Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Calling Quiver from within a Python script

    Hello,

    I need to run Quiver on a large set of *.cmp.h5 files, and so I would like to access the main module from a Python script. I think I might do this similar to how I accessed the CmpH5Select.py module, like this example:
    Code:
    sys.path.append('/smrtanalysis/install/smrtanalysis_2.3.0.140936/analysis/lib/python2.7')
    import pbh5tools.CmpH5Select as select
    ...
    select.cmpH5Select(inputfile, None, idxs = None, groupByStr = "Movie", groupByCsv = None, whereStr = None, outDir = moviedir)
    So I really have two questions: which function in which file can be used to access Quiver (for example, variantcaller.py)? And how should I pass parameters to it?

  • #2
    Originally posted by verheytb View Post
    Hello,

    I need to run Quiver on a large set of *.cmp.h5 files, and so I would like to access the main module from a Python script. I think I might do this similar to how I accessed the CmpH5Select.py module, like this example:
    Code:
    sys.path.append('/smrtanalysis/install/smrtanalysis_2.3.0.140936/analysis/lib/python2.7')
    import pbh5tools.CmpH5Select as select
    ...
    select.cmpH5Select(inputfile, None, idxs = None, groupByStr = "Movie", groupByCsv = None, whereStr = None, outDir = moviedir)
    So I really have two questions: which function in which file can be used to access Quiver (for example, variantcaller.py)? And how should I pass parameters to it?
    To specify the 'quiver' algorithm, you need to invoke variantCaller.py like this:

    'variantCaller.py --algorithm=quiver'

    'variantCaller.py --help' for a full list of options that can be passed in

    See the QUIVER FAQ for details:
    GitHub is where people build software. More than 100 million people use GitHub to discover, fork, and contribute to over 420 million projects.

    Comment


    • #3
      It is not quite as simple as a single function like cmph5select, but the file you are looking for is:
      https://github.com/PacificBioscience...sensus/main.py
      you could always just wrap the system command variantCaller.py as pointed out above.

      Comment

      Latest Articles

      Collapse

      • seqadmin
        Strategies for Sequencing Challenging Samples
        by seqadmin


        Despite advancements in sequencing platforms and related sample preparation technologies, certain sample types continue to present significant challenges that can compromise sequencing results. Pedro Echave, Senior Manager of the Global Business Segment at Revvity, explained that the success of a sequencing experiment ultimately depends on the amount and integrity of the nucleic acid template (RNA or DNA) obtained from a sample. “The better the quality of the nucleic acid isolated...
        03-22-2024, 06:39 AM
      • seqadmin
        Techniques and Challenges in Conservation Genomics
        by seqadmin



        The field of conservation genomics centers on applying genomics technologies in support of conservation efforts and the preservation of biodiversity. This article features interviews with two researchers who showcase their innovative work and highlight the current state and future of conservation genomics.

        Avian Conservation
        Matthew DeSaix, a recent doctoral graduate from Kristen Ruegg’s lab at The University of Colorado, shared that most of his research...
        03-08-2024, 10:41 AM

      ad_right_rmr

      Collapse

      News

      Collapse

      Topics Statistics Last Post
      Started by seqadmin, Yesterday, 06:37 PM
      0 responses
      7 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, Yesterday, 06:07 PM
      0 responses
      7 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 03-22-2024, 10:03 AM
      0 responses
      49 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 03-21-2024, 07:32 AM
      0 responses
      66 views
      0 likes
      Last Post seqadmin  
      Working...
      X