I wrote script to convert cross_match output into gff for use with ACT. Seems to work fine for ACT version 2 [beta] but the stable release of ACT version 2 does not display the gff information, nor is the gff listed under "Entries" after loading using "File:Read and Entry".
I presume something is non-standard in the gff I'm generating but I can't see what it would be. Here are the first 4 lines of a gff file that won't load:
5MCconcat fuzznuc RT5E 59441 59461 21.000 + . Sequence "5MCconcat.1"
5MCconcat fuzznuc RT5E 70888 70908 21.000 + . Sequence "5MCconcat.2"
5MCconcat fuzznuc RT_RNAseH 62560 62622 63.000 - . Sequence "5MCconcat.1"
5MCconcat fuzznuc RT_RNAseH 108752 108820 69.000 - . Sequence "5MCconcat.2"
5MCconcat fuzznuc CCHC 58125 58166 42.000 + . Sequence "5MCconcat.1"
The fields are all tab delimited, although my mail client converted the tabs to spaces.
Any suggestions on what might be wrong? [..]
I have more information. Using ACT version 2 on a Solarix box, I have the same problem. But I can read the exception being thrown when a file containing only the line:
5MCconcat fuzznuc RT5E 59441 59461 21.000 + . Sequence "5MCconcat.1"
is read using the menu "File:Read an Entry".
The exception is:
java.lang.NumberFormatException: For input string: "RT5E"
at java.lang.NumberFormatException.forInputString(NumberFormatException.java:48)
at java.lang.Integer.parseInt(Integer.java:426)
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.MSPcrunchDocumentEntry.<init>(MSPcrunchDocumentEntry.java:53)
at uk.ac.sanger.pathogens.embl.DocumentEntryFactory.makeDocumentEntry(DocumentEntryFactory.java:87)
at diana.components.EntryFileDialog.getEntryFromFileHelper(EntryFileDialog.java:119)
at diana.components.EntryFileDialog.getEntryFromFile(EntryFileDialog.java:206)
at diana.components.EntryFileDialog.getEntry(EntryFileDialog.java:90)
at diana.components.FileDialogEntrySource.getEntryInternal(FileDialogEntrySource.java:209)
at diana.components.FileDialogEntrySource.getEntry(FileDialogEntrySource.java:75)
at diana.components.MultiComparator$8.actionPerformed(MultiComparator.java:700)
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)
When I then try to exit ACT, the display closes but then the program hangs. A zero length "error.log" is created.
Phillip SanMiguel Purdue Genomics Core Facility
