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Old 05-27-2015, 01:48 PM   #1
verheytb
Junior Member
 
Location: Calgary, Alberta

Join Date: Apr 2015
Posts: 5
Default 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?
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Old 05-27-2015, 02:49 PM   #2
gconcepcion
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Location: Menlo Park

Join Date: Dec 2010
Posts: 68
Default

Quote:
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:
https://github.com/PacificBioscience.../QuiverFAQ.rst
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Old 05-28-2015, 08:39 AM   #3
rhall
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Location: San Francisco

Join Date: Aug 2012
Posts: 321
Default

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.
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