BioCyc:Pathway Scheme

None

/ptools-xml/Compound/*/Reaction/@frameid
import java.util.regex.Matcher;
import java.util.regex.Pattern;


import java.util.List;
import java.util.ArrayList;

List tmp = new ArrayList();


for(int i=0; i < in1.size(); i++) {
  
    tmp.add(in1.get(i).toString().replace("#<","#"));
    
    
}
result = tmp;


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);
import java.util.regex.Matcher;
import java.util.regex.Pattern;


import java.util.List;
import java.util.ArrayList;

List tmp = new ArrayList();


for(int i=0; i < in1.size(); i++) {
  
    tmp.add(in1.get(i).toString().replace("#<","#"));
    
    
}
result = tmp;


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);
List strippedlist = new ArrayList();
for (Iterator i = stringlist.iterator(); i.hasNext();) {
	String item = (String) i.next();
	if (strippedlist.contains(item) == false) {
		strippedlist.add(item);
	}
}

import java.util.regex.Matcher;
import java.util.regex.Pattern;


import java.util.List;
import java.util.ArrayList;

List tmp = new ArrayList();


for(int i=0; i < in1.size(); i++) {
  
    tmp.add(in1.get(i).toString().replace("#<","#"));
    
    
}
result = tmp;


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);
List strippedlist = new ArrayList();
for (Iterator i = stringlist.iterator(); i.hasNext();) {
	String item = (String) i.next();
	if (strippedlist.contains(item) == false) {
		strippedlist.add(item);
	}
}

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);
File f = File.createTempFile("taverna", ".tmp");

BufferedWriter writer = new BufferedWriter(new FileWriter(f));
writer.write(content);
writer.close();

filepath = f.getCanonicalPath();
BufferedReader getReader (String fileUrl) throws IOException {
		InputStreamReader reader;
		try {
			reader = new FileReader(fileUrl);
		}
		catch (FileNotFoundException e) {
			// try a real URL instead
			URL url = new URL(fileUrl);
			reader = new InputStreamReader (url.openStream());
		}
		return new BufferedReader(reader);
	}

String NEWLINE = System.getProperty("line.separator");

boolean displayResults = false;
if (displayresults != void) {
	displayResults = Boolean.valueOf(displayresults).booleanValue();
}

StringBuffer sb = new StringBuffer(2000);

if (outputfile == void) {
	throw new RuntimeException("The 'outputfile' parameter cannot be null");
}

if (filelist == null) {
	throw new RuntimeException("The 'filelist' parameter cannot be null");
}

String str = null;

Writer writer = new FileWriter(outputfile);
for (int i = 0; i < filelist.size(); i++) {
	BufferedReader reader = getReader(filelist.get(i));
	while ((str = reader.readLine()) != null) {
		writer.write(str);
		writer.write(NEWLINE);

		if (displayResults) {
			sb.append(str);
			sb.append(NEWLINE);
		}
	}

	reader.close();

}
writer.flush();
writer.close();

if (displayResults) {
	results= sb.toString();
}

out1="[x:y:=human~" + "\"" + in1 + "\"" + ",x<-(pathways-of-reaction y)]"

/ptools-xml/Pathway/@frameid
/ptools-xml/Gene/common-name
import java.util.regex.Matcher;
import java.util.regex.Pattern;


import java.util.List;
import java.util.ArrayList;

List tmp = new ArrayList();


for(int i=0; i < in1.size(); i++) {
   if(!in1.get(i).toString().equals("TRNA-CHARGING-PWY"))
  {
    tmp.add(in1.get(i).toString());
    
   } 
  
}
result = tmp;


out1="[x:y:=human~" + "\"" + in1 + "\"" + ",x<-(genes-of-pathway y)]"

out1="[x:x<-human^^compounds,x^name=" + "\"" + in1 + "\"]"

Name	Description
input_compound_name	The input for the workflow is a Biocyc compound name, for example: L-arginine or L-alanine etc
path_to_output_file	This takes the input of the local directory where the user wants to store the output result of the workflow.

Name	Type	Description
REST_Service_Reactions_I	rest	REST service: The function of this component is to access the BioCyc database with the user input compound and return the details of the compound in the form of an xml document
XPath_Service	xpath	Parse the XML document to extract reactions that the compound participates in. Xpath Expression /ptools-xml/Compound/*/Reaction/@frameid
XML_Error_Check	beanshell	Parse the xml document for possible errors Script import java.util.regex.Matcher; import java.util.regex.Pattern; import java.util.List; import java.util.ArrayList; List tmp = new ArrayList(); for(int i=0; i < in1.size(); i++) { tmp.add(in1.get(i).toString().replace("#<","#")); } result = tmp;
Flatten_List	localworker	Script 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);
REST_Service_Pathways	rest	REST Service: Functions to access the BioCyc database and extract the pathways for the given reactions and return an xml document.
XML_Error_Check_2	beanshell	Check for know errors in the xml document. Script import java.util.regex.Matcher; import java.util.regex.Pattern; import java.util.List; import java.util.ArrayList; List tmp = new ArrayList(); for(int i=0; i < in1.size(); i++) { tmp.add(in1.get(i).toString().replace("#<","#")); } result = tmp;
Flatten_List_2	localworker	Script 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);
Remove_String_Duplicates	localworker	Script List strippedlist = new ArrayList(); for (Iterator i = stringlist.iterator(); i.hasNext();) { String item = (String) i.next(); if (strippedlist.contains(item) == false) { strippedlist.add(item); } }
REST_Service_Genes	rest	REST Service: Functions to access the BioCyc database and extracts the genes for the given set of pathways and returns an xml document.
XML_Error_Check_3	beanshell	Check for known errors in the xml document. Script import java.util.regex.Matcher; import java.util.regex.Pattern; import java.util.List; import java.util.ArrayList; List tmp = new ArrayList(); for(int i=0; i < in1.size(); i++) { tmp.add(in1.get(i).toString().replace("#<","#")); } result = tmp;
hgnc	biomart	Biomart service to convert HGNC symbols to entrez ids.
Flatten_List_6	localworker	Script 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);
Remove_String_Duplicates_4	localworker	Script List strippedlist = new ArrayList(); for (Iterator i = stringlist.iterator(); i.hasNext();) { String item = (String) i.next(); if (strippedlist.contains(item) == false) { strippedlist.add(item); } }
Flatten_List_7	localworker	Script 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);
Create_and_populate_temporary_file_Genes	beanshell	Script File f = File.createTempFile("taverna", ".tmp"); BufferedWriter writer = new BufferedWriter(new FileWriter(f)); writer.write(content); writer.close(); filepath = f.getCanonicalPath();
Concatenate_Files_Genes	localworker	Script BufferedReader getReader (String fileUrl) throws IOException { InputStreamReader reader; try { reader = new FileReader(fileUrl); } catch (FileNotFoundException e) { // try a real URL instead URL url = new URL(fileUrl); reader = new InputStreamReader (url.openStream()); } return new BufferedReader(reader); } String NEWLINE = System.getProperty("line.separator"); boolean displayResults = false; if (displayresults != void) { displayResults = Boolean.valueOf(displayresults).booleanValue(); } StringBuffer sb = new StringBuffer(2000); if (outputfile == void) { throw new RuntimeException("The 'outputfile' parameter cannot be null"); } if (filelist == null) { throw new RuntimeException("The 'filelist' parameter cannot be null"); } String str = null; Writer writer = new FileWriter(outputfile); for (int i = 0; i < filelist.size(); i++) { BufferedReader reader = getReader(filelist.get(i)); while ((str = reader.readLine()) != null) { writer.write(str); writer.write(NEWLINE); if (displayResults) { sb.append(str); sb.append(NEWLINE); } } reader.close(); } writer.flush(); writer.close(); if (displayResults) { results= sb.toString(); }
Query_for_pathways_of_reaction	beanshell	Build a query to extract the pathways that the reactions participate in. Script out1="[x:y:=human~" + "\"" + in1 + "\"" + ",x<-(pathways-of-reaction y)]"
XPath_Service_2	xpath	Parse the xml file Xpath Expression /ptools-xml/Pathway/@frameid
XPath_Service_3	xpath	Parse the xml document and extract the list of genes. Xpath Expression /ptools-xml/Gene/common-name
Filter_pathways	beanshell	Remove certain pathways like "tRNA charging pathway" from consideration. Script import java.util.regex.Matcher; import java.util.regex.Pattern; import java.util.List; import java.util.ArrayList; List tmp = new ArrayList(); for(int i=0; i < in1.size(); i++) { if(!in1.get(i).toString().equals("TRNA-CHARGING-PWY")) { tmp.add(in1.get(i).toString()); } } result = tmp;
Query_for_genes_of_pathway	beanshell	Build a query to extract genes in the given pathway. Script out1="[x:y:=human~" + "\"" + in1 + "\"" + ",x<-(genes-of-pathway y)]"
query_for_REST_service	beanshell	This builds the query with the input compound for the REST interface. Script out1="[x:x<-human^^compounds,x^name=" + "\"" + in1 + "\"]"

Name	Description	Inputs	Outputs
XML_Error_Check	Parse the xml document for possible errors	in1	result
XML_Error_Check_2	Check for know errors in the xml document.	in1	result
XML_Error_Check_3	Check for known errors in the xml document.	in1	result
Create_and_populate_temporary_file_Genes		content	filepath
Query_for_pathways_of_reaction	Build a query to extract the pathways that the reactions participate in.	in1	out1
Filter_pathways	Remove certain pathways like "tRNA charging pathway" from consideration.	in1	result
Query_for_genes_of_pathway	Build a query to extract genes in the given pathway.	in1	out1
query_for_REST_service	This builds the query with the input compound for the REST interface.	in1	out1

Source	Sink
query_for_REST_service:out1	REST_Service_Reactions_I:query
XML_Error_Check:result	XPath_Service:xml_text
REST_Service_Reactions_I:responseBody	XML_Error_Check:in1
XPath_Service:nodelist	Flatten_List:inputlist
Query_for_pathways_of_reaction:out1	REST_Service_Pathways:query
REST_Service_Pathways:responseBody	XML_Error_Check_2:in1
XPath_Service_2:nodelist	Flatten_List_2:inputlist
Flatten_List_2:outputlist	Remove_String_Duplicates:stringlist
Query_for_genes_of_pathway:out1	REST_Service_Genes:query
REST_Service_Genes:responseBody	XML_Error_Check_3:in1
Remove_String_Duplicates_4:strippedlist	hgnc:hgnc.gd_app_sym_filter
XPath_Service_3:nodelist	Flatten_List_6:inputlist
Flatten_List_6:outputlist	Remove_String_Duplicates_4:stringlist
hgnc:hgnc.gd_pub_eg_id	Flatten_List_7:inputlist
Flatten_List_7:outputlist	Create_and_populate_temporary_file_Genes:content
Create_and_populate_temporary_file_Genes:filepath	Concatenate_Files_Genes:filelist
path_to_output_file	Concatenate_Files_Genes:outputfile
Flatten_List:outputlist	Query_for_pathways_of_reaction:in1
XML_Error_Check_2:result	XPath_Service_2:xml_text
XML_Error_Check_3:result	XPath_Service_3:xml_text
Remove_String_Duplicates:strippedlist	Filter_pathways:in1
Filter_pathways:result	Query_for_genes_of_pathway:in1
input_compound_name	query_for_REST_service:in1

BioCyc:Pathway Scheme

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