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Sourcecode: python-biopython version File versions  Download package

# Copyright 2007 by Tiago Antao <tiagoantao@gmail.com>.  All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license.  Please see the LICENSE file that should have been included
# as part of this package.

This module provides code to work with FDist.

See http://www.rubic.rdg.ac.uk/~mab/software.html .

Record           Holds FDist data.

read             Parses a FDist record (file) into a Record object.


def read(handle):
    """Parses FDist data into a Record object.

       handle is a file-like object that contains a FDist record.
    record = Record()
    record.data_org = int(str(handle.next()).rstrip())
    record.num_pops = int(str(handle.next()).rstrip())
    record.num_loci = int(str(handle.next()).rstrip())
    for i in range(record.num_loci):
        num_alleles = int(str(handle.next()).rstrip())
        pops_data = []
        if record.data_org==0:
            for j in range(record.num_pops):
                line_comp = str(handle.next()).rstrip().split(' ')
                pop_dist = map(lambda x: int(x), line_comp)
            raise NotImplementedError('1/alleles by rows not implemented')
        record.loci_data.append((num_alleles, pops_data))
    return record

00048 class Record(object):
    """Holds information from a FDist record.

    data_org    Data organization (0 pops by rows, 1 alleles by rows).
                The Record will behave as if data was 0 (converting if needed)
    num_pops       Number of populations
    num_loci       Number of loci
    loci_data      Loci data
    loci_data is a list, where each element represents a locus. Each element
    is a tuple, the first element is the number of alleles, the second
    element a list. Each element of the list is the count of each allele
    per population.
    def __init__(self):
        self.data_org    = 0
        self.num_pops    = 0
        self.num_loci    = 0
        self.loci_data   = []
    def __str__(self):
        rep  = ['0\n'] #We only export in 0 format, even if originally was 1
        rep.append(str(self.num_pops) + '\n')
        rep.append(str(self.num_loci) + '\n')
        for locus_data in self.loci_data:
            num_alleles, pops_data = locus_data
            rep.append(str(num_alleles) + '\n')
            for pop_data in pops_data:
                for allele_count in pop_data:
                    rep.append(str(allele_count) + ' ')
        return "".join(rep)

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