merge_by_codon.py

#!/usr/bin/env python

'''

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  AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
  IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
  DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
  FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
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Script defining the merging strategy for merging MNPs using a codon
file.

'''

class merge_by_codon:

    codon_dict = {}
    ignore_INDELs = False

    def __init__(self, codon_file, ignore_INDELs=0):
        self.ignore_INDELs = bool(int(ignore_INDELs))
	#load the codon file and create a dictionary of all loci and the codon they belong to
	#the codon file is a tab separated list of locus\tCodonID
        with open(codon_file) as fp:
            for line in fp:
                line_contents = line.rstrip().split('\t')
                self.codon_dict[line_contents[0]] = line_contents[1]

    def get_codon(self, v):
	#return CodonID of all codons the variant covers
        codon_set = set()
        pos = v.pos + 1
        if len(v.ref) > 1:
            #DEL, need to check all codons it stradles
            DEL_length = len(v.ref)
            seqs = [v.chrom + ':' + str(i) for i in range(pos+1, pos+DEL_length)]
            codon_set = set([self.codon_dict[s] for s in seqs if s in self.codon_dict])
        else:
            locus = v.chrom + ':' + str(pos)
            if locus in self.codon_dict:
                codon_set.add(self.codon_dict[locus])
        return codon_set

    def is_merge(self, v1, v2):
        #determine if one of the 2 variants is INDEL, then ignore if ignore_INDELs=True
        isINDEL = False
        if len(v1.ref) > 1 or len(v2.ref) > 1:
            isINDEL = True
        for alt in v1.alt:
            if len(alt) > 1:
                isINDEL = True
        for alt in v2.alt:
            if len(alt) > 1:
                isINDEL = True
        if self.ignore_INDELs and isINDEL:
            return False
        #determine if the variants share a codon
        return bool(self.get_codon(v1).intersection(self.get_codon(v2)))