PRmm (PulseRecognizer minus minus; pronounced perm), is a basic interactive PacBio trace viewer. It is portable and simple.

Additionally, the backend data model of PRmm is designed to be usable for data analysis from the perspective of a ZMW---providing simple access to the collated trace, pulsecall, basecall, and alignment data resulting from the ZMW.

Using the viewer

% prmm --help

Using the model for data analysis

The basic use concept for the model is:

1. Load a "Fixture", which consists of a collated set of files providing traces (tr(c|x).h5), pulses (bam or pl(s|x).h5), bases (bam or bas(s|x).h5) and alignments (bam or cmp.h5). For convenience, a fixture can be specified in an ini file like so:

   [All4Mers-LVP1]
   Comment=All4Mers 1 hour lambda on LVP1 chip
   Traces=/pbi/collections/315/3150005/r54004_20151117_203936/1_A01/m54004_151117_203942.trc.h5
   Analysis=/home/UNIXHOME/dalexander/Projects/git/VariantCallingReports/2015/HQ-Region-Finding/SequelT2B/UnrolledAll4mers
   Bases=%(Analysis)s/m54004_151117_203942.bax.h5
   Pulses=%(Analysis)s/m54004_151117_203942.plx.h5
   Alignment=%(Analysis)s/aligned_reads.cmp.h5
   Reference=%(Analysis)s/All4Mers.fasta
   

   (note the use of format interpolation here, which is inessential (and nonstandard!) but convenient) and then loaded like so:

   >>> readers = Fixture.fromIniFile("~/.pacbio/data-fixtures.ini", "All4Mers-LVP1")
   

2. "Slice" the ReadersFixture by a holenumber of interest, obtaining a "FixtureZmw", which then gives convenient access to the trace and analysis data from that ZMW.

   >>> zmw = readers[55]
   
   >>> zmw.cameraTrace
   array([[  77.40115356,   58.53388214,   58.53388214, ...,   54.8108139 ,
             51.10409546,   51.10409546],
          [ 104.56507874,   73.59329224,   88.93170166, ...,   66.02966309,
             58.53388214,   51.10409546], dtype=float32)
   
   >>> zmw.basecalls
   'AAACATATAACCATGATCAGTAGCTTCTATACAGACAACTAA...'
   
   >>> z.regions  # Frame-delimited "regions"
    [<Region:     INSERT    1239   73519>,
     <Region:         HQ   22749  134882>,
     <Region:  ALIGNMENT   24020   73356>,
     <Region:    ADAPTER   73543   78439>,
     <Region:     INSERT   78485  134882>,
     <Region:  ALIGNMENT   86953  134882>]