Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • 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.

    Comment

    Latest Articles

    Collapse

    • seqadmin
      Genetic Variation in Immunogenetics and Antibody Diversity
      by seqadmin



      The field of immunogenetics explores how genetic variations influence immune responses and susceptibility to disease. In a recent SEQanswers webinar, Oscar Rodriguez, Ph.D., Postdoctoral Researcher at the University of Louisville, and Ruben Martínez Barricarte, Ph.D., Assistant Professor of Medicine at Vanderbilt University, shared recent advancements in immunogenetics. This article discusses their research on genetic variation in antibody loci, antibody production processes,...
      11-06-2024, 07:24 PM
    • seqadmin
      Choosing Between NGS and qPCR
      by seqadmin



      Next-generation sequencing (NGS) and quantitative polymerase chain reaction (qPCR) are essential techniques for investigating the genome, transcriptome, and epigenome. In many cases, choosing the appropriate technique is straightforward, but in others, it can be more challenging to determine the most effective option. A simple distinction is that smaller, more focused projects are typically better suited for qPCR, while larger, more complex datasets benefit from NGS. However,...
      10-18-2024, 07:11 AM

    ad_right_rmr

    Collapse

    News

    Collapse

    Topics Statistics Last Post
    Started by seqadmin, 11-01-2024, 06:09 AM
    0 responses
    30 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 10-30-2024, 05:31 AM
    0 responses
    21 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 10-24-2024, 06:58 AM
    0 responses
    26 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 10-23-2024, 08:43 AM
    0 responses
    57 views
    0 likes
    Last Post seqadmin  
    Working...
    X