mastacembelus armatus
twoBitPath GCA_900324485.2_fMasArm1.2/trackData/addMask/GCA_900324485.2_fMasArm1.2.masked.2bit
organism Zig-Zag eel
defaultPos LR535842.1:14552035-14572034
orderKey 1
scientificName Mastacembelus armatus
htmlPath GCA_900324485.2_fMasArm1.2/html/GCA_900324485.2_fMasArm1.2.description.html
[hiram@hgwdev /hive/data/genomes/asmHubs/VGP/ucscNames] ls */*.trackDb.txt
head -25 GCF_901001135.1_aRhiBiv1.1/download/GCF_901001135.1_aRhiBiv1.1_assembly_report.txt
# Assembly name:  aRhiBiv1.1
# Organism name:  Rhinatrema bivittatum (two-lined caecilian)
# Taxid:          194408
# BioSample:      SAMEA104387956
# BioProject:     PRJEB32111
# Submitter:      SC
# Date:           2019-06-02
# Assembly type:  haploid
# Release type:   major
# Assembly level: Chromosome
# Genome representation: full
# WGS project:    CAAJIB01
# Genome coverage: 43x
# RefSeq category: Representative Genome
# GenBank assembly accession: GCA_901001135.1
# RefSeq assembly accession: GCF_901001135.1
# RefSeq assembly and GenBank assemblies identical: no
#
## Assembly-Units:
## GenBank Unit Accession       RefSeq Unit Accession   Assembly-Unit name
## GCA_901001134.1      GCF_901001134.1 Primary Assembly
##      GCF_006352515.1 non-nuclear
#

__END__
less ../ucscGenomes.txt
genome GCA_900324485.2_fMasArm1.2
trackDb GCA_900324485.2_fMasArm1.2/GCA_900324485.2_fMasArm1.2.trackDb.txt
groups hub.txt
description Mastacembelus armatus
twoBitPath GCA_900324485.2_fMasArm1.2/trackData/addMask/GCA_900324485.2_fMasArm1.2.masked.2bit
organism Zig-Zag eel
defaultPos LR535842.1:14552035-14572034
orderKey 1
scientificName Mastacembelus armatus
htmlPath GCA_900324485.2_fMasArm1.2/html/GCA_900324485.2_fMasArm1.2.description.html
[hiram@hgwdev /hive/data/genomes/asmHubs/VGP/ucscNames] ls */*.trackDb.txt
GCA_900324485.2_fMasArm1.2/GCA_900324485.2_fMasArm1.2.trackDb.txt
GCF_901001135.1_aRhiBiv1.1/GCF_901001135.1_aRhiBiv1.1.trackDb.txt