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MACS 1.4.0beta

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  • MACS 1.4.0beta

    Hi,

    I would like to share with all the MACS (http://liulab.dfci.harvard.edu/MACS/) users a revised version of the program.

    Working with SAM files as input for this last MACS version, we noticed that in case the SAM file has thousands of lines representing unaligned reads at the beginning of it, the program crashes because it is not able to determine the length of the reads. I looked at the source code and modified the Parser.py in order to avoid this error. We tested it with some of our SAM files and it seems to work properly. I also modified the code in order to avoid this error with other input sources but I did not tested it yet. I attached the revised source code.

    Iros Barozzi
    PhD student
    European Institute of Oncology, Milan (Italy)
    Attached Files

  • #2
    Originally posted by iros.barozzi View Post
    Hi,

    I would like to share with all the MACS (http://liulab.dfci.harvard.edu/MACS/) users a revised version of the program.

    Working with SAM files as input for this last MACS version, we noticed that in case the SAM file has thousands of lines representing unaligned reads at the beginning of it, the program crashes because it is not able to determine the length of the reads. I looked at the source code and modified the Parser.py in order to avoid this error. We tested it with some of our SAM files and it seems to work properly. I also modified the code in order to avoid this error with other input sources but I did not tested it yet. I attached the revised source code.

    Iros Barozzi
    PhD student
    European Institute of Oncology, Milan (Italy)
    You should send a patch upstream, directly to the authors.

    See the correponding authors in the Genome Biology paper (2008).
    http://genomebiology.com/content/9/9/R137

    -seb

    Comment


    • #3
      I already tried but I had no reply. So I decided to post it here

      Comment


      • #4
        Problem

        Hello and thanks for this version! I have the same problem with my SAM files so I tried to use this but I get the following error message:

        deepseq:~ schizas$ macs14 -t Data/MTmCmLs_5_1.sam
        Traceback (most recent call last):
        File "/Library/Frameworks/Python.framework/Versions/2.7/bin/macs14", line 336, in <module>
        main()
        File "/Library/Frameworks/Python.framework/Versions/2.7/bin/macs14", line 48, in main
        options = opt_validate(prepare_optparser())
        File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/MACS14/OptValidator.py", line 143, in opt_validate
        if options.keepduplicates != "auto" and options.keepduplicates != "all":
        AttributeError: Values instance has no attribute 'keepduplicates'


        Do you know how I can fix this?

        Thank you
        Michael Schizas

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