Vaccine Targets Workflow

Staphylococcus aureus

String encoded = java.net.URLEncoder.encode(contents_file, "UTF-8");

String url_string = "http://cypher001.ncl.ac.uk:8080/examples/servlets/servlet/HelloWorldExample?contents="+encoded;

String encoded = java.net.URLEncoder.encode(contents_file, "UTF-8");

String url_string = "http://cypher001.ncl.ac.uk:8080/examples/servlets/servlet/HelloWorldExample?contents="+encoded;

String [] lines = in1.split("\n");
List list = new ArrayList();

for (int i =0;i
String [] lines = parsed_uniprot.split("\n");
List list = new ArrayList();


for (String line: lines)
{
	if (line.startsWith(identifier_name))
	{
		list.add(line.substring(3,line.length()).trim());
	}
}

out1 = list;
String [] lines = parsed_uniprot.split("\n");
List list = new ArrayList();


for (String line: lines)
{
	if (line.startsWith(identifier_name))
	{
		list.add(line.substring(identifier_name.length()+1,line.length()).trim());
	}
}

out1 = list;
String input = in1;

String pat = "<[^>]+>[^<]+";

java.util.regex.Pattern p = java.util.regex.Pattern.compile(pat);
java.util.regex.Matcher matcher = p.matcher(input);

String output = "";
List list = new ArrayList();

while(matcher.find())
{
	String match = input.substring(matcher.start()+1, matcher.end());
	if (match.contains("abstractText") || match.contains("fullName")
		|| match.contains("title") || match.contains("dx.doi.org")
		|| match.contains("yearOfPublication") || match.contains("volume")
		|| match.contains("pageInfo"))
	{
		list.add(match);
	}
}
String authors = "";
String abstractText ="";
String year = "";
String volume ="";
String pageInfo ="";
String link ="";
String journal = "";
String title = "";

for (Object o: list)
{
	String word = o.toString();
	int length = word.length();
	if (word.contains("abstractText"))
	{
		abstractText = word.substring(13, length);
	}
	else if (word.contains("fullName"))
	{
		authors += word.substring(9) +", ";
	}
	else if (word.contains("dx.doi.org"))
	{
		link = word.substring(4);
	}
	else if (word.contains("yearOfPublication"))
	{
		year = word.substring(18);
	}
	else if (word.contains("volume"))
	{
		volume = word.substring(7);
	}
	else if (word.contains("pageInfo"))
	{
		pageInfo = word.substring(9);
	}
	else if (word.contains("title") && journal.equals(""))
	{
		journal = word.substring(6);
	}
	else if (word.contains("title"))
	{
		title = word.substring(6);
	}

}


output = authors.substring(0,authors.length()-2) + " ("+year+"). "+title+". "+journal+", "+volume+ " :" + pageInfo+ ". "+link;

out1 = output;

String seperatorString = "\n";
if (seperator != void) {
	seperatorString = seperator;
}
StringBuffer sb = new StringBuffer();
for (Iterator i = data.iterator(); i.hasNext();) {
	String id = (String) i.next();
	sb.append(id);
	if (i.hasNext()) {
		sb.append(seperatorString);
	}
}
concatenated = sb.toString();

flatten(inputs, outputs, depth) {
	for (i = inputs.iterator(); i.hasNext();) {
	    element = i.next();
		if (element instanceof Collection && depth > 0) {
			flatten(element, outputs, depth - 1);
		} else {
			outputs.add(element);
		}
	}
}

outputlist = new ArrayList();

flatten(inputlist, outputlist, 1);
String seperatorString = "\n";
if (seperator != void) {
	seperatorString = seperator;
}
StringBuffer sb = new StringBuffer();
for (Iterator i = stringlist.iterator(); i.hasNext();) {
	String item = (String) i.next();
	sb.append(item);
	if (i.hasNext()) {
		sb.append(seperatorString);
	}
}
concatenated = sb.toString();

path = root + gi_num + ".faa";
//Title:


BufferedWriter out = new BufferedWriter(new FileWriter(outPutFile));

//////////////////////////////////////////////////////////////////
out.write("A-Team | Bioinformatics Solutions  ");

out.write(""+Title+"");


//Design Document Intro
//Beanshell Script:


String[] lines = Intro.split("\n");
String output = "";
for (String line: lines)
{
	output += ""+line+"";
}

out.write(output);


//Target Proteome IDs:
//Beanshell script:


lines = Tid.split("\n");
output = "Target species:";
for (String line: lines)
{
	output+= "    "+line+"";
}

out.write(output);


//Source Proteome IDs:
//Beanshell script:


lines = Sid.split("\n");
output = "Source species:";
for (String line: lines)
{
	output+= "    "+line+"";
}

out.write(output);


//Similarity Measure:
//Beanshell script:


lines = Sim_M.split("\n");
 output = "";
for (String line: lines)
{
	output+= ""+line+"";
}

out.write(output);


//Total List of Identified Proteins:
//Beanshell script:


lines = TotalID_d.split("\n");
output = "Identified proteins:";
for (String line: lines)
{
	output+= "    "+line.split("\t")[0]+"";
}

out.write(output);
//////////////////////////////////////////////////////////////////
out.close();
outputFile = output;

path = root +"-output.html";
out1 = "This comparison was performed with a threshold of "+threshold+" percent identity.";
String seperatorString = "\n";
if (seperator != void) {
	seperatorString = seperator;
}
StringBuffer sb = new StringBuffer();
for (Iterator i = stringlist.iterator(); i.hasNext();) {
	String item = (String) i.next();
	sb.append(item);
	if (i.hasNext()) {
		sb.append(seperatorString);
	}
}
concatenated = sb.toString();

String seperatorString = "\n";
if (seperator != void) {
	seperatorString = seperator;
}
StringBuffer sb = new StringBuffer();
for (Iterator i = stringlist.iterator(); i.hasNext();) {
	String item = (String) i.next();
	sb.append(item);
	if (i.hasNext()) {
		sb.append(seperatorString);
	}
}
concatenated = sb.toString();

BufferedWriter out = new BufferedWriter(new FileWriter(input,true));

if (Title == void)
{Title = "";}
if (Tid == void)
{Tid = "";}
if (TSpecies == void)
{TSpecies = "";}
if (KPI == void)
{KPI = "";}
if (KDiagram == void)
{KDiagram = "";}
if (GO == void)
{GO = "";}
if (InterPro == void)
{InterPro = "";}
if (PubMed == void)
{PubMed = "";}
if (OC_R == void)
{OC_R = "";}
if (OS == void)
{OS = "";}

///////////////////////////////////////////////////////
out.write("
"+Title+"");

String [] lines = Tid.split("\n");
String output ="";
out.write(output);

if (TSpecies != void)
{
	String [] lines = TSpecies.split("\n");
	String output ="";

	for (String line: lines)
	{	
		output += "";
	}
	out.write(output);
}

if (Sid != void)
{
	String [] lines = Sid.split("\n");
	String output ="";
	out.write(output);
}

if (SSpecies != void)
{
	String [] lines = SSpecies.split("\n");
	String output ="";
	
	for (String line: lines)
	{
		output += "";
	}
	out.write(output);
}

String [] lines = KPI.split("\n");
String output ="";

for (String line: lines)
{
	output += "";
}
out.write(output);


String [] lines = KDiagram.split("\n");
String output ="";

for (String line: lines)
{
	output += "";
}
out.write(output);


String [] lines = GO.split("\n");
String output ="";
out.write(output);

String [] lines = InterPro.split("\n");
String output ="";
out.write(output);

String [] lines = PubMed.split("\n");
String output ="";
out.write(output);


String [] lines = OC_R.split("\n");
String output ="";
out.write(output);


String [] lines = OS.split("\n");
String output ="";

for (String line: lines)
{
	output += "";
}
output+="Target Protein IDs 
";

for (String line: lines)
{
	output += line+ "
";
}
output += "
Target Species 
" + line+ "
Source Protein IDs 
";

	for (String line: lines)
	{
		output += line+ "
";
	}
	output+= "
Source Species 
" + line+ "
KEGG Pathway Information 
" + line+ "
KEGG Diagram 
Gene Ontology Annotations 
";

for (String line: lines)
{
	output += line+ "
";
}
output+= "
InterPro 
";

for (String line: lines)
{
	output += line+ "
";
}
output+= "
Publications 
";

for (String line: lines)
{
	output += line+ "
";
}
output+= "
New ONDEX Concepts and Relations 
";

for (String line: lines)
{
	output += line+ "
";
}
output+= "
ONDEX Screenshots 
";
out.write(output);


////////////////////////////////////////////

out.close();
output1 = output;
String seperatorString = "\n";
if (seperator != void) {
	seperatorString = seperator;
}
StringBuffer sb = new StringBuffer();
for (Iterator i = stringlist.iterator(); i.hasNext();) {
	String item = (String) i.next();
	sb.append(item);
	if (i.hasNext()) {
		sb.append(seperatorString);
	}
}
concatenated = sb.toString();

String file = filename;

List output = new ArrayList();

for (Object o : uniprot)
{
	output.add(file);
}

uniprot_ids = uniprot;
filenames = output;

Name	Description
Drug_Target_Protein_FASTA
Target_Proteomes_GI
root_directory
thresholdIdentity

Name	Inputs	Outputs
Get_DrugTarget_Fasta_Url	contents_file	url_string
Get_Target_Fasta_Url	contents_file	url_string
String_to_list	in1	out1
get_identifiers_from_uniprot	parsed_uniprot identifier_name	out1
get_identifiers_from_uniprot_2_2	parsed_uniprot identifier_name	out1
deXMLer	in1	out1
Get_Filename	root gi_num	path
Header_Output	Title Intro Tid Sid Sim_M TotalID_d outPutFile	outputFile
Get_HTML_Filename	root gi_num	path
Sim_Measure_Statement	threshold	out1
Write_Protein_HTML	Tid TSpecies Sid SSpecies KPI input KDiagram GO InterPro PubMed OC_R Title OS	output1
Filename_SHIM	filename uniprot	filenames uniprot_ids
parse_embl_id	input	output
Extraction_of_info	xml_result	fastas_out
remove_Nulls	input	output
extract_gene_ids	input	output
remove_nulls_2	input	output
add_uniprot_to_string	input	output
get_identifiers_from_uniprot_2_2	parsed_uniprot identifier_name	out1
GO_deXMLer	in1	out1
threshold_BLAST_results	blast_file thresholdIdentity	out1
get_identifiers_from_uniprot_2_2	parsed_uniprot identifier_name	out1
to_Lower_Case_2	in1	out1
extract_embl_from_blast	unique_identifiers	out1

Name	Description
protein_ids
NCBIGitoKeggPathways_pathway_descriptions
GO_output_2
NCBIGitoKeggPathways_URL
InterPro
PubMed_Results_2
out
out_2

Source	Sink
Target_Proteomes_GI	Extract_proteins_using_a_gi:id
Get_Filename:path	Extract_proteins_using_a_gi:fasta_file_path
Get_DrugTarget_Fasta_Url:url_string	Microbase_BlastP:subjectURL
Get_Target_Fasta_Url:url_string	Microbase_BlastP:queryURL
Drug_Target_Protein_FASTA	Get_DrugTarget_Fasta_Url:contents_file
Get_Filename:path	Get_Target_Fasta_Url:contents_file
Microbase_BlastP:BlastReport	Threshold_Results:blast_file
thresholdIdentity	Threshold_Results:thresholdIdentity
Get_EMBL_ids:gi_numbers	String_to_list:in1
Threshold_Results:thresholdedBlastResults	Get_EMBL_ids:thresholded_blast
Flatten_List:outputlist	KEGG_Results:Uniprot_ids
String_to_list:out1	Get_Uniprot_Data:SearchTerm
Get_Uniprot_Data:parsed_data	get_identifiers_from_uniprot:parsed_uniprot
AC_identifier:value	get_identifiers_from_uniprot:identifier_name
Get_Uniprot_Data:parsed_data	Gene_Ontology_Results:parsed_uniprot
Get_Uniprot_Data:parsed_data	InterPro_Results:parsed_uniprot
PubMed:value	get_identifiers_from_uniprot_2_2:identifier_name
Get_Uniprot_Data:parsed_data	get_identifiers_from_uniprot_2_2:parsed_uniprot
searchCitations_input:output	searchCitations:parameters
get_identifiers_from_uniprot_2_2:out1	searchCitations_input:luceneQueryString
email:value	searchCitations_input:email
core:value	searchCitations_input:outputFormat
zero:value	searchCitations_input:offSet
searchCitations:parameters	searchCitations_output:input
searchCitations_output:return	deXMLer:in1
deXMLer:out1	Merge_String_List_to_a_String:data
get_identifiers_from_uniprot:out1	Flatten_List:inputlist
KEGG_Results:pathway_descriptions	Merge_String_List_to_a_String_2:stringlist
Target_Proteomes_GI	Get_Filename:gi_num
root_directory	Get_Filename:root
Intro_value:value	Header_Output:Intro
Sid_value:value	Header_Output:Sid
Sim_Measure_Statement:out1	Header_Output:Sim_M
Get_HTML_Filename:path	Header_Output:outPutFile
Title_value:value	Header_Output:Title
Merge_String_List_to_a_String_3:concatenated	Header_Output:Tid
Merge_String_List_to_a_String_4:concatenated	Header_Output:TotalID_d
root_directory	Get_HTML_Filename:root
thresholdIdentity	Sim_Measure_Statement:threshold
Target_Proteomes_GI	Merge_String_List_to_a_String_3:stringlist
Threshold_Results:thresholdedBlastResults	Merge_String_List_to_a_String_4:stringlist
Gene_Ontology_Results:GO_Results	Write_Protein_HTML:GO
InterPro_Results:EB_Eye_Results	Write_Protein_HTML:InterPro
Merge_String_List_to_a_String:concatenated	Write_Protein_HTML:PubMed
Merge_String_List_to_a_String_2:concatenated	Write_Protein_HTML:KPI
Merge_String_List_to_a_String_5:concatenated	Write_Protein_HTML:KDiagram
Filename_SHIM:uniprot_ids	Write_Protein_HTML:Title
Filename_SHIM:filenames	Write_Protein_HTML:input
Get_Uniprot_Data:parsed_data	Write_Protein_HTML:Tid
KEGG_Results:URL	Merge_String_List_to_a_String_5:stringlist
Get_HTML_Filename:path	Filename_SHIM:filename
Flatten_List:outputlist	Filename_SHIM:uniprot
Get_Uniprot_Data:parsed_data	protein_ids
Merge_String_List_to_a_String_2:concatenated	NCBIGitoKeggPathways_pathway_descriptions
Gene_Ontology_Results:GO_Results	GO_output_2
KEGG_Results:URL	NCBIGitoKeggPathways_URL
InterPro_Results:EB_Eye_Results	InterPro
Merge_String_List_to_a_String:concatenated	PubMed_Results_2
Header_Output:outputFile	out
Write_Protein_HTML:output1	out_2

Controller	Target
Extract_proteins_using_a_gi	Get_Target_Fasta_Url
Get_Uniprot_Data	KEGG_Results

Vaccine Targets Workflow

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"+Title+"

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"+Title+"

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