Retrieve details on genetic marker by UniSTS numerical UID
Created: 2009-08-19 17:27:42
The workflow retrieves the marker's primers and the organism name - if available. The organism name may not be unique for a given marker. The primers should be.
It would be nice if some good soul could investigate how to retrieve the various mappings from the site. The retrieval of the primers is thought to prepare for a manual mapping of the marker's chromosomal location.
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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 (10)
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));
}
}
|
say_group_is_1 |
stringconstant |
Value1 |
Outputs (5)
Name |
Description |
Primer_Forward |
|
Primer_Reverse |
|
UniSTS_URL |
|
Organism |
|
Raw_HTML_of_NCBI_website |
|
Datalinks (16)
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 |
say_group_is_1:value |
Filter_list_of_strings_extracting_match_to_organism:group |
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 |
say_group_is_1:value |
Filter_list_of_strings_extracting_match_to_reverse_primer:group |
Nested_workflow:filtered_values |
Primer_Forward |
Filter_list_of_strings_extracting_match_to_reverse_primer:filteredlist |
Primer_Reverse |
Concatenate_two_strings:output |
UniSTS_URL |
Filter_list_of_strings_extracting_match_to_organism:filteredlist |
Organism |
Get_Web_Page_from_URL:contents |
Raw_HTML_of_NCBI_website |
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licensed under:
Version 3 (latest)
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