Jason, The LAJ tool is something we deprecated and removed from production a while back, recommending MAF over AXT. Something you might be able to try would be converting your AXT file to MAF and then use GMAJ for visualization. Thanks! -Dannon On May 17, 2011, at 8:32 PM, Ellul Jason wrote:
Hi All,
I have been able to workaround the problem I was having by modifying the LAJ_code.py to include 'and data != None' on each of the elif statements. i.e.
if name == "maf_input": params["alignfile1"] = "display?id=%s" % data.id elif name == "seq_file1" and data != None and data.state == data.states.OK and data.has_data(): params["file1seq1"] = "display?id=%s" % data.id elif name == "seq_file2" and data != None and data.state == data.states.OK and data.has_data(): params["file1seq2"] = "display?id=%s" % data.id elif name == "exonfile" and data != None and data.state == data.states.OK and data.has_data(): params["exonfile"] = "display?id=%s" % data.id elif name == "repeatfile" and data != None and data.state == data.states.OK and data.has_data(): params["repeatfile"] = "display?id=%s" % data.id elif name == "annotationfile" and data != None and data.state == data.states.OK and data.has_data(): params["annotationfile"] = "display?id=%s" % data.id elif name == "underlayfile" and data != None and data.state == data.states.OK and data.has_data(): params["underlayfile"] = "display?id=%s" % data.id elif name == "highlightfile" and data != None and data.state == data.states.OK and data.has_data(): params["highlightfile"] = "display?id=%s" % data.id
For some reason, even though repeatfile is optional the script always thinks that a file has been selected, even when one has not. Hence data is equal to None and it throws a 'nonetype has no attribute state' error when it checks data.state==data.states.OK.
Could a developer please look into why it would think a file for the option repeatfile had been selected when one hasn't.
Cheers, --
Jason Ellul Bioinformatician Cancer Research Division
Peter MacCallum Cancer Centre TEL: +61 3 9656 1512 FAX: +61 3 9656 1411 EMAIL: jason.ellul@petermac.org
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