Compile Protein FASTA from Target to Drug file

None

String input = protein_to_drug_file;
String [] lines = input.split("\n");
HashSet set = new HashSet();

for (int i = 1; i
if ((id == void) || (id == null) || id.equals("")) {
	throw new RunTimeException("port id must have a non-empty value");
}

URL url = new URL ("http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?rettype=fasta&db=protein&retmode=text&id=" + id);

BufferedReader reader = new BufferedReader (new InputStreamReader(url.openStream()));
StringWriter writer = new StringWriter();

char[] buffer = new char[1024];
    while (true) {
        int r = reader.read(buffer);
        if (r <= 0) {
            break;
        }
        writer.write(buffer, 0, r);
    }
outputText = writer.toString();

BufferedWriter out = new BufferedWriter(new FileWriter(outputFile,true));
out.write(filecontents);
out.close();
outputFile = filecontents;

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);
	}


StringBuffer sb = new StringBuffer(4000);

BufferedReader in = getReader(fileurl);
String str;
String lineEnding = System.getProperty("line.separator");

while ((str = in.readLine()) != null) {
	sb.append(str);
	sb.append(lineEnding);
}
in.close();
filecontents = sb.toString();
  

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);
	}


StringBuffer sb = new StringBuffer(4000);

BufferedReader in = getReader(fileurl);
String str;
String lineEnding = System.getProperty("line.separator");

while ((str = in.readLine()) != null) {
	sb.append(str);
	sb.append(lineEnding);
}
in.close();
filecontents = sb.toString();

Name	Description
protein_to_drug_file	The tab-delimited file with a header that shows UniProt identiifers in the first column and DrugBank identifiers in the second.
protein_fasta_file	The location where the FASTA file should be saved on disk.

Name	Type	Description
Uniprot_Splitter	beanshell	Script String input = protein_to_drug_file; String [] lines = input.split("\n"); HashSet set = new HashSet(); for (int i = 1; i
Get_Protein_FASTA	localworker	Script if ((id == void) \|\| (id == null) \|\| id.equals("")) { throw new RunTimeException("port id must have a non-empty value"); } URL url = new URL ("http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?rettype=fasta&db=protein&retmode=text&id=" + id); BufferedReader reader = new BufferedReader (new InputStreamReader(url.openStream())); StringWriter writer = new StringWriter(); char[] buffer = new char[1024]; while (true) { int r = reader.read(buffer); if (r <= 0) { break; } writer.write(buffer, 0, r); } outputText = writer.toString();
Append_To_Text_File	localworker	Script BufferedWriter out = new BufferedWriter(new FileWriter(outputFile,true)); out.write(filecontents); out.close(); outputFile = filecontents;
Read_Text_File	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); } StringBuffer sb = new StringBuffer(4000); BufferedReader in = getReader(fileurl); String str; String lineEnding = System.getProperty("line.separator"); while ((str = in.readLine()) != null) { sb.append(str); sb.append(lineEnding); } in.close(); filecontents = sb.toString();
Read_Text_File_2	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); } StringBuffer sb = new StringBuffer(4000); BufferedReader in = getReader(fileurl); String str; String lineEnding = System.getProperty("line.separator"); while ((str = in.readLine()) != null) { sb.append(str); sb.append(lineEnding); } in.close(); filecontents = sb.toString();

Source	Sink
Read_Text_File_2:filecontents	Uniprot_Splitter:protein_to_drug_file
Uniprot_Splitter:targets	Get_Protein_FASTA:id
protein_fasta_file	Append_To_Text_File:outputFile
Get_Protein_FASTA:outputText	Append_To_Text_File:filecontents
protein_fasta_file	Read_Text_File:fileurl
protein_to_drug_file	Read_Text_File_2:fileurl
Read_Text_File:filecontents	fasta

Compile Protein FASTA from Target to Drug file

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