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Commit 63243469 authored by Thomas Faraut's avatar Thomas Faraut
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variant improvment

parent 042230b9
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......@@ -30,6 +30,24 @@ def complement(seq):
return ''.join(seq_list)
class VariantGraph():
def __init__(self, chromosome):
self.chromosome = chromosome
self.segments = []
def length(self):
return len(self.chromosome)
def new_segment(self, haplotype1, haplotype2=NONE ):
segment = [haplotype1, haplotype2]
self.segment.append(segment)
def get_haplotype_segment(self, num, genotype):
return self.
class Fragment:
"""
A fragment is a chromosomal segment witha start and end are
......@@ -90,9 +108,6 @@ def read_vcf(vcf_file):
offset = record.stop + 1
def main():
parser = argparse.ArgumentParser(description="Reformat data for plink",
formatter_class=argparse.RawTextHelpFormatter)
......
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