Fetch EMBL File
Created: 2010-03-19 13:23:40
Fetches an EMBL file using the EMBL id. Creates file to a specified location.
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Authors (4)
| baywatch |
| Alan R Williams |
| Baywatch Solutions |
|
Titles (3)
| fetch embl file |
| Fetch embl file. |
| Read GenBank file |
Descriptions (4)
| Fetches an embl file from ebi, displaysannotations. |
|
| The Get_web_page_from_URL downloads a file from myExperiment that contains GenBank data. That data is then saved to a temporary file generated by the create_and_populate_temporary_file beanshell. The path to the temporary file is then passed to the Read_GenBank_file service. That service reads the file and converts the GenBank data into Agave format. The result is then sent to the workflow's out port. |
| Fetches an embl file from ebi given an idenfier,e.g., CP000256, displays annotations. |
Dependencies (0)
Inputs (1)
| Name |
Description |
| embl_id |
EMBL ID
|
Processors (3)
| Name |
Type |
Description |
| save_to_file |
beanshell |
ScriptStringBuffer sb = new StringBuffer();sb.append("D:/data/demo/");sb.append(embl_id);sb.append(".embl");File f = new File( sb.toString() );BufferedWriter writer = new BufferedWriter (new FileWriter(f));writer.write(content);writer.close();String filePath = f.getCanonicalPath(); |
| fetch_embl_file |
localworker |
ScriptURL inputURL = null;if (base != void) { inputURL = new URL(base + embl_id);}else { inputURL = new URL(embl_id);}URLConnection con = inputURL.openConnection();InputStream in = con.getInputStream();InputStreamReader isr = new InputStreamReader(in);Reader inReader = new BufferedReader(isr);StringBuffer buf = new StringBuffer();int ch;while ((ch = inReader.read()) > -1) { buf.append((char)ch);}inReader.close();content = buf.toString();//String NEWLINE = System.getProperty("line.separator");////URL inputURL = null;//if (base != void) {// inputURL = new URL(new URL(base), url);//} else {// inputURL = new URL(url);//}//StringBuffer result = new StringBuffer();//BufferedReader reader = new BufferedReader(new InputStreamReader(inputURL.openStream()));//String line = null;//while ((line = reader.readLine()) != null) {// result.append(line);// result.append(NEWLINE);//}////contents = result.toString(); |
| base |
stringconstant |
Valuehttp://www.ebi.ac.uk/Tools/webservices/rest/dbfetch/embl/ |
Beanshells (1)
| Name |
Description |
Inputs |
Outputs |
| save_to_file |
|
content
embl_id
|
filePath
content
|
Outputs (2)
| Name |
Description |
| emb_file |
Embl file name
|
| file_location |
Location of the generated EMBL file
|
Datalinks (6)
| Source |
Sink |
| fetch_embl_file:content |
save_to_file:content |
| fetch_embl_file:embl_id |
save_to_file:embl_id |
| base:value |
fetch_embl_file:base |
| embl_id |
fetch_embl_file:embl_id |
| save_to_file:content |
emb_file |
| save_to_file:filePath |
file_location |
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licensed under:
Version 1
(of 1)
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