Hi!
After going to the Artemis workshop in Dublin I really see more and more
good things about the program. But I have a few queries still that I
hope you could help me with: (I'm running Artemis v5 on Linux RH9 by the
way...)
1. I can't read blastall outputs in Artemis. I ran a blastp(ver2.2.5)
against nr with -m 8, which generated something like this:
1733:1942 gi|23464690|ref|NP_695293.1| 97.14 70 2
0 1 70 197 266 1.5e-31 135.61733:1942
gi|23336054|ref|ZP_00121283.1| 91.43 70 6 0 1
70 197 266 6.1e-30 130.21733:1942
gi|23473454|ref|ZP_00128750.1| 48.28 58 30 0 1
58 204 261 4.6e-09 60.851733:1942
gi|16331056|ref|NP_441784.1| 44.83 58 32 0 6
63 199 256 1.9e-07 55.451733:1942
gi|22983842|ref|ZP_00029010.1| 41.27 63 37 0 2
64 249 311 2.5e-07 55.07
When I tried to open it in Artemis nothing happend except these shell
messages:
java.lang.NumberFormatException: For input string: "34.62"
at
java.lang.NumberFormatException.forInputString(NumberFormatException.java:48)
at java.lang.Integer.parseInt(Integer.java:435)
at java.lang.Integer.valueOf(Integer.java:532)
at
uk.ac.sanger.pathogens.embl.MSPcrunchStreamFeature.<init>(MSPcrunchStreamFeature.java:121)
at
uk.ac.sanger.pathogens.embl.MSPcrunchStreamFeature.readFromStream(MSPcrunchStreamFeature.java:299)
at
uk.ac.sanger.pathogens.embl.LineGroup.readNextLineGroup(LineGroup.java:104)
at
uk.ac.sanger.pathogens.embl.SimpleDocumentEntry.<init>(SimpleDocumentEntry.java:69)
at
uk.ac.sanger.pathogens.embl.BlastDocumentEntry.<init>(BlastDocumentEntry.java:53)
at
uk.ac.sanger.pathogens.embl.DocumentEntryFactory.makeDocumentEntry(DocumentEntryFactory.java:89)
at
diana.components.EntryFileDialog.getEntryFromFileHelper(EntryFileDialog.java:138)
at
diana.components.EntryFileDialog.getEntryFromFile(EntryFileDialog.java:225)
at
diana.components.EntryFileDialog.getEntry(EntryFileDialog.java:109)
at
diana.components.FileDialogEntrySource.getEntryInternal(FileDialogEntrySource.java:209)
at
diana.components.FileDialogEntrySource.getEntry(FileDialogEntrySource.java:93)
at
diana.components.ArtemisMain.getEntryEditFromEntrySource(ArtemisMain.java:400)
at diana.components.ArtemisMain.access$0(ArtemisMain.java)
at
diana.components.ArtemisMain$1.actionPerformed(ArtemisMain.java:82)
at java.awt.MenuItem.processActionEvent(MenuItem.java:588)
at java.awt.MenuItem.processEvent(MenuItem.java:548)
at
java.awt.MenuComponent.dispatchEventImpl(MenuComponent.java:285)
at java.awt.MenuComponent.dispatchEvent(MenuComponent.java:273)
at java.awt.EventQueue.dispatchEvent(EventQueue.java:452)
at
java.awt.EventDispatchThread.pumpOneEventForHierarchy(EventDispatchThread.java:197)
at
java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:150)
at
java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:144)
at
java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:136)
at java.awt.EventDispatchThread.run(EventDispatchThread.java:99)
Am I doing something wrong?
2. All the 'run_ programs' except run_jalview works fine. I installed
Jalview-1.7.5b which works fine standalone for MSF files, but
run_jalview is still not happy... Any advice?
3. If I want to make a run_InterPrsScan tool as well (I have installed
it locally), is it enough just to use eg run_smart as a template and
write a new shell script, or must I change something else too?
4. In for example the SMART output there are many URLs. Is it possible
to include some HTML viewer in Artemis or to start up a web-browser for
viewing these links?
Thanks alot for any input!
Regards,
Marcus Claesson
University College Cork
