88-89.sh

analyse(){
   geneSetFilePath=$1
   outputFile=$2
   analyticsFile=$ATLAS_EXPS/E-GEOD-59831/E-GEOD-59831-analytics.tsv
   echo irap_GSE_piano --tsv=$analyticsFile --pvalue-col=3 --foldchange-col=4 --title="title" --pvalue=0.05 --gs_fdr=0.1 --method=fisher-exact --dup-use-best --plot-annot-only --top=10 --minsize 0 --maxsize 100 --descr $ATLAS_PROD/bioentity_properties/go/goIDToTerm.tsv.decorate.aux --go=$geneSetFilePath --out=$outputFile
   irap_GSE_piano --tsv=$analyticsFile --pvalue-col=3 --foldchange-col=4 --title="title" --pvalue=0.05 --gs_fdr=0.1 --method=fisher-exact --dup-use-best --plot-annot-only --top=10 --minsize 0 --maxsize 100 --descr $ATLAS_PROD/bioentity_properties/go/goIDToTerm.tsv.decorate.aux --go=$geneSetFilePath --out=$outputFile
}

comm -12 /nfs/production3/ma/home/atlas3-production/bioentity_properties/archive/ensembl_88_35/mus_musculus.ensgene.go.tsv /nfs/production3/ma/home/atlas3-production/bioentity_properties/archive/ensembl_89_36/mus_musculus.ensgene.go.tsv > annotations/ensembl-88-89comm-12-mus_musculus.ensgene.go.tsv
comm -23 /nfs/production3/ma/home/atlas3-production/bioentity_properties/archive/ensembl_88_35/mus_musculus.ensgene.go.tsv /nfs/production3/ma/home/atlas3-production/bioentity_properties/archive/ensembl_89_36/mus_musculus.ensgene.go.tsv > annotations/ensembl-88-89comm-23-mus_musculus.ensgene.go.tsv
comm -13 /nfs/production3/ma/home/atlas3-production/bioentity_properties/archive/ensembl_88_35/mus_musculus.ensgene.go.tsv /nfs/production3/ma/home/atlas3-production/bioentity_properties/archive/ensembl_89_36/mus_musculus.ensgene.go.tsv > annotations/ensembl-88-89comm-13-mus_musculus.ensgene.go.tsv
cat annotations/ensembl-88-89comm-12-mus_musculus.ensgene.go.tsv annotations/ensembl-88-89comm-13-mus_musculus.ensgene.go.tsv > annotations/ensembl-88-89comm-1-mus_musculus.ensgene.go.tsv
cat annotations/ensembl-88-89comm-12-mus_musculus.ensgene.go.tsv annotations/ensembl-88-89comm-23-mus_musculus.ensgene.go.tsv > annotations/ensembl-88-89comm-2-mus_musculus.ensgene.go.tsv



mkdir -p ensembl-88-89-comm
analyse annotations/ensembl-88-89comm-12-mus_musculus.ensgene.go.tsv ensembl-88-89-comm/12 | tee ensembl-88-89-comm/12.out
analyse annotations/ensembl-88-89comm-1-mus_musculus.ensgene.go.tsv ensembl-88-89-comm/1 | tee ensembl-88-89-comm/1.out
analyse annotations/ensembl-88-89comm-2-mus_musculus.ensgene.go.tsv ensembl-88-89-comm/2 | tee ensembl-88-89-comm/2.out

#input sizes
wc -l annotations/*
  304880 annotations/ensembl-88-89comm-12-mus_musculus.ensgene.go.tsv
   41488 annotations/ensembl-88-89comm-13-mus_musculus.ensgene.go.tsv
  346368 annotations/ensembl-88-89comm-1-mus_musculus.ensgene.go.tsv
    3566 annotations/ensembl-88-89comm-23-mus_musculus.ensgene.go.tsv
  308446 annotations/ensembl-88-89comm-2-mus_musculus.ensgene.go.tsv

#output sizes
wc -l ensembl-88-89-comm/*tsv
  14303 ensembl-88-89-comm/12.tsv
   9595 ensembl-88-89-comm/1.tsv
  14323 ensembl-88-89-comm/2.tsv