abifpy is a python module that extracts sequence and various other data from Applied Biosystem's, Inc. format (ABIF) file. The module is made based on the official spec released by Applied Biosystem.
import abifpy
yummy = abifpy.Trace('tracefile.ab1')
By default, only these tags are extracted:
yummy.seq # sequence data as called by the basecaller yummy.qual # quality values after basecalling yummy.sampleid # sample id entered before the run yummy.well # well coordinate of the sample (A1-K12, if using a 96-well plate) yummy.instrument # sequencing machine model
You can invoke the all_tags=True option when instantiating the class to get all tags available. These tags can then be viewed using as the yummy.tags attribute. Be warned that the module are only able to read data from the five tags above. If you want to make sense of the extra tags, all the information is in the official spec.
Copyright (c) 2011 by Wibowo Arindrarto
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