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.el...@petermac.org
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