#########################################################################
# SGP GENES (DONE - 2015-07-30 - Hiram)
    mkdir /hive/data/genomes/hg38/bed/sgpGene
    cd /hive/data/genomes/hg38/bed/sgpGene
    mkdir genome.crg.es
    cd genome.crg.es
    wget --timestamping \
      http://genome.crg.es/genepredictions/H.sapiens/hg38_x_mm10/SGP/00readme
time for C in `cut -f1 ../../../chrom.sizes`
do
  echo $C
  wget --timestamping \
    http://genome.crg.es/genepredictions/H.sapiens/hg38_x_mm10/SGP/${C}.gtf
  wget --timestamping \
   http://genome.crg.es/genepredictions/H.sapiens/hg38_x_mm10/SGP/${C}.sgp2.gff3
done
    # real    16m38.232s

    cd ..
    cat genome.crg.es/*.gtf | ldHgGene -gtf -genePredExt hg38 sgpGene stdin
    # Read 36030 transcripts in 537030 lines in 1 files
    #   36030 groups 350 seqs 1 sources 3 feature types
    # 36030 gene predictions

    featureBits -enrichment hg38 refGene:CDS sgpGene
# refGene:CDS 1.211%, sgpGene 1.284%, both 1.002%, cover 82.76%, enrich 64.43x
    featureBits -enrichment hg19 refGene:CDS sgpGene
# refGene:CDS 1.216%, sgpGene 1.295%, both 1.029%, cover 84.56%, enrich 65.28x

###########################################################################
# GENEID GENE PREDICTIONS (DONE - 2015-07-30 - Hiram)
    ssh hgwdev
    mkdir /hive/data/genomes/hg38/bed/geneid
    cd /hive/data/genomes/hg38/bed/geneid
    mkdir genome.crg.es
    cd genome.crg.es
    wget --timestamping \
      http://genome.crg.es/genepredictions/H.sapiens/hg38/geneid_v1.4/00readme
time for C in `cut -f1 ../../../chrom.sizes`
do
  echo $C
  wget --timestamping \
    http://genome.crg.es/genepredictions/H.sapiens/hg38/geneid_v1.4/${C}.gtf
  wget --timestamping \
    http://genome.crg.es/genepredictions/H.sapiens/hg38/geneid_v1.4/${C}.gff3
done
    # real    16m08.759s

    cd ..
    cat genome.crg.es/*.gtf | ldHgGene -gtf -genePredExt hg38 geneid stdin
    #   Read 35910 transcripts in 290394 lines in 1 files
    #     35910 groups 364 seqs 1 sources 3 feature types
    #   35910 gene predictions

    featureBits -enrichment hg38 refGene:CDS geneid
  # refGene:CDS 1.211%, geneid 1.352%, both 0.942%, cover 77.80%, enrich 57.56x
    featureBits -enrichment hg19 refGene:CDS geneid
  # refGene:CDS 1.216%, geneid 1.363%, both 0.972%, cover 79.87%, enrich 58.59x

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