Mouse430A_2
org.embl.ebi.escience.scuflworkers.java.StringListMerge
mus_musculus
44592504
19592504
17
\n
org.embl.ebi.escience.scuflworkers.java.SplitByRegex
,
http://xml.nig.ac.jp/wsdl/Ensembl.wsdl
getGeneInfo
org.embl.ebi.escience.scuflworkers.java.SplitByRegex
\n
Retrieves a list of Ensembl genes for a given species, chromosome and position
http://phoebus.cs.man.ac.uk:1977/axis/services/qtl_analysis.getgenesbyspecies
Retrieves the current databases from ENSEMBL for a species
http://phoebus.cs.man.ac.uk:1977/axis/services/qtl_analysis.getcurrentdatabase
String[] split = input.split("\n");
Vector nonEmpty = new Vector();
for (int i = 0; i < split.length; i++)
{
String trimmed = split[i].trim();
String[] trimmedSplit = trimmed.split("\t");
System.out.println(trimmedSplit.length);
if (trimmedSplit.length == 4){
nonEmpty.add(trimmedSplit[3].trim());
}
}
String output = "";
for (int i = 0; i < nonEmpty.size(); i++)
{
output = output + (String) (nonEmpty.elementAt(i) + "\n");
}
input
output
gene_name
extract information from geneGeneInfo processor at http://xml.nig.ac.jp/wsdl/Ensembl.wsdl
http://phoebus.cs.man.ac.uk:1977/axis/services/seq_analysis.parse_ddbj_gene_info
Gets ENSEMBL gene IDS that are based on the probeset names passed to it
http://phoebus.cs.man.ac.uk:1977/axis/services/qtl_analysis.probeset_to_gene
Gets the probesets that are in a region of a chromosome e.g. in a QTL or based on 2 marker names
http://phoebus.cs.man.ac.uk:1977/axis/services/qtl_analysis.probeset_in_qtl
swiss
String[] split = input.split("\n");
Vector nonEmpty = new Vector();
for (int i = 0; i < split.length; i++)
{
String trimmed = split[i].trim();
String[] trimmedSplit = trimmed.split(":");
System.out.println(trimmedSplit.length);
if (trimmedSplit.length == 2){
nonEmpty.add(trimmedSplit[1].trim());
}
}
String output = "";
for (int i = 0; i < nonEmpty.size(); i++)
{
output = output + (String) (nonEmpty.elementAt(i) + "\n");
}
//String[] split2 = intermediate.split(":");
//Vector nonEmpty2 = new Vector();
//for (int i = 0; i < split2.length; i++)
//{
// String trimmed2 = split2[i].trim();
// String[] trimmedSplit2 = trimmed2.split(":");
// nonEmpty2.add(trimmedSplit2[1].trim());
//}
//String output = "";
//for (int i = 0; i < nonEmpty2.size(); i++)
//{
// output = output + (String) (nonEmpty2.elementAt(i) + "\n");
//}
input
output
extract information from geneGeneInfo processor at http://xml.nig.ac.jp/wsdl/Ensembl.wsdl
http://phoebus.cs.man.ac.uk:1977/axis/services/seq_analysis.parse_ddbj_gene_info
http://localhost/maxdBrowse_export/geneHunt2.wsdl
hunt
Parses the text based output from maxdBrowse query to list the probeset ids and expression values
http://phoebus.cs.man.ac.uk:1977/axis/services/qtl_analysis.maxdbrowse_expressions
text