Calling Quiver from within a Python script

[verheytb]

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:

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?

[gconcepcion]

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:

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/PacificBiosciences/GenomicConsensus/blob/master/doc/QuiverFAQ.rst

[rhall]

It is not quite as simple as a single function like cmph5select, but the file you are looking for is:

https://github.com/PacificBiosciences/GenomicConsensus/blob/master/GenomicConsensus/main.py

you could always just wrap the system command variantCaller.py as pointed out above.