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  • driver identification using CHASM in cancer

    Hello,

    I am trying to run CHASM "BuildClassifier" command. But it always return error saying:

    Traceback (most recent call last):
    File "<string>", line 31, in <module>
    File "/home/andywong86/pyinstaller-1.4/iu.py", line 436, in importHook
    File "/home/andywong86/pyinstaller-1.4/iu.py", line 521, in doimport
    File "./build/pyi.linux2/BuildClassifier/outPYZ1.pyz/util.makemuts", line 23, in <module>
    File "./build/pyi.linux2/BuildClassifier/outPYZ1.pyz/util.genes", line 59, in __init__
    IOError: [Errno 2] No such file or directory: './ClassifierPack/refseq.info'

    I don't know what's happening. Anyone used CHASM before?

    Thank you very much!

  • #2
    I assume you have to set the CHASMDIR evironment variable, because I got a similar error when I did not do that, if I remember correctly.
    Because I'm going to use CHASM from a script, I add the setting of that variable before the BuildClassifier command. Like this:
    CHASMDIR=/opt/CHASM /opt/CHASM/BuildClassifier -m /opt/CHASM/ClassifierPack/contexts/BR.context -i /opt/CHASM/ClassifierPack/calibrate.tmps -o breast_cancer

    I also have a question:
    Is it the idea to use the "calibrate" set of mutations for building the classifier, like I did in the above command? And then use RunChasm on the mutation-list of cancer samples I want to test?
    Or should the model be calibrated on the *same* set of mutations I will use RunChasm on?
    Last edited by nyk; 09-28-2011, 02:08 PM.

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