netco4biomed.and

#!/usr/bin/env anduril-runner

//$ -b /opt/moksiskaan/db/pipeline
//$ -b $ANDURIL_BUNDLES/NetCon4BioMed


// Settings

reexecute="changed"

// Init

checkpoint_init=BashEvaluate(script="echo exec-1- > ../../progress.txt",failOnErr=false)

moksiskaanInit = MoksiskaanInit()
include moksiskaanPipelines+"/Studies.and"

linkStyles = INPUT(path = moksiskaanBundle+"/functions/CandidateReport/LinkTypeProperties.csv")
linkFunctions = INPUT(path = moksiskaanBundle+"/functions/CandidateReport/LinkTypeFunctions.csv")

linkRules = "Keggonen"
linkTypes =  //LinkType_pathway_precedence+","+
            //LinkType_protein_protein_interaction+","+
            LinkType_protein_activation+","+
            LinkType_protein_inhibition+","+
            LinkType_protein_state_change+","+
            //LinkType_protein_binding+","+
            //LinkType_protein_dissociation+","+
            LinkType_gene_expression+","+
            LinkType_gene_repression+","+
            LinkType_phosphorylation+","+
            LinkType_dephosphorylation+","+
            LinkType_glycosylation+","+
            LinkType_ubiquitination+","+
            LinkType_methylation

// We provide heuristics
//heuristics_in = INPUT(path="controllable.txt")

// Script tha creates the zip file
zip_sc=INPUT(path="makezip.sh")

// Script for coloring detail file
color_script = INPUT(path="detail_ex.sh")

// Gene name to Ensembl ID mapping
name_ensembl_map=INPUT(path="mart_export.txt")

// User input
organism = Organism_Homo_sapiens

//check_target = BashEvaluate(script="touch "+$PWD+"/target_genes")
if(std.exists($PWD+"/target_genes", type="file")){
    target_genes_pre = INPUT(path=$PWD+"/target_genes")
    target_genes=SearchReplace(file=target_genes_pre,key00="\\s",value00="\n")
}else{
    target_genes=StringInput(content="")
}


target_genes_header = CSVCleaner(original=target_genes, columnsIn="Target Gene")

if(std.exists($PWD+"/network", type="file")){
    listGenes_pre=INPUT(path=$PWD+"/network")
    listGenes_pre2=SearchReplace(file=listGenes_pre,key00="\\s",value00="\n")
    listGenes=BashEvaluate(var1=listGenes_pre2,var2=target_genes,script="cat @var1@ > @optOut1@; echo '\n' >> @optOut1@; cat @var2@ >> @optOut1@")
//    listGenes=CSVJoin(csv1=listGenes_pre,csv2=target_genes, useKeys=false)
    listGenes_header = CSVCleaner(original=listGenes.optOut1, columnsIn="Target Gene")
}else{
    listGenes=StringInput(content="")
    listGenes_header=StringInput(content="Target Gene\nnone")
}



//check_cancer_include = BashEvaluate(script="touch "+$PWD+"/cancer_checkbox")
if(std.exists($PWD+"/cancer_checkbox", type="file")){
    cancer_include = INPUT(path=$PWD+"/cancer_checkbox")
}else{
    cancer_include=StringInput(content="")
}
//cancer_include = INPUT(path=$PWD+"/cancer_checkbox",@bind=check_cancer_include)
cancer_include_file = std.fRead(cancer_include)
cancer_include_file_fil = std.strReplace(cancer_include_file, " ", "")

cancer_cells = std.fRead($PWD+"/cancers")
if (cancer_cells != "none")
{
cancer_file_path = std.concat("cancer_data/", cancer_cells,".csv")
cancer_file_path_fil = std.strReplace(cancer_file_path, " ", "")
cell_file = INPUT(path=cancer_file_path_fil)
cell_file_header = CSVCleaner(original=cell_file, columns="Gene name")
cell_file_header_pr = CSVCleaner(original=cell_file_header, columnsIn="Target Gene")
target_gene_comb = CSVJoin(csv1=target_genes_header, csv2=cell_file_header_pr, useKeys=false) // List of target genes
    if (cancer_include_file_fil == "on") {
	all_genes = CSVJoin(csv1=listGenes_header,csv2=cell_file_header_pr, useKeys=false) // List of genes to build the network
    }
    else
    {
	all_genes = listGenes_header // List of genes to build the network
    }
}
else
{
    all_genes = listGenes_header // List of genes to build the network
    target_gene_comb=target_genes_header // List of target genes
}

gap_file = std.fRead($PWD+"/gap")
gap_file_fil = std.strReplace(gap_file, " ", "")
gap = std.convert(gap_file_fil, type="int")
if (gap > 6) {gap = 6}
if (gap < 1) {gap = 1}

if(std.exists($PWD+"/drug", type="file")){
    drug_input = INPUT(path=$PWD+"/drug")
}else{
    drug_input=StringInput(content="")
}

//check_drug=BashEvaluate(script="touch "+$PWD+"/drug")
//drug_input=INPUT(path=$PWD+"/drug",@bind=check_drug)
drugable_file = std.fRead(drug_input)
drugable = std.strReplace(drugable_file, " ", "")

missedGenes=""

skip_net_gen=0

if (std.exists($PWD+"/graphml", type="file")) {
    pathway = INPUT(path=$PWD+"/graphml")
    annotationPathway = GraphAnnotator(graph = pathway)
    checkpoint_12=BashEvaluate(script="echo done-1- > ../../progress.txt; echo skip-2- >> ../../progress.txt; echo exec-3- >> ../../progress.txt",failOnErr=false,@bind=annotationPathway)
    skip_net_gen=1
} else {
    
/*    geneConvert=KorvasieniAnnotator(sourceKeys=all_genes,
                    //connection=Properties,
                    indicator=true,
                    inputDB=".GeneName",
                    inputType="Gene",
                    targetDB=".GeneId",
                    unique=true)*/
      geneConvert=CSVFilter(csv=name_ensembl_map,auxiliary=all_genes,idColumn="GeneName",matchColumn="Target Gene",includeColumns=".GeneId,GeneName",rename="GeneName=Target Gene")
                    
                    
    EnsemblId=CSVFilter(csv=geneConvert, includeColumns=".GeneId", nonMissing=1)

    missingGenes_pre=CSVFilter(csv=all_genes, auxiliary=geneConvert, idColumn="Target Gene", matchColumn="Target Gene",negate=true,includeColumns="")
    missingGenes=CSVFilter(csv=missingGenes_pre,includeColumns="Target Gene")

    nMissed=std.nRows(missingGenes)
    if(nMissed>0){
	missedGenes="<pre>THE FOLLOWING GENES CANNOT BE VALIDATED:\n"
	for row: std.itercsv(missingGenes){
	    missedGenes=missedGenes+std.recordToString(row,keys=false)+"\n"
	}
	missedGenes=missedGenes+"</pre>"
    }

    FilEnsemblId=SearchReplace(file=EnsemblId,key00=",",value00="\"\n\"")

    expandType="connected"
//    expandType="both"

    // Generating the pathway
    xrefCol=".GeneId"


//    FilEnsemblId=SearchReplace(file=all_genes,key00="Target Gene",value00=xrefCol)

    checkpoint_1=BashEvaluate(script="echo done-1- > ../../progress.txt; echo exec-2- >> ../../progress.txt",failOnErr=false,@bind=FilEnsemblId)
      
    pathway = CandidatePathway(hits = FilEnsemblId,
				linkTypes = linkTypes,
				linkStyles = linkStyles,
				annotRules = linkRules, 
				organism = Organism_Homo_sapiens,
				xrefType = 10,
				xrefCol = xrefCol,
				maxGap=gap,
				expand=expandType,
				hitProperties="isHit=true,color=#00EE00,penwidth=3",
				@execute=reexecute
				)

    graphml_output = BashEvaluate(script="cp @var1@ ../../network.graphml;cp @var2@ ../../legend.graphml",var1=pathway.graph,var2=pathway.legend,failOnErr=false)

    annotationPathway = GraphAnnotator(graph = pathway.graph)

//    vis_graphml = GraphVisualizer(graph=pathway.graph)

//    graphml_pdf = LatexPDF(document=vis_graphml)

//    pdf_output = BashEvaluate(script="cp @var1@ ../../network.pdf",var1=graphml_pdf.document,failOnErr=false)
    vis_graph_gen = BashEvaluate(script="cd ../../; ../../vis_graphml.and &",failOnErr=false,@bind=graphml_output)

    checkpoint_2=BashEvaluate(script="echo done-1- > ../../progress.txt; echo done-2- >> ../../progress.txt; echo exec-3- >> ../../progress.txt",failOnErr=false,@bind=annotationPathway)
}


vertexLabel=CSVFilter(csv=annotationPathway.vertexAttributes, includeColumns="Vertex, label")

edgeNumbers=CSVFilter(csv=annotationPathway.edgeAttributes, includeColumns="Vertex1, Vertex2")

edgeVertex=CSVJoin(csv1=edgeNumbers,csv2=vertexLabel, keyColumnNames="Vertex1, Vertex")
edgeVertexRename=CSVCleaner(original=edgeVertex, rename="label=label1")
edgeVertexClean=CSVJoin(csv1=edgeVertexRename,csv2=vertexLabel, keyColumnNames="Vertex2, Vertex")
network=CSVCleaner(original=edgeVertexClean, columns="label1, label",rename="label1=Source, label=Target")

netSize=std.nRows(network)

// Filtering the input to NetControl component
fil_case_source = CSVFilter(csv=target_gene_comb, auxiliary=network, matchColumn="Source")

fil_case_target = CSVFilter(csv=target_gene_comb, auxiliary=network, matchColumn="Target")

fil_case_both = CSVJoin(csv1=fil_case_source,csv2=fil_case_target, useKeys=false)

fil_case_both_no_header = CSVCleaner(original=fil_case_both, dropHeader=true, skipQuotes="*")

network_no_header = CSVCleaner(original=network, dropHeader=true, skipQuotes="*")

net_output = BashEvaluate(script="cp @var1@ ../../network.txt",var1=network_no_header,failOnErr=false)


// NetControl component
// there can be more conditions in running NetControl, change when decided on final specification


drugSize=0
if(std.exists($PWD+"/drug_targets", type="file")){
    additional_drug_targets_pre=INPUT(path=$PWD+"/drug_targets")
    additional_drug_targets_pre2=SearchReplace(file=additional_drug_targets_pre,key00="\\s",value00="\n")
    additional_target_genes=CSVCleaner(original=additional_drug_targets_pre2,columnsIn="targets",trim=true)
    drugSize=std.nRows(additional_target_genes)
}else{
    additional_target_genes=StringInput(content="targets")
}

if (skip_net_gen == 1)
{
    checkpoint_3=BashEvaluate(script="echo done-1- > ../../progress.txt; echo skip-2- >> ../../progress.txt; echo done-3- >> ../../progress.txt; echo exec-4- >> ../../progress.txt",failOnErr=false,@bind=network_no_header)
}else{
    checkpoint_3=BashEvaluate(script="echo done-1- > ../../progress.txt; echo done-2- >> ../../progress.txt; echo done-3- >> ../../progress.txt; echo exec-4- >> ../../progress.txt",failOnErr=false,@bind=network_no_header)
}

if (drugable == "on") {
    drug_targets_pre = INPUT(path="Drug-Target_Approved_Proteins.txt")
    if(drugSize>0){
	drug_targets_pre2=CSV2IDList(table1=drug_targets_pre,table2=additional_target_genes)
	heuristics_in=INPUT(path="drug_targets_heuristics.txt")
    }
    else{
	drug_targets_pre2=CSV2IDList(table1=drug_targets_pre)
	heuristics_in=INPUT(path="drug_targets_heuristics.txt")
    }
    drug_targets=CSVCleaner(original=drug_targets_pre2,dropHeader=true,skipQuotes="*")
    if (netSize>0){
        nc_result = NetControl(graph=network_no_header, targets=fil_case_both_no_header, heuristics=heuristics_in, controllable=drug_targets)
    }
}
else {
    if(drugSize>0){
	drug_targets_pre2=CSV2IDList(table1=additional_target_genes)
	drug_targets=CSVCleaner(original=drug_targets_pre2,dropHeader=true,skipQuotes="*")
	heuristics_in=INPUT(path="drug_targets_heuristics.txt")
	if (netSize>0){
	    nc_result = NetControl(graph=network_no_header, targets=fil_case_both_no_header, heuristics=heuristics_in, controllable=drug_targets)
        }
    }
    else{
	heuristics_in=INPUT(path="simple_fast.txt")
	if (netSize>0){
	    nc_result = NetControl(graph=network_no_header, targets=fil_case_both_no_header, heuristics=heuristics_in)
        }
    }
}

if(netSize==0){
    // Creating the result zip file

    checkpoint_5=BashEvaluate(script="echo done-1- > ../../progress.txt; echo fail-2- >> ../../progress.txt; echo fail-3- >> ../../progress.txt; echo fail-4- >> ../../progress.txt; echo exec-5- >> ../../progress.txt",failOnErr=false,@bind=network)


    message=StringInput(content="<em><font color=red>Not enough data to build the network</font></em><br><font color=red>"+missedGenes+"</font>")

    cp_zip = BashEvaluate(script=zip_sc,var6=message,failOnErr=false)

    // Copying resulting files to the top of the $workingdir
    cp_output = BashEvaluate(script="cp @var1@.zip ../../result.zip; cp @var2@ ../../res",
		var1=cp_zip.optOut1, var2=message)

    OUTPUT(cp_zip.optOut1)

    checkpoint_6=BashEvaluate(script="echo done-1- > ../../progress.txt; echo fail-2- >> ../../progress.txt; echo fail-3- >> ../../progress.txt; echo fail-4- >> ../../progress.txt; echo done-5- >> ../../progress.txt",failOnErr=false,@bind=cp_output)

}else{

    if (skip_net_gen == 1)
    {
	checkpoint_5=BashEvaluate(script="echo done-1- > ../../progress.txt; echo skip-2- >> ../../progress.txt; echo done-3- >> ../../progress.txt; echo done-4- >> ../../progress.txt; echo exec-5- >> ../../progress.txt",failOnErr=false,@bind=nc_result)
    }else{
	checkpoint_5=BashEvaluate(script="echo done-1- > ../../progress.txt; echo done-2- >> ../../progress.txt; echo done-3- >> ../../progress.txt; echo done-4- >> ../../progress.txt; echo exec-5- >> ../../progress.txt",failOnErr=false,@bind=nc_result)
    }

    message=StringInput(content="<em><font color=green>Status: OK</font></em><br><font color=red>"+missedGenes+"</font>")

    nc_result_details=BashEvaluate(script="tail -n +3 @var1@", var1=nc_result.detail)

    cp_output_nc_result_details = BashEvaluate(script="cp @var6@ ../../result/details.txt; ",
		var6=nc_result_details.stdOut,failOnErr=false)
    

    // Filtering the output of NetControl component to make it suitable for creating a graph 
    nc_result_split = TextFileSplitter(file=nc_result.count,
                 splitRegexp=".*\\bExtra\\b.*")
                 

    cp_output_nc_result_split = BashEvaluate(script="cp @var4@ ../../result/driven.csv;",
		var4=nc_result_split.array["1"],failOnErr=false)
    
    nc_extra = CSVCleaner(original=nc_result_split.array["2"], dropHeader=true)

    cp_output_nc_extra = BashEvaluate(script="cp @var5@ ../../result/extra.csv;",
		var5=nc_extra, failOnErr=false)
    
    nc_extra_clean = CSVCleaner(original=nc_extra, rename="Extra=name, Targets=fillcolor")
    nc_extra_color = CSVCleaner(original=nc_extra_clean, replace="fillcolor\n([0-9])\n#ff0000")

    nc_driver = CSVCleaner(original=nc_result_split.array["1"], rename="Driven=name, Targets=fillcolor")
    nc_driver_color = CSVCleaner(original=nc_driver, replace="fillcolor\n([0-9])\n#00ffff")


    nc_driver_color_col = CSVCleaner(original=nc_driver_color, columns="name", dropHeader=true, skipQuotes="*")

    check_driver = std.fRead(nc_driver_color_col)
    if (check_driver != "") {
	driver_sh = BashEvaluate(script=color_script,var1=nc_driver_color_col, var2=nc_result.detail, failOnErr=false)
	driver_col = CSVCleaner(original=driver_sh.optOut2, columnsIn="name")
	driver_join = CSVJoin(csv1=driver_col, csv2=nc_driver_color, intersection=false)
	driver_join_clean = CSVCleaner(original=driver_join, naSymbol="\"#BF5FFF\"")
    }
    else {
	driver_join_clean = nc_driver_color
    }

    nc_extra_color_col = CSVCleaner(original=nc_extra_color, columns="name", dropHeader=true, skipQuotes="*")

    check_extra = std.fRead(nc_extra_color_col)
    if (check_extra != "") {
	extra_sh = BashEvaluate(script=color_script,var1=nc_extra_color_col, var2=nc_result.detail, failOnErr=false)
	extra_col = CSVCleaner(original=extra_sh.optOut2, columnsIn="name")
	extra_join = CSVJoin(csv1=extra_col, csv2=nc_extra_color, intersection=false)
	extra_join_clean = CSVCleaner(original=extra_join, naSymbol="\"#FFA500\"")
    }
    else {
	extra_join_clean = nc_extra_color
    }

    nc_both_color = CSVJoin(csv1=driver_join_clean,csv2=extra_join_clean, useKeys=false)

    // Annotating moksiskaan graph
    mok_vertex_att = CSVJoin(csv1=annotationPathway.vertexAttributes,csv2=nc_both_color, intersection=false, keyColumnNames="label,name")

    mok_vertex_att_clean = CSVCleaner(original=mok_vertex_att, columns="Vertex, BioentityId, EnsemblGeneId, color, fillcolor, isHit, label, penwidth, originalID", naSymbol="")

    mok_graph_ant_color = GraphAnnotator(graph=annotationPathway.graph, vertexAttributes=mok_vertex_att_clean)

    cp_output_graphml = BashEvaluate(script="cp @var3@ ../../result/network.graphml; ",
		var3=mok_graph_ant_color.graph,failOnErr=false)


    cp_zip_no_pdf = BashEvaluate(script=zip_sc,var2=mok_graph_ant_color.graph, 
			var3=nc_result_split.array["1"], var4=nc_extra, var5=nc_result_details.stdOut,failOnErr=false)

    // Copying resulting files to the top of the $workingdir
    cp_output_no_pdf = BashEvaluate(script="cp @var1@.zip ../../result.zip;",
		var1=cp_zip_no_pdf.optOut1,failOnErr=false)
    

    mok_vis_graph = GraphVisualizer(graph=mok_graph_ant_color.graph)

    mok_nc_pdf = LatexPDF(document=mok_vis_graph)

    // This does not work at the moment
    /* 
    mok_cyto = Pathway2Cytoscape(pathway=mok_graph_ant_color.graph,
                  //groups=SetList,
                  edgeCopy="arrowhead,color",
                  linkAttr="LinkTypeId",
                  nameAttr="label",
                  title="MyPathway",
                  tooltipAttr="",
                  vertexCopy="BioentityId,EnsemblGeneId,color,isHit,fillcolor",
                  weightAttr="LinkWeight")
    */



    // Creating the result zip file
    cp_zip = BashEvaluate(script=zip_sc,var1=mok_nc_pdf.document, var2=mok_graph_ant_color.graph, 
			var3=nc_result_split.array["1"], var4=nc_extra, var5=nc_result_details.stdOut,failOnErr=false)

    // Copying resulting files to the top of the $workingdir
    cp_output = BashEvaluate(script="cp @var1@.zip ../../result.zip; cp @var2@ ../../result/network.pdf; cp @var3@ ../../result/network.graphml; cp @var4@ ../../result/driven.csv; cp @var5@ ../../result/extra.csv; cp @var6@ ../../result/details.txt; ",
		var1=cp_zip.optOut1,var2=mok_nc_pdf.document, var3=mok_graph_ant_color.graph, 
			var4=nc_result_split.array["1"], var5=nc_extra, var6=nc_result_details.stdOut,failOnErr=false)
    cp_res = BashEvaluate(script="cp @var1@ ../../res", var1=message)
    OUTPUT(cp_zip.optOut1)
    OUTPUT(mok_nc_pdf.document)
    OUTPUT(mok_graph_ant_color.graph)
    OUTPUT(nc_result_split.array["1"])
    OUTPUT(nc_extra)
    OUTPUT(nc_result.detail)

    if (skip_net_gen == 1)
    {
	checkpoint_6=BashEvaluate(script="echo done-1- > ../../progress.txt; echo skip-2- >> ../../progress.txt; echo done-3- >> ../../progress.txt; echo done-4- >> ../../progress.txt; echo done-5- >> ../../progress.txt",failOnErr=false,@bind=cp_output)
    }else{
	checkpoint_6=BashEvaluate(script="echo done-1- > ../../progress.txt; echo done-2- >> ../../progress.txt; echo done-3- >> ../../progress.txt; echo done-4- >> ../../progress.txt; echo done-5- >> ../../progress.txt",failOnErr=false,@bind=cp_output)
    }
}