gsea-empty-spaces.sh

analyse(){    
	geneSetFilePath=$1;    
	outputFile=$2;    
	analyticsFile=$ATLAS_EXPS/E-GEOD-59831/E-GEOD-59831-analytics.tsv
	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 5 --maxsize 100 --descr $ATLAS_PROD/bioentity_properties/go/goIDToTerm.tsv.decorate.aux --go=$geneSetFilePath --out=$outputFile; 
}


# a "normal" analysis
analyse /nfs/production3/ma/home/atlas3-production/bioentity_properties/archive/ensembl_88_35/mus_musculus.ensgene.go.tsv /var/tmp/out1


#There are some IDs with no go terms: 
comm -23 <( cut -f 1 /nfs/production3/ma/home/atlas3-production/bioentity_properties/archive/ensembl_88_35/mus_musculus.ensgene.go.tsv | sort -u ) <(cut -f1 $ATLAS_EXPS/E-GEOD-59831/E-GEOD-59831-analytics.tsv | sort -u ) | wc -l
#	289

#Make a version of the annotations file with these terms added to the end
cat /nfs/production3/ma/home/atlas3-production/bioentity_properties/archive/ensembl_88_35/mus_musculus.ensgene.go.tsv <( comm -23 <( cut -f 1 /nfs/production3/ma/home/atlas3-production/bioentity_properties/archive/ensembl_88_35/mus_musculus.ensgene.go.tsv | sort -u ) <(cut -f1 $ATLAS_EXPS/E-GEOD-59831/E-GEOD-59831-analytics.tsv | sort -u ) | sed 's/$/\t/'  ) > /var/tmp/mus_musculus.ensgene.go.tsv-ids-at-the-end


analyse  /var/tmp/mus_musculus.ensgene.go.tsv-ids-at-the-end /var/tmp/out2

# No results as predicted!
diff /var/tmp/out1.tsv /var/tmp/out2.tsv | wc -l
#	0

#filter out all the gene id -> empty
grep -ve "[[:space:]]$" /nfs/production3/ma/home/atlas3-production/bioentity_properties/archive/ensembl_88_35/mus_musculus.ensgene.go.tsv > /var/tmp/mus_musculus.ensgene.go.tsv-no-empty-goterms

analyse  /var/tmp/mus_musculus.ensgene.go.tsv-no-empty-goterms /var/tmp/out3

# Lots of results!
diff /var/tmp/out1.tsv /var/tmp/out3.tsv | wc -l 
#	9724

A lot of the change between ensembl 88 and 89 can be accounted as "gene id to empty" :

[fg_atlas@ebi-cli-002 ~]$ 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 | wc -l
41488
[fg_atlas@ebi-cli-002 ~]$ 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 | grep -e "[[:space:]]$" | wc -l
36400