63 lines
1.8 KiB
Python
Executable File
63 lines
1.8 KiB
Python
Executable File
#!/usr/bin/env python3
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"""
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Caution : At the moment for gzipped files only.
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"""
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import gzip
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import sys
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# default folded SFS
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folded = True
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diploid = True
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# PARAM : Nb of indiv
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n = int(sys.argv[2])
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if diploid and not folded:
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n *= 2
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SFS_values = dict.fromkeys(range(n),0)
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with gzip.open(sys.argv[1], "rb") as inputgz:
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line = inputgz.readline()
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genotypes = []
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#SFS_values = {}
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while line:
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line = line.decode('utf-8').strip()
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if not line.startswith("##") and not line.startswith("#"):
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FORMAT = line.split("\t")[8:9]
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SAMPLES = line.split("\t")[9:]
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snp_genotypes = []
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allele_counts = {}
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for sample in SAMPLES:
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# for UNPHASED data
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smpl_genotype = [int(a) for a in sample.split(':')[0].split('/') if a != '.']
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nb_alleles = set(smpl_genotype)
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snp_genotypes += smpl_genotype
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if len(set(snp_genotypes)) == 1:
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line = inputgz.readline()
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continue
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#print(snp_genotypes)
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for k in set(snp_genotypes):
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allele_counts[snp_genotypes.count(k)] = k
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if 7 in allele_counts.keys():
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print(allele_counts)
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#print(allele_counts)
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if folded :
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#for count in allele_counts.keys():
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# for count in allele_counts.keys():
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# if count <= len(snp_genotypes)/2 :
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# SFS_values[count-1] += 1
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# else:
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# SFS_values[len(snp_genotypes)-count-1] += 1
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SFS_values[min(allele_counts.keys())-1] += 1
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line = inputgz.readline()
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#print(SFS_values)
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# Note : tout est doublé là
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