Retrieve details on genetic marker by UniSTS numerical UID
Created: 2009-08-19 17:27:42
This upload shell help to locate a bug in Taverna, which may have crippled the contents of this file and only half displays it now.
Preview
Not available
Run
Run this Workflow in the Taverna Workbench...
Workflow Components
Authors (1)
Steffen Möller <moeller@inb.uni-luebeck.de> |
Titles (1)
Retrieve details on UniSTS Unique ID |
Descriptions (1)
Upon submission of the numerical ID for the genetic marker, the web site is parsed for a series of details, i.e. the chromosome and the primer sequences, to allow a sequence similarity search with that data. |
Dependencies (0)
Inputs (1)
Name |
Description |
UniSTS_UID |
The Unique ID for the marker.
|
Processors (9)
Name |
Type |
Description |
UniSTS_access_url_for_uid |
stringconstant |
Valuehttp://www.ncbi.nlm.nih.gov/genome/sts/sts.cgi?uid= |
Concatenate_two_strings |
localworker |
Scriptoutput = string1 + string2; |
Get_Web_Page_from_URL |
localworker |
ScriptURL inputURL = null;
if (base != void) {
inputURL = new URL(new URL(base), url);
}
else {
inputURL = new URL(url);
}
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();
contents = 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();
|
selection_forward |
stringconstant |
Value.*Forward primer:.*([A-Za-z]+).* |
selection_reverse |
stringconstant |
Value.*Reverse primer:.*([A-Za-z]+).* |
Nested_workflow |
workflow |
|
selection_organism |
stringconstant |
ValuePCR product size:.*([A-Za-z0-9 ]+) |
Filter_list_of_strings_extracting_match_to_organism |
localworker |
Scriptimport java.util.regex.*;
filteredlist = new ArrayList();
Pattern thePat = Pattern.compile(regex);
int theGroup = Integer.parseInt(group);
for (Iterator i = stringlist.iterator(); i.hasNext();) {
String item = (String) i.next();
Matcher matcher = thePat.matcher(item);
if (matcher.find()) {
filteredlist.add(matcher.group(theGroup));
}
}
|
Filter_list_of_strings_extracting_match_to_reverse_primer |
localworker |
Scriptimport java.util.regex.*;
filteredlist = new ArrayList();
Pattern thePat = Pattern.compile(regex);
int theGroup = Integer.parseInt(group);
for (Iterator i = stringlist.iterator(); i.hasNext();) {
String item = (String) i.next();
Matcher matcher = thePat.matcher(item);
if (matcher.find()) {
filteredlist.add(matcher.group(theGroup));
}
}
|
Outputs (5)
Name |
Description |
Primer_Forward |
|
Primer_Reverse |
|
Chromosome |
|
Organism |
|
Raw_HTML_of_NCBI_website |
|
Datalinks (13)
Source |
Sink |
UniSTS_access_url_for_uid:value |
Concatenate_two_strings:string1 |
UniSTS_UID |
Concatenate_two_strings:string2 |
Concatenate_two_strings:output |
Get_Web_Page_from_URL:url |
Get_Web_Page_from_URL:contents |
Nested_workflow:string_with_lines_to_be_filtered |
selection_forward:value |
Nested_workflow:regex_to_filter_lines_for |
Nested_workflow:lines |
Filter_list_of_strings_extracting_match_to_organism:stringlist |
selection_organism:value |
Filter_list_of_strings_extracting_match_to_organism:regex |
selection_reverse:value |
Filter_list_of_strings_extracting_match_to_reverse_primer:regex |
Nested_workflow:lines |
Filter_list_of_strings_extracting_match_to_reverse_primer:stringlist |
Nested_workflow:filtered_values |
Primer_Forward |
Concatenate_two_strings:output |
Chromosome |
Filter_list_of_strings_extracting_match_to_organism:filteredlist |
Organism |
Get_Web_Page_from_URL:contents |
Raw_HTML_of_NCBI_website |
Uploader
License
All versions of this Workflow are
licensed under:
Version 1 (earliest)
(of 3)
Credits (1)
(People/Groups)
Attributions (0)
(Workflows/Files)
None
Shared with Groups (0)
None
Featured In Packs (0)
None
Log in to add to one of your Packs
Attributed By (0)
(Workflows/Files)
None
Favourited By (0)
No one
Statistics
Other workflows that use similar services
(0)
There are no workflows in myExperiment that use similar services to this Workflow.
Comments (0)
No comments yet
Log in to make a comment