Large file parsing of Genepop files.
The standard parser loads the whole file into memory. This parser provides an iterator over data.
Classes: - LargeRecord - Holds GenePop data.
Functions: - read - Parses a GenePop record (file) into a Record object.
Get individual’s data from line.
Parse a handle containing a GenePop file.
Arguments: - handle is a file-like object that contains a GenePop record.
- class Bio.PopGen.GenePop.LargeFileParser.Record(handle)
Hold information from a GenePop record.
Members: marker_len The marker length (2 or 3 digit code per allele).
comment_line Comment line.
loci_list List of loci names.
data_generator Iterates over population data.
The generator will only work once. If you want to read a handle twice you have to re-open it!
data_generator can either be () - an empty tuple - marking a new population or an individual. An individual is something like (‘Ind1’, [(1,1), (3,None), (200,201)], In the case above the individual is called Ind1, has three diploid loci. For the second loci, one of the alleles is unknown.
Initialize the class.
Extract population data.