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(a)petermac.org
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