Query based tools in BACNET

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drbecavin edited this page May 20, 2020 · 5 revisions

In this tutorial, we will explain how-to use BACNET architecture to make query-base multi-omics analysis.

We have added a test function which is ran when the BannerView loaded. Open ''bacnet.e4.rap.TestPart.java'' -> go to runTests() function, and add

System.out.println("test run");

script_multiomics

When running "bacnet.e4.rap", you will see ''test run'' displayed in the console.

test_run

Here are a list of BACNET script to add in runTests() to browse ListeriomicsSample database.

(If you need help for BACNET API go on the JavaDoc)

How-to get List of genomes?
How-to get List of transcriptomes?
How-to get List of proteomes?
How-to get list of genes and ncRNA?
How-to search gene and print available information?
How-to search gene and print its sequences?
How-to search gene and print its homologs?
How-to search gene and relevant omics datasets?
How-to show expression of gene in different omics dataset?
How-to correlate omics datasets?
How-to load table and add annotation?
How-to display omics dataset on GenomeViewer?

List of genomes

ArrayList<String> genomes = Genome.getAvailableGenomes();
for(String genome : genomes) {
     System.out.println(genome);
}

Expected output with ListeriomicsSample

Listeria monocytogenes EGD-e
Listeria monocytogenes EGD
Listeria monocytogenes 10403S

List of biological conditions

ArrayList<BioCondition> bioconditions = BioCondition.getAllBioConditions();
for(BioCondition biocond : bioconditions) {
    System.out.println(biocond.getName() +" "+ biocond.getGenomeName() +" "+ biocond.getTypeDataContained());
}

Expected output with ListeriomicsSample

BHI_2014_EGDe Listeria monocytogenes EGD-e [RNASeq]
CellWall_2004_EGDe Listeria monocytogenes EGD-e [Proteome]
EGD_WT Listeria monocytogenes EGD-e [GeneExpr, Tiling]
EGDe_280212 Listeria monocytogenes EGD-e [GeneExpr, Tiling]
EGDe_30C Listeria monocytogenes EGD-e [TSS]
EGDe_37C_RiboSeq Listeria monocytogenes EGD-e [RiboSeq]
EGDe_37C_TSS Listeria monocytogenes EGD-e [TSS]
EGDe_37C_TermSeq Listeria monocytogenes EGD-e [TermSeq]
Exoproteome_2010_EGDe Listeria monocytogenes EGD-e [Proteome]
Extracellular_BHI_2011_EGDe Listeria monocytogenes EGD-e [Proteome]
Extracellular_UGiessen_2010 Listeria monocytogenes EGD-e [ExpressionMatrix]
IFN_Intracellular_UGiessen_2010 Listeria monocytogenes EGD-e [ExpressionMatrix]
Intracellular_UGiessen_2010 Listeria monocytogenes EGD-e [ExpressionMatrix]
Macrophages_2014_EGDe Listeria monocytogenes EGD-e [RNASeq]
Stat_2009_EGDe Listeria monocytogenes EGD-e [Proteome]
prfA_Star Listeria monocytogenes EGD-e [GeneExpr, Tiling]

List of transcriptomes

ArrayList<BioCondition> bioconditions = BioCondition.getAllBioConditions();
for(BioCondition biocond : bioconditions) {
    for(OmicsData omics : biocond.getTranscriptomesData()){
        System.out.println(biocond.getGenomeName() + " " + omics.getName());
    }
}

Expected output with ListeriomicsSample

Listeria monocytogenes EGD-e BHI_2014_EGDe_f
Listeria monocytogenes EGD-e BHI_2014_EGDe_r
Listeria monocytogenes EGD-e EGD_WT.ge
Listeria monocytogenes EGD-e EGD_WT.+.gr
Listeria monocytogenes EGD-e EGD_WT.-.gr
Listeria monocytogenes EGD-e EGDe_280212.ge
Listeria monocytogenes EGD-e EGDe_280212.+.gr
Listeria monocytogenes EGD-e EGDe_280212.-.gr
Listeria monocytogenes EGD-e EGDe_30C_f
Listeria monocytogenes EGD-e EGDe_30C_r
Listeria monocytogenes EGD-e EGDe_37C_RiboSeq_f
Listeria monocytogenes EGD-e EGDe_37C_RiboSeq_r
Listeria monocytogenes EGD-e EGDe_37C_TSS_f
Listeria monocytogenes EGD-e EGDe_37C_TSS_r
Listeria monocytogenes EGD-e EGDe_37C_TermSeq_f
Listeria monocytogenes EGD-e EGDe_37C_TermSeq_r
Listeria monocytogenes EGD-e Macrophages_2014_EGDe_f
Listeria monocytogenes EGD-e Macrophages_2014_EGDe_r
Listeria monocytogenes EGD-e prfA_Star.ge
Listeria monocytogenes EGD-e prfA_Star.+.gr
Listeria monocytogenes EGD-e prfA_Star.-.gr

List of proteomes

ArrayList<BioCondition> bioconditions = BioCondition.getAllBioConditions();
for(BioCondition biocond : bioconditions) {
    for(OmicsData omics : biocond.getProteomicsData()){
        System.out.println(biocond.getGenomeName() + " " + omics.getName());
    }
}

Expected output with ListeriomicsSample

Listeria monocytogenes EGD-e CellWall_2004_EGDe
Listeria monocytogenes EGD-e Exoproteome_2010_EGDe
Listeria monocytogenes EGD-e Extracellular_BHI_2011_EGDe
Listeria monocytogenes EGD-e Stat_2009_EGDe

Get list of genes and ncRNA

Search them in a genome (ex: Listeria monocytogenes EGD-e)

// get genome
String genomeName = Genome.EGDE_NAME;
System.out.println("Open: "+genomeName);
Genome genome = Genome.loadGenome(genomeName);
// get list of genes and print all
LinkedHashMap<String, Gene> genes = genome.getGenes();
for(String geneName : genes.keySet()) {
    Gene gene = genes.get(geneName);
    System.out.println(gene + " ("+gene.getGeneName()+")");
}
// get list of ncRNA
LinkedHashMap<String, NcRNA> ncrnas = genome.getNcRNAs();
for(String ncrnaName : ncrnas.keySet()) {
    NcRNA ncrna = ncrnas.get(ncrnaName);
    System.out.println(ncrna + " ("+ncrna.getGeneName()+")");
}

Expected output with ListeriomicsSample

Open: Listeria monocytogenes EGD-e
Load Listeria monocytogenes EGD-e
/Users/christophebecavin/Documents/BACNET/ListeriomicsSample/Database/Genomes/Listeria monocytogenes EGD-e/GCF_000196035.1_ASM19603v1.fna
/Users/christophebecavin/Documents/BACNET/ListeriomicsSample/Database/Genomes/Listeria monocytogenes EGD-e/GCF_000196035.1_ASM19603v1_genomic.fna
Number of chromosomes found 1
lmo0001	318	1673	1356	+ (dnaA)
lmo0002	1867	3012	1146	+ (dnaN)
lmo0003	3121	4464	1344	+ ()
lmo0004	4644	4865	222	+ ()
lmo0005	4869	5981	1113	+ (recF)
lmo0006	6030	7970	1941	+ (gyrB)
lmo0007	8065	10593	2529	+ (gyrA)
lmo0008	10728	12242	1515	+ ()
lmo0009	12258	12776	519	+ ()
lmo0010	12918	13886	969	+ ()
........
lmot01	82705	82777	73	+ ()
lmor01	237466	239020	1555	+ ()
lmor02	239265	242195	2931	+ ()
lmor03	242276	242385	110	+ ()
........

Search gene and print available information

String geneName = "lmo0200";
String genomeName = Genome.EGDE_NAME;
Genome genome = Genome.loadGenome(genomeName);
// search gene
Gene gene = genome.getGeneFromName(geneName);
// print general information
System.out.println(gene + " " + gene.getInfo());

Expected output with ListeriomicsSample

Load Listeria monocytogenes EGD-e
/Users/christophebecavin/Documents/BACNET/ListeriomicsSample/Database/Genomes/Listeria monocytogenes EGD-e/GCF_000196035.1_ASM19603v1.fna
/Users/christophebecavin/Documents/BACNET/ListeriomicsSample/Database/Genomes/Listeria monocytogenes EGD-e/GCF_000196035.1_ASM19603v1_genomic.fna
Number of chromosomes found 1
lmo0200	203640	204353	714	- prfA, listeriolysin positive regulatory protein

Search gene and print its sequence

(DNA and AA)

String geneName = "lmo0200";
String genomeName = Genome.EGDE_NAME;
Genome genome = Genome.loadGenome(genomeName);
// search gene
Gene gene = genome.getGeneFromName(geneName);
// print gene nucleotide sequence
System.out.println(gene.getSequence());
// print gene amino acid sequence
System.out.println(gene.getSequenceAA());

Expected output with ListeriomicsSample

Load Listeria monocytogenes EGD-e
/Users/christophebecavin/Documents/BACNET/ListeriomicsSample/Database/Genomes/Listeria monocytogenes EGD-e/GCF_000196035.1_ASM19603v1.fna
/Users/christophebecavin/Documents/BACNET/ListeriomicsSample/Database/Genomes/Listeria monocytogenes EGD-e/GCF_000196035.1_ASM19603v1_genomic.fna
Number of chromosomes found 1
ATGAACGCTCAAGCAGAAGAATTCAAAAAATATTTAGAAACTAACGGGATAAAACCAAAACAATTTCATAAAAAAGAACTTATTTTTAACCAATGGGATCCACAAGAATATTGTATTTTTCTATATGATGGTATCACAAAGCTCACGAGTATTAGCGAGAACGGGACCATCATGAATTTACAATACTACAAAGGGGCTTTCGTTATAATGTCTGGCTTTATTGATACAGAAACATCGGTTGGCTATTATAATTTAGAAGTCATTAGCGAGCAGGCTACCGCATACGTTATCAAAATAAACGAACTAAAAGAACTACTGAGCAAAAATCTTACGCACTTTTTCTATGTTTTCCAAACCCTACAAAAACAAGTTTCATACAGTCTAGCTAAATTTAATGATTTTTCGATTAACGGGAAGCTTGGCTCTATTTGCGGTCAACTTTTAATCCTGACCTATGTGTATGGTAAAGAAACTCCTGATGGCATCAAGATTACACTGGATAATTTAACAATGCAGGAGTTAGGATATTCAAGTGGCATCGCACATAGCTCAGCTGTTAGCAGAATTATTTCCAAATTAAAGCAAGAGAAAGTTATCGTGTATAAAAATTCATGCTTTTATGTACAAAATCTTGATTATCTCAAAAGATATGCCCCTAAATTAGATGAATGGTTTTATTTAGCATGTCCTGCTACTTGGGGAAAATTAAATTAA
MNAQAEEFKKYLETNGIKPKQFHKKELIFNQWDPQEYCIFLYDGITKLTSISENGTIMNLQYYKGAFVIMSGFIDTETSVGYYNLEVISEQATAYVIKINELKELLSKNLTHFFYVFQTLQKQVSYSLAKFNDFSINGKLGSICGQLLILTYVYGKETPDGIKITLDNLTMQELGYSSGIAHSSAVSRIISKLKQEKVIVYKNSCFYVQNLDYLKRYAPKLDEWFYLACPATWGKLN

Search gene and print its homologs

Print result as fasta file

String geneName = "lmo0200";
String genomeName = Genome.EGDE_NAME;
Genome genome = Genome.loadGenome(genomeName);
// search gene
Gene gene = genome.getGeneFromName(geneName);
ArrayList<String> listResults = new ArrayList<String>();
// go trough all homologs
for(String genomeNameHomolog : gene.getConservationHashMap().keySet()) {
    Genome genomeHomolog = Genome.loadGenome(genomeNameHomolog);
    String homologInfo = gene.getConservationHashMap().get(genomeNameHomolog);
    String genehomologName = homologInfo.split(";")[0];
    String similarity = homologInfo.split(";")[2];
    Gene genehomolog = genomeHomolog.getGeneFromName(genehomologName);
    listResults.add("> "+ genehomologName + " - "+genomeNameHomolog + " - similarity="+similarity);
    listResults.add(genehomolog.getSequenceAA());
}
for(String result : listResults) {
    System.out.println(result);
}

Expected output with ListeriomicsSample

Load Listeria monocytogenes EGD-e
/Users/christophebecavin/Documents/BACNET/ListeriomicsSample/Database/Genomes/Listeria monocytogenes EGD-e/GCF_000196035.1_ASM19603v1.fna
/Users/christophebecavin/Documents/BACNET/ListeriomicsSample/Database/Genomes/Listeria monocytogenes EGD-e/GCF_000196035.1_ASM19603v1_genomic.fna
Number of chromosomes found 1
Load Listeria monocytogenes EGD
/Users/christophebecavin/Documents/BACNET/ListeriomicsSample/Database/Genomes/Listeria monocytogenes EGD/GCF_000582845.1_SV_1.fna
/Users/christophebecavin/Documents/BACNET/ListeriomicsSample/Database/Genomes/Listeria monocytogenes EGD/GCF_000582845.1_SV_1_genomic.fna
Number of chromosomes found 1
Load Listeria monocytogenes 10403S
/Users/christophebecavin/Documents/BACNET/ListeriomicsSample/Database/Genomes/Listeria monocytogenes 10403S/GCF_000168695.2_ASM16869v2_genomic.fna
/Users/christophebecavin/Documents/BACNET/ListeriomicsSample/Database/Genomes/Listeria monocytogenes 10403S/GCF_000168695.2_ASM16869v2.fna
Number of chromosomes found 1
> lmo0200 - Listeria monocytogenes EGD-e - similarity=1.0
MNAQAEEFKKYLETNGIKPKQFHKKELIFNQWDPQEYCIFLYDGITKLTSISENGTIMNLQYYKGAFVIMSGFIDTETSVGYYNLEVISEQATAYVIKINELKELLSKNLTHFFYVFQTLQKQVSYSLAKFNDFSINGKLGSICGQLLILTYVYGKETPDGIKITLDNLTMQELGYSSGIAHSSAVSRIISKLKQEKVIVYKNSCFYVQNLDYLKRYAPKLDEWFYLACPATWGKLN
> LMON_RS00965 - Listeria monocytogenes EGD - similarity=0.9915612
MNAQAEEFKKYLETNGIKPKQFHKKELIFNQWDPQEYCIFLYDGITKLTSISENGTIMNLQYYKGAFVIMSGFIDTETSVGYYNLEVISEQATAYVIKINELKELLSKNLTHFFYVFQTLQKQVSYSLAKFNDFSINGKLGSICSQLLILTYVYGKETPDGIKITLDNLTMQELGYSSGIAHSSAVSRIISKLKQEKVIVYKNSCFYVQNLDYLKRYAPKLDEWFYLAYPATWGKLN
> LMRG_RS00965 - Listeria monocytogenes 10403S - similarity=1.0
MNAQAEEFKKYLETNGIKPKQFHKKELIFNQWDPQEYCIFLYDGITKLTSISENGTIMNLQYYKGAFVIMSGFIDTETSVGYYNLEVISEQATAYVIKINELKELLSKNLTHFFYVFQTLQKQVSYSLAKFNDFSINGKLGSICGQLLILTYVYGKETPDGIKITLDNLTMQELGYSSGIAHSSAVSRIISKLKQEKVIVYKNSCFYVQNLDYLKRYAPKLDEWFYLACPATWGKLN

Search gene and relevant omics datasets

Get transcriptomes and proteomes in which the gene is found.

String geneName = "lmo0200";
String genomeName = Genome.EGDE_NAME;
Genome genome = Genome.loadGenome(genomeName);
// search gene
Gene gene = genome.getGeneFromName(geneName);

// get transcriptomics datasets
double cutoffLogFC = GenomeElementAtlas.DEFAULT_LOGFC_CUTOFF;
Filter filter = new Filter();
filter.setCutOff1(cutoffLogFC);
GenomeElementAtlas atlas = new GenomeElementAtlas(gene, filter);
System.out.println("Over expressed in " + atlas.getOverBioConds().size() + " transcriptomic datasets");
for(String bioCond : atlas.getOverBioConds()) {
    System.out.println(bioCond);
}
System.out.println("Under expressed in " + atlas.getUnderBioConds().size() + " transcriptomic datasets");
// Print datasets over expressed
for(String bioCond : atlas.getUnderBioConds()) {
    System.out.println(bioCond);     
}
System.out.println("Not diff expressed in " + atlas.getNotDiffExpresseds().size() + " transcriptomic datasets");
for(String bioCond : atlas.getNotDiffExpresseds()) {
    System.out.println(bioCond); 
}

// get proteomics datasets 
ExpressionMatrix exprProteomesMatrix = Database.getInstance().getExprProteomesTable(genomeName);
System.out.println(gene.getName());
if (exprProteomesMatrix.getRowNames().containsKey(gene.getName())) {
    for (String header : exprProteomesMatrix.getHeaders()) {
        double value = exprProteomesMatrix.getValue(gene.getName(), header);
        if (value > 0) {
            System.out.println("Found in " + header + " proteome");
        }
    }
}

Expected output with ListeriomicsSample

Load Listeria monocytogenes EGD-e
/Users/christophebecavin/Documents/BACNET/ListeriomicsSample/Database/Genomes/Listeria monocytogenes EGD-e/GCF_000196035.1_ASM19603v1.fna
/Users/christophebecavin/Documents/BACNET/ListeriomicsSample/Database/Genomes/Listeria monocytogenes EGD-e/GCF_000196035.1_ASM19603v1_genomic.fna
Number of chromosomes found 1
Listeria monocytogenes EGD-e
/Users/christophebecavin/Documents/BACNET/ListeriomicsSample/Database/Transcriptomes/Table_LOGFC_Listeria monocytogenes EGD-e
Over expressed in 2 transcriptomic datasets
EGD_WT vs EGDe_280212
prfA_Star vs EGDe_280212
Under expressed in 3 transcriptomic datasets
Extracellular_UGiessen_2010 vs IFN_Intracellular_UGiessen_2010
Extracellular_UGiessen_2010 vs Intracellular_UGiessen_2010
Macrophages_2014_EGDe vs BHI_2014_EGDe
Not diff expressed in 0 transcriptomic datasets
/Users/christophebecavin/Documents/BACNET/ListeriomicsSample/Database/Proteomes/Table_Expr_Listeria monocytogenes EGD-e
lmo0200
Found in Stat_2009_EGDe proteome

Show expression of gene in different omics dataset

String geneName = "lmo0196";
String genomeName = Genome.EGDE_NAME;
Genome genome = Genome.loadGenome(genomeName);
// search gene
Gene gene = genome.getGeneFromName(geneName);

/*
 * Select some datasets
 */
ArrayList<String> bioConditions = new ArrayList<>();
bioConditions.add("BHI_2014_EGDe"); // RNASeq data
bioConditions.add("EGDe_280212"); // Tiling array data
bioConditions.add("Extracellular_BHI_2011_EGDe"); // proteomics data

/*
 * Load all datasets (Load absolute expression values)
 * Modified from: bacnet.genomeBrowser.core.DataTrack.loadData()
 */
ArrayList<OmicsData> omics = new ArrayList<OmicsData>();
for (String bioCondName : bioConditions) {
    BioCondition bioCond = BioCondition.getBioCondition(bioCondName);
    for (Tiling tiling : bioCond.getTilings()) {
        if (!tiling.isInfoRead()) {
            tiling.read();
            omics.add(tiling);
        }
    }
    for (OmicsData tscData : bioCond.getOmicsData()) {
        if (tscData.getType() == TypeData.RNASeq) {
            ExpressionData rnaseq = (ExpressionData) tscData;
            rnaseq.load();
            omics.add(rnaseq);
        }
    }
    for (ProteomicsData proteome : bioCond.getProteomes()) {
        if (!proteome.isLoaded()) {
            proteome.load();
            omics.add(proteome);
        }
    }
}

// Get expression of the gene in each omics dataset
for(OmicsData omic : omics) {
    if(omic instanceof ExpressionData) {
        if(omic.getType() == TypeData.RNASeq) {
            ExpressionData ngs = (ExpressionData) omic;
            double[] values = ngs.read(gene.getBegin(), gene.getEnd());
            double value = VectorUtils.mean(values);
            System.out.println("RNA expression of " +gene.getName() + " = "+ ngs.getName()+ " " + value);
        }else if(omic.getType() == TypeData.Tiling) {
            Tiling tiling = (Tiling) omic;
            double[] values = tiling.get(gene.getBegin(), gene.getEnd(), true);
            double value = VectorUtils.mean(values);
            System.out.println("Tiling expression of " +gene.getName() + " = "+ tiling.getName()+ " " + value);
        }
    }else if(omic instanceof ProteomicsData) {
        ProteomicsData proteome = (ProteomicsData) omic;
        double value = proteome.getValue(gene.getName(), ""+ColNames.VALUE);
        System.out.println("Proteome expression of " +gene.getName() + " = " + proteome.getName()+ " " + value);
    }
}

Expected output with ListeriomicsSample

RNA expression of lmo0196 = BHI_2014_EGDe_f 8.947220907622064
RNA expression of lmo0196 = BHI_2014_EGDe_r 0.0
Tiling expression of lmo0196 = EGDe_280212.+.gr 7.040657774895381
Tiling expression of lmo0196 = EGDe_280212.-.gr 1.9403730330008202
Proteome expression of lmo0196 = Extracellular_BHI_2011_EGDe 2.0

Correlate omics datasets

Get transcriptome and proteome and correlate their expression value

String genomeName = Genome.EGDE_NAME;
Genome genome = Genome.loadGenome(genomeName);

//Select some datasets
ArrayList<String> bioConditions = new ArrayList<>();
bioConditions.add("BHI_2014_EGDe"); // RNASeq data
bioConditions.add("EGDe_280212"); // Tiling array data
bioConditions.add("Extracellular_BHI_2011_EGDe"); // proteomics data

/*
 * Load all datasets (Load absolute expression values)
 * Modified from: bacnet.genomeBrowser.core.DataTrack.loadData()
 */
ArrayList<OmicsData> omics = new ArrayList<OmicsData>();
for (String bioCondName : bioConditions) {
    BioCondition bioCond = BioCondition.getBioCondition(bioCondName);
    for (Tiling tiling : bioCond.getTilings()) {
        if (!tiling.isInfoRead()) {
            tiling.read();
            omics.add(tiling);
        }
    }
    for (OmicsData tscData : bioCond.getOmicsData()) {
        if (tscData.getType() == TypeData.RNASeq) {
            ExpressionData rnaseq = (ExpressionData) tscData;
            rnaseq.load();
            omics.add(rnaseq);
        }
    }
    for (ProteomicsData proteome : bioCond.getProteomes()) {
        if (!proteome.isLoaded()) {
            proteome.load();
            omics.add(proteome);
        }
    }
}


// Get expression of the genes in each omics dataset
HashMap<String, double[]> dataTOvalue = new HashMap<String, double[]>();
for(OmicsData omic : omics) {
    System.out.println("Get expression value from "+omic.getName());
    double[] valueOmic = new double[genome.getGeneNames().size()];
    int k = 0;
    for(String geneName : genome.getGeneNames()) {
        Gene gene = genome.getGeneFromName(geneName);
        if(omic instanceof ExpressionData) {
            if(omic.getType() == TypeData.RNASeq) {
                ExpressionData ngs = (ExpressionData) omic;
                double[] values = ngs.read(gene.getBegin(), gene.getEnd());
                double value = VectorUtils.mean(values);
                valueOmic[k] = value;
            }else if(omic.getType() == TypeData.Tiling) {
                Tiling tiling = (Tiling) omic;
                double[] values = tiling.get(gene.getBegin(), gene.getEnd(), true);
                double value = VectorUtils.mean(values);
                valueOmic[k] = value;
            }
        }else if(omic instanceof ProteomicsData) {
            ProteomicsData proteome = (ProteomicsData) omic;
            double value = proteome.getValue(gene.getName(), ""+ColNames.VALUE);
            valueOmic[k] = value;
        }
        k++;
    }
    dataTOvalue.put(omic.getName(), valueOmic);
}

// calculate correlation
System.out.println(dataTOvalue.size());
for(int i=0;i<dataTOvalue.size();i++) {
    String data1 = (String) dataTOvalue.keySet().toArray()[i];
    for(int j=i+1;j<dataTOvalue.size();j++) {
        String data2 = (String) dataTOvalue.keySet().toArray()[j];
        double pearson = VectorUtils.pearsonCorrelation(dataTOvalue.get(data1), dataTOvalue.get(data2));
        System.out.println("Pearson correlation " + data1 + " vs " + data2 + " = "+pearson);
    }
}

Expected output with ListeriomicsSample

Get expression value from BHI_2014_EGDe_f
Get expression value from BHI_2014_EGDe_r
Get expression value from EGDe_280212.+.gr
Get expression value from EGDe_280212.-.gr
Get expression value from Extracellular_BHI_2011_EGDe
5
Pearson correlation BHI_2014_EGDe_r vs BHI_2014_EGDe_f = -0.41445242767486445
Pearson correlation BHI_2014_EGDe_r vs Extracellular_BHI_2011_EGDe = 0.18967716183382038
Pearson correlation BHI_2014_EGDe_r vs EGDe_280212.+.gr = -0.1271332697577054
Pearson correlation BHI_2014_EGDe_r vs EGDe_280212.-.gr = 0.8343485426119056
Pearson correlation BHI_2014_EGDe_f vs Extracellular_BHI_2011_EGDe = 0.09040552038115299
Pearson correlation BHI_2014_EGDe_f vs EGDe_280212.+.gr = 0.7916789004459144
Pearson correlation BHI_2014_EGDe_f vs EGDe_280212.-.gr = -0.24692357602934614
Pearson correlation Extracellular_BHI_2011_EGDe vs EGDe_280212.+.gr = 0.13169483731106035
Pearson correlation Extracellular_BHI_2011_EGDe vs EGDe_280212.-.gr = 0.15163077495892452
Pearson correlation EGDe_280212.+.gr vs EGDe_280212.-.gr = 0.04453016177144432

Load table and add annotation

ExpressionMatrix matrix = ExpressionMatrix.loadTab("/Users/user/exprMatrix.txt", true);
matrix = Annotation.addAnnotation(matrix, Genome.loadEgdeGenome());
matrix.saveTab("/Users/user/exprMatrix_Annot.txt","Locustag");

Display omics dataset on GenomeViewer

This last piece of script has to be put in another function. It has be added to TestPart.runPostTests(EPartService partService). This is explained by the fact that GenomeViewer should be ran after the InitPage is created. All displays should be ran at the end of bacnet.e4.rap startup.

ArrayList<String> bioConditions = new ArrayList<>();
bioConditions.add("EGDe_280212");
bioConditions.add("BHI_2014_EGDe");
bioConditions.add("EGDe_37C_TSS");
bioConditions.add("EGDe_37C_RiboSeq");
bioConditions.add("EGDe_37C_TermSeq");
GenomeTranscriptomeView.displayGenomeElementAndBioConditions(partService, Genome.EGDE_NAME, bioConditions, "");

Expected output with ListeriomicsSample multi_omics_viewer