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Vaccine drug targeting

Created: 2011-04-01 09:23:14 Last updated: 2011-04-01 09:24:37

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Workflow Components

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Titles (0)

Descriptions (0)

Dependencies (0)

Inputs (3)

Name	Description
FileName
PathogenicStrain
NonPathogenicStrain

Processors (6)

Name	Type	Description
Beanshell_2	beanshell	Script String[] seq1 = VariantsInSubject.split("\n"); ArrayList seq3 = Kegg_descriptions; ArrayList seq4 = pathdescr; ArrayList seq5 = URL; ArrayList extra = extrainfo; fileOut=""; for (int i=0;i<=seq1.length-1;i++){ if(!seq3.get(i).contains("hypothetical")){ if((pathdescr.get(0)).get(i).contains("path:")){ fileOut = fileOut +"gi accesion: "+seq1[i]+"\nKegg ID & Cell. Funct.: "+seq3.get(i)+"\nKEGG "+seq4.get(0).get(i)+"\n"+extra.get(0).get(i); for(int j=0;j<=seq5.get(i).size()-1;j++){ fileOut = fileOut+"\n-URL:"+seq5.get(i).get(j); } fileOut = fileOut+"\n\n"; } else{ fileOut = fileOut +"gi accession: "+seq1[i]+"\nKegg ID & Cell. Funct.: "+seq3.get(i)+"\n"+extra.get(0).get(i)+"\n\n"; } } }
Write_Text_File	localworker	Script BufferedWriter out = new BufferedWriter(new FileWriter(outputFile)); out.write(filecontents); out.close(); outputFile = filecontents;
NCBIGitoKeggPathways	workflow
Beanshell	beanshell	Script List split = new ArrayList(); String[] result = string.split("\n"); for (int i = 0; i < result.length; i++) { split.add(result[i]); }
Workflow1	workflow
Workflow62	workflow

Beanshells (11)

Name	Inputs	Outputs
Beanshell_2	Kegg_descriptions VariantsInSubject URL pathdescr extrainfo	fileOut
Beanshell	string	split
Beanshell	input	output
Beanshell_2	input	output
Beanshell_3	GOterm pubmed	extrainfo
Beanshell_4	gilist	output
remove_Nulls	input	output
extract_gene_ids	input	output
remove_nulls_2	input	output
add_ncbi_to_string	input	output
Beanshell	BlastReport	filtered

Outputs (0)

Datalinks (12)

Source	Sink
NCBIGitoKeggPathways:kegg_descriptions	Beanshell_2:Kegg_descriptions
NCBIGitoKeggPathways:pathway_descriptions	Beanshell_2:pathdescr
NCBIGitoKeggPathways:URL	Beanshell_2:URL
Workflow1:VariantsInSubject	Beanshell_2:VariantsInSubject
Workflow62:extrainfo	Beanshell_2:extrainfo
Beanshell_2:fileOut	Write_Text_File:filecontents
FileName	Write_Text_File:outputFile
Beanshell:split	NCBIGitoKeggPathways:Gi_numbers
Workflow1:VariantsInSubject	Beanshell:string
NonPathogenicStrain	Workflow1:SubjectURL
PathogenicStrain	Workflow1:queryURL
Workflow1:VariantsInSubject	Workflow62:GiNumber