Estimate the channel gating duration in a single molecule nanopore experiment analyzed with MOSAIC (https://github.com/usnistgov/mosaic).

channelGating.py

"""
	Estimate the channel gating duration in a single molecule nanopore experiment.
	
	:Created:	02/26/2015
 	:Author: 	Arvind Balijepalli <[email protected]>
	:ChangeLog:
	.. line-block::
		02/26/15	AB	Initial version
"""
import mosaic.abfTrajIO as abf
import numpy as np

def estimateGatingDuration( trajioobj, gatingcurrentpa, blocksz, totaltime, fshz ):
    npts = int((fshz)*blocksz)
    nblk = int(totaltime/blocksz)-1

    # Iterate over the blocks of data and check if the channel was in a gated state.
    # The code below returns the mean ionic current of blocks that are below the gating
    # threshold (gatingcurrentpa)
    gEvents = filter(  lambda x:x<float(gatingcurrentpa),
                       [ np.mean(trajioobj.popdata(npts)) for i in range(nblk) ])

    return len(gEvents)*blocksz

abfObj=abf.abfTrajIO(dirname='~/abfSet1',filter='*.abf')
print estimateGatingDuration( abfObj, 20., 0.25, 100, abfObj.FsHz )