/
conRadNullDistribution.py
4347 lines (4327 loc) · 407 KB
/
conRadNullDistribution.py
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# -*- coding: utf-8 -*-
import sys
import random
def polSub(fasta,code='invertebrateMt'):
geneticCodes = {'standard':{"TTT":"F", "TTC":"F", "TTA":"L", "TTG":"L", "TCT":"S", "TCC":"S", "TCA":"S", "TCG":"S", "TAT":"Y", "TAC":"Y", "TAA":"*", "TAG":"*", "TGT":"C", "TGC":"C", "TGA":"*", "TGG":"W", "CTT":"L", "CTC":"L", "CTA":"L", "CTG":"L", "CCT":"P", "CCC":"P", "CCA":"P", "CCG":"P", "CAT":"H", "CAC":"H", "CAA":"Q", "CAG":"Q", "CGT":"R", "CGC":"R", "CGA":"R", "CGG":"R", "ATT":"I", "ATC":"I", "ATA":"I", "ATG":"M", "ACT":"T", "ACC":"T", "ACA":"T", "ACG":"T", "AAT":"N", "AAC":"N", "AAA":"K", "AAG":"K", "AGT":"S", "AGC":"S", "AGA":"R", "AGG":"R", "GTT":"V", "GTC":"V", "GTA":"V", "GTG":"V", "GCT":"A", "GCC":"A", "GCA":"A", "GCG":"A", "GAT":"D", "GAC":"D", "GAA":"E", "GAG":"E", "GGT":"G", "GGC":"G", "GGA":"G", "GGG":"G"},'invertebrateMt':{'CTT': 'L', 'TAG': '*', 'ACA': 'T', 'ACG': 'T', 'ATC': 'I', 'AAC': 'N', 'ATA': 'M', 'AGG': 'S', 'CCT': 'P', 'ACT': 'T', 'AGC': 'S', 'AAG': 'K', 'AGA': 'S', 'CAT': 'H', 'AAT': 'N', 'ATT': 'I', 'CTG': 'L', 'CTA': 'L', 'CTC': 'L', 'CAC': 'H', 'AAA': 'K', 'CCG': 'P', 'AGT': 'S', 'CCA': 'P', 'CAA': 'Q', 'CCC': 'P', 'TAT': 'Y', 'GGT': 'G', 'TGT': 'C', 'CGA': 'R', 'CAG': 'Q', 'TCT': 'S', 'GAT': 'D', 'CGG': 'R', 'TTT': 'F', 'TGC': 'C', 'GGG': 'G', 'TGA': 'W', 'GGA': 'G', 'TGG': 'W', 'GGC': 'G', 'TAC': 'Y', 'TTC': 'F', 'TCG': 'S', 'TTA': 'L', 'TTG': 'L', 'TCC': 'S', 'ACC': 'T', 'TAA': '*', 'GCA': 'A', 'GTA': 'V', 'GCC': 'A', 'GTC': 'V', 'GCG': 'A', 'GTG': 'V', 'GAG': 'E', 'GTT': 'V', 'GCT': 'A', 'GAC': 'D', 'CGT': 'R', 'GAA': 'E', 'TCA': 'S', 'ATG': 'M', 'CGC': 'R'},'vertebrateMt':{'CTT': 'L', 'TAG': '*', 'ACA': 'T', 'ACG': 'T', 'ATC': 'I', 'AAC': 'N', 'ATA': 'M', 'AGG': '*', 'CCT': 'P', 'ACT': 'T', 'AGC': 'S', 'AAG': 'K', 'AGA': '*', 'CAT': 'H', 'AAT': 'N', 'ATT': 'I', 'CTG': 'L', 'CTA': 'L', 'CTC': 'L', 'CAC': 'H', 'AAA': 'K', 'CCG': 'P', 'AGT': 'S', 'CCA': 'P', 'CAA': 'Q', 'CCC': 'P', 'TAT': 'Y', 'GGT': 'G', 'TGT': 'C', 'CGA': 'R', 'CAG': 'Q', 'TCT': 'S', 'GAT': 'D', 'CGG': 'R', 'TTT': 'F', 'TGC': 'C', 'GGG': 'G', 'TGA': 'W', 'GGA': 'G', 'TGG': 'W', 'GGC': 'G', 'TAC': 'Y', 'TTC': 'F', 'TCG': 'S', 'TTA': 'L', 'TTG': 'L', 'TCC': 'S', 'ACC': 'T', 'TAA': '*', 'GCA': 'A', 'GTA': 'V', 'GCC': 'A', 'GTC': 'V', 'GCG': 'A', 'GTG': 'V', 'GAG': 'E', 'GTT': 'V', 'GCT': 'A', 'GAC': 'D', 'CGT': 'R', 'GAA': 'E', 'TCA': 'S', 'ATG': 'M', 'CGC': 'R'}, 'yeastMt':{'CTT': 'T', 'TAG': '*', 'ACA': 'T', 'ACG': 'T', 'ATC': 'I', 'AAC': 'N', 'ATA': 'M', 'AGG': 'R', 'CCT': 'P', 'ACT': 'T', 'AGC': 'S', 'AAG': 'K', 'AGA': 'R', 'CAT': 'H', 'AAT': 'N', 'ATT': 'I', 'CTG': 'T', 'CTA': 'T', 'CTC': 'T', 'CAC': 'H', 'AAA': 'K', 'CCG': 'P', 'AGT': 'S', 'CCA': 'P', 'CAA': 'Q', 'CCC': 'P', 'TAT': 'Y', 'GGT': 'G', 'TGT': 'C', 'CGA': 'R', 'CAG': 'Q', 'TCT': 'S', 'GAT': 'D', 'CGG': 'R', 'TTT': 'F', 'TGC': 'C', 'GGG': 'G', 'TGA': 'W', 'GGA': 'G', 'TGG': 'W', 'GGC': 'G', 'TAC': 'Y', 'TTC': 'F', 'TCG': 'S', 'TTA': 'L', 'TTG': 'L', 'TCC': 'S', 'ACC': 'T', 'TAA': '*', 'GCA': 'A', 'GTA': 'V', 'GCC': 'A', 'GTC': 'V', 'GCG': 'A', 'GTG': 'V', 'GAG': 'E', 'GTT': 'V', 'GCT': 'A', 'GAC': 'D', 'CGT': 'R', 'GAA': 'E', 'TCA': 'S', 'ATG': 'M', 'CGC': 'R'}, 'coelenterateMt':{'CTT': 'L', 'TAG': '*', 'ACA': 'T', 'ACG': 'T', 'ATC': 'I', 'AAC': 'N', 'ATA': 'I', 'AGG': 'R', 'CCT': 'P', 'ACT': 'T', 'AGC': 'S', 'AAG': 'K', 'AGA': 'R', 'CAT': 'H', 'AAT': 'N', 'ATT': 'I', 'CTG': 'L', 'CTA': 'L', 'CTC': 'L', 'CAC': 'H', 'AAA': 'K', 'CCG': 'P', 'AGT': 'S', 'CCA': 'P', 'CAA': 'Q', 'CCC': 'P', 'TAT': 'Y', 'GGT': 'G', 'TGT': 'C', 'CGA': 'R', 'CAG': 'Q', 'TCT': 'S', 'GAT': 'D', 'CGG': 'R', 'TTT': 'F', 'TGC': 'C', 'GGG': 'G', 'TGA': 'W', 'GGA': 'G', 'TGG': 'W', 'GGC': 'G', 'TAC': 'Y', 'TTC': 'F', 'TCG': 'S', 'TTA': 'L', 'TTG': 'L', 'TCC': 'S', 'ACC': 'T', 'TAA': '*', 'GCA': 'A', 'GTA': 'V', 'GCC': 'A', 'GTC': 'V', 'GCG': 'A', 'GTG': 'V', 'GAG': 'E', 'GTT': 'V', 'GCT': 'A', 'GAC': 'D', 'CGT': 'R', 'GAA': 'E', 'TCA': 'S', 'ATG': 'M', 'CGC': 'R'},'ciliateNuc':{'CTT': 'L', 'TAG': 'Q', 'ACA': 'T', 'ACG': 'T', 'ATC': 'I', 'AAC': 'N', 'ATA': 'I', 'AGG': 'R', 'CCT': 'P', 'ACT': 'T', 'AGC': 'S', 'AAG': 'K', 'AGA': 'R', 'CAT': 'H', 'AAT': 'N', 'ATT': 'I', 'CTG': 'L', 'CTA': 'L', 'CTC': 'L', 'CAC': 'H', 'AAA': 'K', 'CCG': 'P', 'AGT': 'S', 'CCA': 'P', 'CAA': 'Q', 'CCC': 'P', 'TAT': 'Y', 'GGT': 'G', 'TGT': 'C', 'CGA': 'R', 'CAG': 'Q', 'TCT': 'S', 'GAT': 'D', 'CGG': 'R', 'TTT': 'F', 'TGC': 'C', 'GGG': 'G', 'TGA': '*', 'GGA': 'G', 'TGG': 'W', 'GGC': 'G', 'TAC': 'Y', 'TTC': 'F', 'TCG': 'S', 'TTA': 'L', 'TTG': 'L', 'TCC': 'S', 'ACC': 'T', 'TAA': 'Q', 'GCA': 'A', 'GTA': 'V', 'GCC': 'A', 'GTC': 'V', 'GCG': 'A', 'GTG': 'V', 'GAG': 'E', 'GTT': 'V', 'GCT': 'A', 'GAC': 'D', 'CGT': 'R', 'GAA': 'E', 'TCA': 'S', 'ATG': 'M', 'CGC': 'R'},'echinodermMt':{'CTT': 'L', 'TAG': '*', 'ACA': 'T', 'ACG': 'T', 'ATC': 'I', 'AAC': 'N', 'ATA': 'I', 'AGG': 'S', 'CCT': 'P', 'ACT': 'T', 'AGC': 'S', 'AAG': 'K', 'AGA': 'S', 'CAT': 'H', 'AAT': 'N', 'ATT': 'I', 'CTG': 'L', 'CTA': 'L', 'CTC': 'L', 'CAC': 'H', 'AAA': 'N', 'CCG': 'P', 'AGT': 'S', 'CCA': 'P', 'CAA': 'Q', 'CCC': 'P', 'TAT': 'Y', 'GGT': 'G', 'TGT': 'C', 'CGA': 'R', 'CAG': 'Q', 'TCT': 'S', 'GAT': 'D', 'CGG': 'R', 'TTT': 'F', 'TGC': 'C', 'GGG': 'G', 'TGA': 'W', 'GGA': 'G', 'TGG': 'W', 'GGC': 'G', 'TAC': 'Y', 'TTC': 'F', 'TCG': 'S', 'TTA': 'L', 'TTG': 'L', 'TCC': 'S', 'ACC': 'T', 'TAA': '*', 'GCA': 'A', 'GTA': 'V', 'GCC': 'A', 'GTC': 'V', 'GCG': 'A', 'GTG': 'V', 'GAG': 'E', 'GTT': 'V', 'GCT': 'A', 'GAC': 'D', 'CGT': 'R', 'GAA': 'E', 'TCA': 'S', 'ATG': 'M', 'CGC': 'R'}, 'euplotidNuc':{'CTT': 'L', 'TAG': '*', 'ACA': 'T', 'ACG': 'T', 'ATC': 'I', 'AAC': 'N', 'ATA': 'I', 'AGG': 'R', 'CCT': 'P', 'ACT': 'T', 'AGC': 'S', 'AAG': 'K', 'AGA': 'R', 'CAT': 'H', 'AAT': 'N', 'ATT': 'I', 'CTG': 'L', 'CTA': 'L', 'CTC': 'L', 'CAC': 'H', 'AAA': 'K', 'CCG': 'P', 'AGT': 'S', 'CCA': 'P', 'CAA': 'Q', 'CCC': 'P', 'TAT': 'Y', 'GGT': 'G', 'TGT': 'C', 'CGA': 'R', 'CAG': 'Q', 'TCT': 'S', 'GAT': 'D', 'CGG': 'R', 'TTT': 'F', 'TGC': 'C', 'GGG': 'G', 'TGA': 'C', 'GGA': 'G', 'TGG': 'W', 'GGC': 'G', 'TAC': 'Y', 'TTC': 'F', 'TCG': 'S', 'TTA': 'L', 'TTG': 'L', 'TCC': 'S', 'ACC': 'T', 'TAA': '*', 'GCA': 'A', 'GTA': 'V', 'GCC': 'A', 'GTC': 'V', 'GCG': 'A', 'GTG': 'V', 'GAG': 'E', 'GTT': 'V', 'GCT': 'A', 'GAC': 'D', 'CGT': 'R', 'GAA': 'E', 'TCA': 'S', 'ATG': 'M', 'CGC': 'R'}, 'bacterial':{'CTT': 'L', 'TAG': '*', 'ACA': 'T', 'ACG': 'T', 'ATC': 'I', 'AAC': 'N', 'ATA': 'I', 'AGG': 'R', 'CCT': 'P', 'ACT': 'T', 'AGC': 'S', 'AAG': 'K', 'AGA': 'R', 'CAT': 'H', 'AAT': 'N', 'ATT': 'I', 'CTG': 'L', 'CTA': 'L', 'CTC': 'L', 'CAC': 'H', 'AAA': 'K', 'CCG': 'P', 'AGT': 'S', 'CCA': 'P', 'CAA': 'Q', 'CCC': 'P', 'TAT': 'Y', 'GGT': 'G', 'TGT': 'C', 'CGA': 'R', 'CAG': 'Q', 'TCT': 'S', 'GAT': 'D', 'CGG': 'R', 'TTT': 'F', 'TGC': 'C', 'GGG': 'G', 'TGA': '*', 'GGA': 'G', 'TGG': 'W', 'GGC': 'G', 'TAC': 'Y', 'TTC': 'F', 'TCG': 'S', 'TTA': 'L', 'TTG': 'L', 'TCC': 'S', 'ACC': 'T', 'TAA': '*', 'GCA': 'A', 'GTA': 'V', 'GCC': 'A', 'GTC': 'V', 'GCG': 'A', 'GTG': 'V', 'GAG': 'E', 'GTT': 'V', 'GCT': 'A', 'GAC': 'D', 'CGT': 'R', 'GAA': 'E', 'TCA': 'S', 'ATG': 'M', 'CGC': 'R'},'yeastNuc':{'CTT': 'L', 'TAG': '*', 'ACA': 'T', 'ACG': 'T', 'ATC': 'I', 'AAC': 'N', 'ATA': 'I', 'AGG': 'R', 'CCT': 'P', 'ACT': 'T', 'AGC': 'S', 'AAG': 'K', 'AGA': 'R', 'CAT': 'H', 'AAT': 'N', 'ATT': 'I', 'CTG': 'S', 'CTA': 'L', 'CTC': 'L', 'CAC': 'H', 'AAA': 'K', 'CCG': 'P', 'AGT': 'S', 'CCA': 'P', 'CAA': 'Q', 'CCC': 'P', 'TAT': 'Y', 'GGT': 'G', 'TGT': 'C', 'CGA': 'R', 'CAG': 'Q', 'TCT': 'S', 'GAT': 'D', 'CGG': 'R', 'TTT': 'F', 'TGC': 'C', 'GGG': 'G', 'TGA': '*', 'GGA': 'G', 'TGG': 'W', 'GGC': 'G', 'TAC': 'Y', 'TTC': 'F', 'TCG': 'S', 'TTA': 'L', 'TTG': 'L', 'TCC': 'S', 'ACC': 'T', 'TAA': '*', 'GCA': 'A', 'GTA': 'V', 'GCC': 'A', 'GTC': 'V', 'GCG': 'A', 'GTG': 'V', 'GAG': 'E', 'GTT': 'V', 'GCT': 'A', 'GAC': 'D', 'CGT': 'R', 'GAA': 'E', 'TCA': 'S', 'ATG': 'M', 'CGC': 'R'}, 'ascidianMt':{'CTT': 'L', 'TAG': '*', 'ACA': 'T', 'ACG': 'T', 'ATC': 'I', 'AAC': 'N', 'ATA': 'M', 'AGG': 'G', 'CCT': 'P', 'ACT': 'T', 'AGC': 'S', 'AAG': 'K', 'AGA': 'G', 'CAT': 'H', 'AAT': 'N', 'ATT': 'I', 'CTG': 'L', 'CTA': 'L', 'CTC': 'L', 'CAC': 'H', 'AAA': 'K', 'CCG': 'P', 'AGT': 'S', 'CCA': 'P', 'CAA': 'Q', 'CCC': 'P', 'TAT': 'Y', 'GGT': 'G', 'TGT': 'C', 'CGA': 'R', 'CAG': 'Q', 'TCT': 'S', 'GAT': 'D', 'CGG': 'R', 'TTT': 'F', 'TGC': 'C', 'GGG': 'G', 'TGA': 'W', 'GGA': 'G', 'TGG': 'W', 'GGC': 'G', 'TAC': 'Y', 'TTC': 'F', 'TCG': 'S', 'TTA': 'L', 'TTG': 'L', 'TCC': 'S', 'ACC': 'T', 'TAA': '*', 'GCA': 'A', 'GTA': 'V', 'GCC': 'A', 'GTC': 'V', 'GCG': 'A', 'GTG': 'V', 'GAG': 'E', 'GTT': 'V', 'GCT': 'A', 'GAC': 'D', 'CGT': 'R', 'GAA': 'E', 'TCA': 'S', 'ATG': 'M', 'CGC': 'R'},'flatwormMt':{'CTT': 'L', 'TAG': '*', 'ACA': 'T', 'ACG': 'T', 'ATC': 'I', 'AAC': 'N', 'ATA': 'I', 'AGG': 'S', 'CCT': 'P', 'ACT': 'T', 'AGC': 'S', 'AAG': 'K', 'AGA': 'S', 'CAT': 'H', 'AAT': 'N', 'ATT': 'I', 'CTG': 'L', 'CTA': 'L', 'CTC': 'L', 'CAC': 'H', 'AAA': 'N', 'CCG': 'P', 'AGT': 'S', 'CCA': 'P', 'CAA': 'Q', 'CCC': 'P', 'TAT': 'Y', 'GGT': 'G', 'TGT': 'C', 'CGA': 'R', 'CAG': 'Q', 'TCT': 'S', 'GAT': 'D', 'CGG': 'R', 'TTT': 'F', 'TGC': 'C', 'GGG': 'G', 'TGA': 'W', 'GGA': 'G', 'TGG': 'W', 'GGC': 'G', 'TAC': 'Y', 'TTC': 'F', 'TCG': 'S', 'TTA': 'L', 'TTG': 'L', 'TCC': 'S', 'ACC': 'T', 'TAA': 'Y', 'GCA': 'A', 'GTA': 'V', 'GCC': 'A', 'GTC': 'V', 'GCG': 'A', 'GTG': 'V', 'GAG': 'E', 'GTT': 'V', 'GCT': 'A', 'GAC': 'D', 'CGT': 'R', 'GAA': 'E', 'TCA': 'S', 'ATG': 'M', 'CGC': 'R'},'chlorophyceanMt':{'CTT': 'L', 'TAG': 'L', 'ACA': 'T', 'ACG': 'T', 'ATC': 'I', 'AAC': 'N', 'ATA': 'I', 'AGG': 'R', 'CCT': 'P', 'ACT': 'T', 'AGC': 'S', 'AAG': 'K', 'AGA': 'R', 'CAT': 'H', 'AAT': 'N', 'ATT': 'I', 'CTG': 'L', 'CTA': 'L', 'CTC': 'L', 'CAC': 'H', 'AAA': 'K', 'CCG': 'P', 'AGT': 'S', 'CCA': 'P', 'CAA': 'Q', 'CCC': 'P', 'TAT': 'Y', 'GGT': 'G', 'TGT': 'C', 'CGA': 'R', 'CAG': 'Q', 'TCT': 'S', 'GAT': 'D', 'CGG': 'R', 'TTT': 'F', 'TGC': 'C', 'GGG': 'G', 'TGA': '*', 'GGA': 'G', 'TGG': 'W', 'GGC': 'G', 'TAC': 'Y', 'TTC': 'F', 'TCG': 'S', 'TTA': 'L', 'TTG': 'L', 'TCC': 'S', 'ACC': 'T', 'TAA': '*', 'GCA': 'A', 'GTA': 'V', 'GCC': 'A', 'GTC': 'V', 'GCG': 'A', 'GTG': 'V', 'GAG': 'E', 'GTT': 'V', 'GCT': 'A', 'GAC': 'D', 'CGT': 'R', 'GAA': 'E', 'TCA': 'S', 'ATG': 'M', 'CGC': 'R'},'trematodeMt':{'CTT': 'L', 'TAG': '*', 'ACA': 'T', 'ACG': 'T', 'ATC': 'I', 'AAC': 'N', 'ATA': 'M', 'AGG': 'S', 'CCT': 'P', 'ACT': 'T', 'AGC': 'S', 'AAG': 'K', 'AGA': 'S', 'CAT': 'H', 'AAT': 'N', 'ATT': 'I', 'CTG': 'L', 'CTA': 'L', 'CTC': 'L', 'CAC': 'H', 'AAA': 'N', 'CCG': 'P', 'AGT': 'S', 'CCA': 'P', 'CAA': 'Q', 'CCC': 'P', 'TAT': 'Y', 'GGT': 'G', 'TGT': 'C', 'CGA': 'R', 'CAG': 'Q', 'TCT': 'S', 'GAT': 'D', 'CGG': 'R', 'TTT': 'F', 'TGC': 'C', 'GGG': 'G', 'TGA': 'W', 'GGA': 'G', 'TGG': 'W', 'GGC': 'G', 'TAC': 'Y', 'TTC': 'F', 'TCG': 'S', 'TTA': 'L', 'TTG': 'L', 'TCC': 'S', 'ACC': 'T', 'TAA': '*', 'GCA': 'A', 'GTA': 'V', 'GCC': 'A', 'GTC': 'V', 'GCG': 'A', 'GTG': 'V', 'GAG': 'E', 'GTT': 'V', 'GCT': 'A', 'GAC': 'D', 'CGT': 'R', 'GAA': 'E', 'TCA': 'S', 'ATG': 'M', 'CGC': 'R'},'pterobranchiaMt':{'CTT': 'L', 'TAG': '*', 'ACA': 'T', 'ACG': 'T', 'ATC': 'I', 'AAC': 'N', 'ATA': 'I', 'AGG': 'K', 'CCT': 'P', 'ACT': 'T', 'AGC': 'S', 'AAG': 'K', 'AGA': 'S', 'CAT': 'H', 'AAT': 'N', 'ATT': 'I', 'CTG': 'L', 'CTA': 'L', 'CTC': 'L', 'CAC': 'H', 'AAA': 'K', 'CCG': 'P', 'AGT': 'S', 'CCA': 'P', 'CAA': 'Q', 'CCC': 'P', 'TAT': 'Y', 'GGT': 'G', 'TGT': 'C', 'CGA': 'R', 'CAG': 'Q', 'TCT': 'S', 'GAT': 'D', 'CGG': 'R', 'TTT': 'F', 'TGC': 'C', 'GGG': 'G', 'TGA': 'W', 'GGA': 'G', 'TGG': 'W', 'GGC': 'G', 'TAC': 'Y', 'TTC': 'F', 'TCG': 'S', 'TTA': 'L', 'TTG': 'L', 'TCC': 'S', 'ACC': 'T', 'TAA': '*', 'GCA': 'A', 'GTA': 'V', 'GCC': 'A', 'GTC': 'V', 'GCG': 'A', 'GTG': 'V', 'GAG': 'E', 'GTT': 'V', 'GCT': 'A', 'GAC': 'D', 'CGT': 'R', 'GAA': 'E', 'TCA': 'S', 'ATG': 'M', 'CGC': 'R'}}
geneticCode = geneticCodes[code]
startCodons = ['ATT','ATC','ATA','ATG','GTG'] #invertebrateMt code
positionDict = {(0,1533):'COI',(1533,2217):'COII',(2217,2373):'ATP8',(2373,3066):'ATP6',(3066,4005):'ND1',(4005,4509):'ND6',(4509,5646):'CYTB',(5646,5940):'ND4L',(5940,7314):'ND4',(7314,9030):'ND5',(9030,9807):'COIII',(9807,10158):'ND3',(10158,11214):'ND2'} #{(start,stop):gene}
seqDict, seqList, codonDict = buildCodonDict(fasta)
popList = []
sexList = []
outList = []
synSites = {">$Duluth":2591.52083333, ">$Heron2":2598, ">$McGregor":2599, ">$Waik36":2586.91666667, ">$WalesC":2584.91666667, ">$clone_1":2598, ">$AC51":2598.33333333, ">$Heron_mitochondrion":2599, ">$clone_7":2592.85416667, ">$Waik37":2586.58333333, ">$Gunn":2597.66666667, ">$DenmarkA":2593.125, ">$Waik372":2589.25, ">$Tarawera":2586.58333333, ">$Poerua_triploid":2597, ">$Kaniere_triploid":2586.58333333, ">$Waik_lane4_TCCTGAGC_trimmed_paired_contig_237":2593.79166667, ">$Brunner_2_4n":2593.60416674, ">$Brunner_6_3n":2592.9583334, ">$Grasmere_1_4n":2628.66666703, ">$Grasmere_6_3n":2599.62500001, ">$Poerua_72_4n":2605.47916675, ">$Rotoiti_1_4n":2594.35416672, ">$*Kaniere_1_2n":2598.33333333, ">$*Ianthe_lane1_TAAGGCGA_trimmed_paired_contig_309":2595, ">$*Yellow_Contig_56":2592.33333333, ">$*Alexsex":2592.33333333, ">$*AlexMap":2592.33333333, ">$*Lady":2598.66666667, ">$*Ianthe":2597, ">$*Rotoroa_1_2n":2598.58333338}
C1Sites = {">$Duluth":6323.85416667, ">$Heron2":6320.33333333, ">$McGregor":6319, ">$Waik36":6330.25, ">$WalesC":6333.25, ">$clone_1":6319.66666667, ">$AC51":6318.66666667, ">$Heron_mitochondrion":6319.33333333, ">$clone_7":6322.52083333, ">$Waik37":6327.25, ">$Gunn":6324.33333333, ">$DenmarkA":6322.45833333, ">$Waik372":6330.58333333, ">$Tarawera":6329.25, ">$Poerua_triploid":6321.66666667, ">$Kaniere_triploid":6330.58333333, ">$Waik_lane4_TCCTGAGC_trimmed_paired_contig_237":6320.125, ">$Brunner_2_4n":6259.27083326, ">$Brunner_6_3n":6262.95833327, ">$Grasmere_1_4n":5990.99999963, ">$Grasmere_6_3n":6307.62499999, ">$Poerua_72_4n":6232.81249992, ">$Rotoiti_1_4n":6264.68749995, ">$*Kaniere_1_2n":6320.33333333, ">$*Ianthe_lane1_TAAGGCGA_trimmed_paired_contig_309":6321, ">$*Yellow_Contig_56":6326.33333333, ">$*Alexsex":6326.33333333, ">$*AlexMap":6326.33333333, ">$*Lady":6318, ">$*Ianthe":6321.33333333, ">$*Rotoroa_1_2n":6271.58333329}
R1Sites = {">$Duluth":2298.625, ">$Heron2":2295.66666667, ">$McGregor":2296, ">$Waik36":2296.83333333, ">$WalesC":2295.83333333, ">$clone_1":2296.33333333, ">$AC51":2297, ">$Heron_mitochondrion":2295.66666667, ">$clone_7":2298.625, ">$Waik37":2300.16666667, ">$Gunn":2292, ">$DenmarkA":2298.41666667, ">$Waik372":2294.16666667, ">$Tarawera":2298.16666667, ">$Poerua_triploid":2295.33333333, ">$Kaniere_triploid":2296.83333333, ">$Waik_lane4_TCCTGAGC_trimmed_paired_contig_237":2300.08333333, ">$Brunner_2_4n":2361.125, ">$Brunner_6_3n":2358.08333333, ">$Grasmere_1_4n":2594.33333333, ">$Grasmere_6_3n":2306.75, ">$Poerua_72_4n":2375.70833333, ">$Rotoiti_1_4n":2354.95833333, ">$*Kaniere_1_2n":2295.33333333, ">$*Ianthe_lane1_TAAGGCGA_trimmed_paired_contig_309":2298, ">$*Yellow_Contig_56":2295.33333333, ">$*Alexsex":2295.33333333, ">$*AlexMap":2295.33333333, ">$*Lady":2297.33333333, ">$*Ianthe":2295.66666667, ">$*Rotoroa_1_2n":2343.83333333}
C2Sites = {">$Duluth":5093.47916667, ">$Heron2":5090.33333333, ">$McGregor":5089.66666667, ">$Waik36":5100.75, ">$WalesC":5101.75, ">$clone_1":5091.33333333, ">$AC51":5089.33333333, ">$Heron_mitochondrion":5088.66666667, ">$clone_7":5092.14583333, ">$Waik37":5096.75, ">$Gunn":5090.33333333, ">$DenmarkA":5091.875, ">$Waik372":5097.41666667, ">$Tarawera":5097.08333333, ">$Poerua_triploid":5092, ">$Kaniere_triploid":5096.75, ">$Waik_lane4_TCCTGAGC_trimmed_paired_contig_237":5091.20833333, ">$Brunner_2_4n":5082.39583326, ">$Brunner_6_3n":5076.37499994, ">$Grasmere_1_4n":4999.33333297, ">$Grasmere_6_3n":5084.70833332, ">$Poerua_72_4n":5059.52083325, ">$Rotoiti_1_4n":5085.97916662, ">$*Kaniere_1_2n":5090, ">$*Ianthe_lane1_TAAGGCGA_trimmed_paired_contig_309":5095.33333333, ">$*Yellow_Contig_56":5097.33333333, ">$*Alexsex":5097.33333333, ">$*AlexMap":5097.33333333, ">$*Lady":5089, ">$*Ianthe":5093, ">$*Rotoroa_1_2n":5078.41666662}
R2Sites = {">$Duluth":3529, ">$Heron2":3525.66666667, ">$McGregor":3525.33333333, ">$Waik36":3526.33333333, ">$WalesC":3527.33333333, ">$clone_1":3524.66666667, ">$AC51":3526.33333333, ">$Heron_mitochondrion":3526.33333333, ">$clone_7":3529, ">$Waik37":3530.66666667, ">$Gunn":3526, ">$DenmarkA":3529, ">$Waik372":3527.33333333, ">$Tarawera":3530.33333333, ">$Poerua_triploid":3525, ">$Kaniere_triploid":3530.66666667, ">$Waik_lane4_TCCTGAGC_trimmed_paired_contig_237":3529, ">$Brunner_2_4n":3538, ">$Brunner_6_3n":3544.66666667, ">$Grasmere_1_4n":3586, ">$Grasmere_6_3n":3529.66666667, ">$Poerua_72_4n":3549, ">$Rotoiti_1_4n":3533.66666667, ">$*Kaniere_1_2n":3525.66666667, ">$*Ianthe_lane1_TAAGGCGA_trimmed_paired_contig_309":3523.66666667, ">$*Yellow_Contig_56":3524.33333333, ">$*Alexsex":3524.33333333, ">$*AlexMap":3524.33333333, ">$*Lady":3526.33333333, ">$*Ianthe":3524, ">$*Rotoroa_1_2n":3537}
C3Sites = {">$Duluth":2949.125, ">$Heron2":2945, ">$McGregor":2945, ">$Waik36":2947.16666667, ">$WalesC":2950.83333333, ">$clone_1":2944.66666667, ">$AC51":2945, ">$Heron_mitochondrion":2944.66666667, ">$clone_7":2949.79166667, ">$Waik37":2950.5, ">$Gunn":2944, ">$DenmarkA":2949.75, ">$Waik372":2952.83333333, ">$Tarawera":2950.5, ">$Poerua_triploid":2945.66666667, ">$Kaniere_triploid":2950.83333333, ">$Waik_lane4_TCCTGAGC_trimmed_paired_contig_237":2948.75, ">$Brunner_2_4n":2917.29166659, ">$Brunner_6_3n":2925.4166666, ">$Grasmere_1_4n":2832.33333297, ">$Grasmere_6_3n":2941.74999999, ">$Poerua_72_4n":2926.20833325, ">$Rotoiti_1_4n":2932.12499995, ">$*Kaniere_1_2n":2945.66666667, ">$*Ianthe_lane1_TAAGGCGA_trimmed_paired_contig_309":2945.33333333, ">$*Yellow_Contig_56":2946.66666667, ">$*Alexsex":2946.66666667, ">$*AlexMap":2946.66666667, ">$*Lady":2947.33333333, ">$*Ianthe":2945.33333333, ">$*Rotoroa_1_2n":2928.16666662}
R3Sites = {">$Duluth":5673.35416667, ">$Heron2":5671, ">$McGregor":5670, ">$Waik36":5679.91666667, ">$WalesC":5678.25, ">$clone_1":5671.33333333, ">$AC51":5670.66666667, ">$Heron_mitochondrion":5670.33333333, ">$clone_7":5671.35416667, ">$Waik37":5676.91666667, ">$Gunn":5672.33333333, ">$DenmarkA":5671.125, ">$Waik372":5671.91666667, ">$Tarawera":5676.91666667, ">$Poerua_triploid":5671.33333333, ">$Kaniere_triploid":5676.58333333, ">$Waik_lane4_TCCTGAGC_trimmed_paired_contig_237":5671.45833333, ">$Brunner_2_4n":5703.10416667, ">$Brunner_6_3n":5695.625, ">$Grasmere_1_4n":5753, ">$Grasmere_6_3n":5672.625, ">$Poerua_72_4n":5682.3125, ">$Rotoiti_1_4n":5687.52083333, ">$*Kaniere_1_2n":5670, ">$*Ianthe_lane1_TAAGGCGA_trimmed_paired_contig_309":5673.66666667, ">$*Yellow_Contig_56":5675, ">$*Alexsex":5675, ">$*AlexMap":5675, ">$*Lady":5668, ">$*Ianthe":5671.66666667, ">$*Rotoroa_1_2n":5687.25}
C4Sites = {">$Duluth":3422.02083333, ">$Heron2":3419.66666667, ">$McGregor":3420, ">$Waik36":3420.25, ">$WalesC":3423.25, ">$clone_1":3419.33333333, ">$AC51":3419, ">$Heron_mitochondrion":3419, ">$clone_7":3422.6875, ">$Waik37":3424.58333333, ">$Gunn":3420, ">$DenmarkA":3422.45833333, ">$Waik372":3428.25, ">$Tarawera":3424.91666667, ">$Poerua_triploid":3421, ">$Kaniere_triploid":3423.58333333, ">$Waik_lane4_TCCTGAGC_trimmed_paired_contig_237":3421.79166667, ">$Brunner_2_4n":3405.10416659, ">$Brunner_6_3n":3421.95833327, ">$Grasmere_1_4n":3382.99999963, ">$Grasmere_6_3n":3416.95833332, ">$Poerua_72_4n":3422.97916658, ">$Rotoiti_1_4n":3422.85416662, ">$*Kaniere_1_2n":3420.33333333, ">$*Ianthe_lane1_TAAGGCGA_trimmed_paired_contig_309":3420, ">$*Yellow_Contig_56":3420.66666667, ">$*Alexsex":3420.66666667, ">$*AlexMap":3420.66666667, ">$*Lady":3423, ">$*Ianthe":3419.33333333, ">$*Rotoroa_1_2n":3414.91666662}
R4Sites = {">$Duluth":5200.45833333, ">$Heron2":5196.33333333, ">$McGregor":5195, ">$Waik36":5206.83333333, ">$WalesC":5205.83333333, ">$clone_1":5196.66666667, ">$AC51":5196.66666667, ">$Heron_mitochondrion":5196, ">$clone_7":5198.45833333, ">$Waik37":5202.83333333, ">$Gunn":5196.33333333, ">$DenmarkA":5198.41666667, ">$Waik372":5196.5, ">$Tarawera":5202.5, ">$Poerua_triploid":5196, ">$Kaniere_triploid":5203.83333333, ">$Waik_lane4_TCCTGAGC_trimmed_paired_contig_237":5198.41666667, ">$Brunner_2_4n":5215.29166667, ">$Brunner_6_3n":5199.08333333, ">$Grasmere_1_4n":5202.33333333, ">$Grasmere_6_3n":5197.41666667, ">$Poerua_72_4n":5185.54166667, ">$Rotoiti_1_4n":5196.79166667, ">$*Kaniere_1_2n":5195.33333333, ">$*Ianthe_lane1_TAAGGCGA_trimmed_paired_contig_309":5199, ">$*Yellow_Contig_56":5201, ">$*Alexsex":5201, ">$*AlexMap":5201, ">$*Lady":5192.33333333, ">$*Ianthe":5197.66666667, ">$*Rotoroa_1_2n":5200.5}
C5Sites = {">$Duluth":4384.85416667, ">$Heron2":4382.33333333, ">$McGregor":4382, ">$Waik36":4383.58333333, ">$WalesC":4385.58333333, ">$clone_1":4382.33333333, ">$AC51":4382, ">$Heron_mitochondrion":4382.33333333, ">$clone_7":4385.1875, ">$Waik37":4385.58333333, ">$Gunn":4382.66666667, ">$DenmarkA":4385.125, ">$Waik372":4390.58333333, ">$Tarawera":4385.58333333, ">$Poerua_triploid":4383.33333333, ">$Kaniere_triploid":4386.25, ">$Waik_lane4_TCCTGAGC_trimmed_paired_contig_237":4383.79166667, ">$Brunner_2_4n":4338.9375, ">$Brunner_6_3n":4354.95833333, ">$Grasmere_1_4n":4238, ">$Grasmere_6_3n":4375.95833333, ">$Poerua_72_4n":4354.14583333, ">$Rotoiti_1_4n":4363.35416667, ">$*Kaniere_1_2n":4383.33333333, ">$*Ianthe_lane1_TAAGGCGA_trimmed_paired_contig_309":4384, ">$*Yellow_Contig_56":4381.66666667, ">$*Alexsex":4381.66666667, ">$*AlexMap":4381.66666667, ">$*Lady":4385.33333333, ">$*Ianthe":4384.66666667, ">$*Rotoroa_1_2n":4354.91666667}
R5Sites = {">$Duluth":4237.625, ">$Heron2":4233.66666667, ">$McGregor":4233, ">$Waik36":4243.5, ">$WalesC":4243.5, ">$clone_1":4233.66666667, ">$AC51":4233.66666667, ">$Heron_mitochondrion":4232.66666667, ">$clone_7":4235.95833333, ">$Waik37":4241.83333333, ">$Gunn":4233.66666667, ">$DenmarkA":4235.75, ">$Waik372":4234.16666667, ">$Tarawera":4241.83333333, ">$Poerua_triploid":4233.66666667, ">$Kaniere_triploid":4241.16666667, ">$Waik_lane4_TCCTGAGC_trimmed_paired_contig_237":4236.41666667, ">$Brunner_2_4n":4281.45833326, ">$Brunner_6_3n":4266.08333327, ">$Grasmere_1_4n":4347.33333297, ">$Grasmere_6_3n":4238.41666665, ">$Poerua_72_4n":4254.37499992, ">$Rotoiti_1_4n":4256.29166662, ">$*Kaniere_1_2n":4232.33333333, ">$*Ianthe_lane1_TAAGGCGA_trimmed_paired_contig_309":4235, ">$*Yellow_Contig_56":4240, ">$*Alexsex":4240, ">$*AlexMap":4240, ">$*Lady":4230, ">$*Ianthe":4232.33333333, ">$*Rotoroa_1_2n":4260.49999996}
C6Sites = {">$Duluth":4128.5625, ">$Heron2":4124.66666667, ">$McGregor":4124.33333333, ">$Waik36":4130.08333333, ">$WalesC":4129.75, ">$clone_1":4125.66666667, ">$AC51":4124.66666667, ">$Heron_mitochondrion":4125, ">$clone_7":4126.89583333, ">$Waik37":4123.41666667, ">$Gunn":4126.33333333, ">$DenmarkA":4127.04166667, ">$Waik372":4126.08333333, ">$Tarawera":4124.08333333, ">$Poerua_triploid":4126, ">$Kaniere_triploid":4125.75, ">$Waik_lane4_TCCTGAGC_trimmed_paired_contig_237":4126.04166667, ">$Brunner_2_4n":4078.47916674, ">$Brunner_6_3n":4075.2083334, ">$Grasmere_1_4n":3848.3333337, ">$Grasmere_6_3n":4112.54166668, ">$Poerua_72_4n":4050.43750008, ">$Rotoiti_1_4n":4084.39583338, ">$*Kaniere_1_2n":4126.33333333, ">$*Ianthe_lane1_TAAGGCGA_trimmed_paired_contig_309":4125, ">$*Yellow_Contig_56":4127.33333333, ">$*Alexsex":4127.33333333, ">$*AlexMap":4127.33333333, ">$*Lady":4121, ">$*Ianthe":4123.66666667, ">$*Rotoroa_1_2n":4085.08333338}
R6Sites = {">$Duluth":4493.91666667, ">$Heron2":4491.33333333, ">$McGregor":4490.66666667, ">$Waik36":4497, ">$WalesC":4499.33333333, ">$clone_1":4490.33333333, ">$AC51":4491, ">$Heron_mitochondrion":4490, ">$clone_7":4494.25, ">$Waik37":4504, ">$Gunn":4490, ">$DenmarkA":4493.83333333, ">$Waik372":4498.66666667, ">$Tarawera":4503.33333333, ">$Poerua_triploid":4491, ">$Kaniere_triploid":4501.66666667, ">$Waik_lane4_TCCTGAGC_trimmed_paired_contig_237":4494.16666667, ">$Brunner_2_4n":4541.91666674, ">$Brunner_6_3n":4545.8333334, ">$Grasmere_1_4n":4737.00000037, ">$Grasmere_6_3n":4501.83333335, ">$Poerua_72_4n":4558.08333342, ">$Rotoiti_1_4n":4535.25000005, ">$*Kaniere_1_2n":4489.33333333, ">$*Ianthe_lane1_TAAGGCGA_trimmed_paired_contig_309":4494, ">$*Yellow_Contig_56":4494.33333333, ">$*Alexsex":4494.33333333, ">$*AlexMap":4494.33333333, ">$*Lady":4494.33333333, ">$*Ianthe":4493.33333333, ">$*Rotoroa_1_2n":4530.33333338}
C7Sites = {">$Duluth":3873.77083333, ">$Heron2":3870.66666667, ">$McGregor":3870, ">$Waik36":3879.91666667, ">$WalesC":3880.58333333, ">$clone_1":3871.66666667, ">$AC51":3870.66666667, ">$Heron_mitochondrion":3870.33333333, ">$clone_7":3872.10416667, ">$Waik37":3874.25, ">$Gunn":3872.33333333, ">$DenmarkA":3871.625, ">$Waik372":3875.91666667, ">$Tarawera":3874.58333333, ">$Poerua_triploid":3872.66666667, ">$Kaniere_triploid":3875.91666667, ">$Waik_lane4_TCCTGAGC_trimmed_paired_contig_237":3870.29166667, ">$Brunner_2_4n":3832.85416667, ">$Brunner_6_3n":3825.79166667, ">$Grasmere_1_4n":3635.33333333, ">$Grasmere_6_3n":3860.45833333, ">$Poerua_72_4n":3801.89583333, ">$Rotoiti_1_4n":3832.9375, ">$*Kaniere_1_2n":3871.66666667, ">$*Ianthe_lane1_TAAGGCGA_trimmed_paired_contig_309":3873.66666667, ">$*Yellow_Contig_56":3877, ">$*Alexsex":3877, ">$*AlexMap":3877, ">$*Lady":3869, ">$*Ianthe":3872.33333333, ">$*Rotoroa_1_2n":3832.58333333}
R7Sites = {">$Duluth":4748.70833333, ">$Heron2":4745.33333333, ">$McGregor":4745, ">$Waik36":4747.16666667, ">$WalesC":4748.5, ">$clone_1":4744.33333333, ">$AC51":4745, ">$Heron_mitochondrion":4744.66666667, ">$clone_7":4749.04166667, ">$Waik37":4753.16666667, ">$Gunn":4744, ">$DenmarkA":4749.25, ">$Waik372":4748.83333333, ">$Tarawera":4752.83333333, ">$Poerua_triploid":4744.33333333, ">$Kaniere_triploid":4751.5, ">$Waik_lane4_TCCTGAGC_trimmed_paired_contig_237":4749.91666667, ">$Brunner_2_4n":4787.54166659, ">$Brunner_6_3n":4795.24999994, ">$Grasmere_1_4n":4949.99999963, ">$Grasmere_6_3n":4753.91666665, ">$Poerua_72_4n":4806.62499992, ">$Rotoiti_1_4n":4786.70833328, ">$*Kaniere_1_2n":4744, ">$*Ianthe_lane1_TAAGGCGA_trimmed_paired_contig_309":4745.33333333, ">$*Yellow_Contig_56":4744.66666667, ">$*Alexsex":4744.66666667, ">$*AlexMap":4744.66666667, ">$*Lady":4746.33333333, ">$*Ianthe":4744.66666667, ">$*Rotoroa_1_2n":4782.83333329}
meanCSites = {">$Duluth":4310.80952381, ">$Heron2":4307.57142857143, ">$McGregor":4307.14285714286, ">$Waik36":4313.14285714286, ">$WalesC":4314.99999999857, ">$clone_1":4307.80952381, ">$AC51":4307.04761904857, ">$Heron_mitochondrion":4307.04761904714, ">$clone_7":4310.19047619, ">$Waik37":4311.76190476143, ">$Gunn":4308.57142857, ">$DenmarkA":4310.04761904714, ">$Waik372":4314.52380952286, ">$Tarawera":4312.28571428429, ">$Poerua_triploid":4308.90476190571, ">$Kaniere_triploid":4312.80952380857, ">$Waik_lane4_TCCTGAGC_trimmed_paired_contig_237":4308.85714285857, ">$Brunner_2_4n":4273.47619044429, ">$Brunner_6_3n":4277.52380949714, ">$Grasmere_1_4n":4132.47619031857, ">$Grasmere_6_3n":4299.99999999429, ">$Poerua_72_4n":4263.99999996286, ">$Rotoiti_1_4n":4283.76190474143, ">$*Kaniere_1_2n":4308.23809523714, ">$*Ianthe_lane1_TAAGGCGA_trimmed_paired_contig_309":4309.19047619, ">$*Yellow_Contig_56":4311, ">$*Alexsex":4311, ">$*AlexMap":4311, ">$*Lady":4307.52380952286, ">$*Ianthe":4308.52380952286, ">$*Rotoroa_1_2n":4280.80952379}
meanRSites = {">$Duluth":4311.66964285714, ">$Heron2":4308.42857142857, ">$McGregor":4307.85714285714, ">$Waik36":4313.94047619, ">$WalesC":4314.08333333143, ">$clone_1":4308.19047619, ">$AC51":4308.61904762, ">$Heron_mitochondrion":4307.95238095286, ">$clone_7":4310.95535714286, ">$Waik37":4315.65476190571, ">$Gunn":4307.76190476143, ">$DenmarkA":4310.82738095286, ">$Waik372":4310.22619047714, ">$Tarawera":4315.13095238, ">$Poerua_triploid":4308.09523809429, ">$Kaniere_triploid":4314.60714285714, ">$Waik_lane4_TCCTGAGC_trimmed_paired_contig_237":4311.35119047714, ">$Brunner_2_4n":4346.91964284714, ">$Brunner_6_3n":4343.51785713429, ">$Grasmere_1_4n":4452.85714280429, ">$Grasmere_6_3n":4314.37499999857, ">$Poerua_72_4n":4344.52083332286, ">$Rotoiti_1_4n":4335.88392856429, ">$*Kaniere_1_2n":4307.42857142714, ">$*Ianthe_lane1_TAAGGCGA_trimmed_paired_contig_309":4309.80952381, ">$*Yellow_Contig_56":4310.66666666571, ">$*Alexsex":4310.66666666571, ">$*AlexMap":4310.66666666571, ">$*Lady":4307.80952380714, ">$*Ianthe":4308.47619047714, ">$*Rotoroa_1_2n":4334.60714285143}
D1 = {'mean':[],1:[],2:[],3:[],4:[],5:[],6:[],7:[]}#πC/πS
D2 = {'mean':[],1:[],2:[],3:[],4:[],5:[],6:[],7:[]}#πR/πS
D3 = {'mean':[],1:[],2:[],3:[],4:[],5:[],6:[],7:[]}#thetaC/thetaS
D4 = {'mean':[],1:[],2:[],3:[],4:[],5:[],6:[],7:[]}#thetaR/thetaS
D5 = {'piS':[]} #πS
logfile = open('mt_nullDistribution_IantheAnalysis.log','w')
for seq in seqList:
if '$' in seq:
popList.append(seq)
else:
outList.append(seq)
seqNums = range(len(popList))
currPCT = 0
sexN = 6
asexN = 16
sexAn = aN(sexN)
asexAn = aN(asexN)
logfile.write('Calculating population genetic parameters:\n')
logfile.close()
while len(D1['mean']) < 10000:
newPCT = int(round(100*len(D1['mean'])/10000.0))
if newPCT > currPCT:
logfile = open('mt_nullDistribution_πS.log','a')
logfile.write('\t' + str(newPCT) + '% complete\n')
logfile.close()
currPCT = newPCT
sexList = []
asexList = []
while len(sexList) < sexN:
currNum = random.choice(seqNums)
if popList[currNum] not in sexList:
sexList.append(popList[currNum])
while len(asexList) < asexN:
currNum = random.choice(seqNums)
if popList[currNum] not in asexList and popList[currNum] not in sexList:
asexList.append(popList[currNum])
sexSynSites = 0.0
asexSynSites = 0.0
sexC1Sites = 0.0
sexC2Sites = 0.0
sexC3Sites = 0.0
sexC4Sites = 0.0
sexC5Sites = 0.0
sexC6Sites = 0.0
sexC7Sites = 0.0
sexMeanCSites = 0.0
sexR1Sites = 0.0
sexR2Sites = 0.0
sexR3Sites = 0.0
sexR4Sites = 0.0
sexR5Sites = 0.0
sexR6Sites = 0.0
sexR7Sites = 0.0
sexMeanRSites = 0.0
asexC1Sites = 0.0
asexC2Sites = 0.0
asexC3Sites = 0.0
asexC4Sites = 0.0
asexC5Sites = 0.0
asexC6Sites = 0.0
asexC7Sites = 0.0
asexMeanCSites = 0.0
asexR1Sites = 0.0
asexR2Sites = 0.0
asexR3Sites = 0.0
asexR4Sites = 0.0
asexR5Sites = 0.0
asexR6Sites = 0.0
asexR7Sites = 0.0
asexMeanRSites = 0.0
for sexual in sexList:
sexSynSites += synSites[sexual]
sexC1Sites += C1Sites[sexual]
sexC2Sites += C2Sites[sexual]
sexC3Sites += C3Sites[sexual]
sexC4Sites += C4Sites[sexual]
sexC5Sites += C5Sites[sexual]
sexC6Sites += C6Sites[sexual]
sexC7Sites += C7Sites[sexual]
sexMeanCSites += meanCSites[sexual]
sexR1Sites += R1Sites[sexual]
sexR2Sites += R2Sites[sexual]
sexR3Sites += R3Sites[sexual]
sexR4Sites += R4Sites[sexual]
sexR5Sites += R5Sites[sexual]
sexR6Sites += R6Sites[sexual]
sexR7Sites += R7Sites[sexual]
sexMeanRSites += meanRSites[sexual]
for asexual in asexList:
asexSynSites += synSites[asexual]
asexC1Sites += C1Sites[asexual]
asexC2Sites += C2Sites[asexual]
asexC3Sites += C3Sites[asexual]
asexC4Sites += C4Sites[asexual]
asexC5Sites += C5Sites[asexual]
asexC6Sites += C6Sites[asexual]
asexC7Sites += C7Sites[asexual]
asexMeanCSites += meanCSites[asexual]
asexR1Sites += R1Sites[asexual]
asexR2Sites += R2Sites[asexual]
asexR3Sites += R3Sites[asexual]
asexR4Sites += R4Sites[asexual]
asexR5Sites += R5Sites[asexual]
asexR6Sites += R6Sites[asexual]
asexR7Sites += R7Sites[asexual]
asexMeanRSites += meanRSites[asexual]
asexSynSites /= len(asexList)
asexC1Sites /= len(asexList)
asexC2Sites /= len(asexList)
asexC3Sites /= len(asexList)
asexC4Sites /= len(asexList)
asexC5Sites /= len(asexList)
asexC6Sites /= len(asexList)
asexC7Sites /= len(asexList)
asexMeanCSites /= len(asexList)
asexR1Sites /= len(asexList)
asexR2Sites /= len(asexList)
asexR3Sites /= len(asexList)
asexR4Sites /= len(asexList)
asexR5Sites /= len(asexList)
asexR6Sites /= len(asexList)
asexR7Sites /= len(asexList)
asexMeanRSites /= len(asexList)
sexSynSites /= len(sexList)
sexC1Sites /= len(sexList)
sexC2Sites /= len(sexList)
sexC3Sites /= len(sexList)
sexC4Sites /= len(sexList)
sexC5Sites /= len(sexList)
sexC6Sites /= len(sexList)
sexC7Sites /= len(sexList)
sexMeanCSites /= len(sexList)
sexR1Sites /= len(sexList)
sexR2Sites /= len(sexList)
sexR3Sites /= len(sexList)
sexR4Sites /= len(sexList)
sexR5Sites /= len(sexList)
sexR6Sites /= len(sexList)
sexR7Sites /= len(sexList)
sexMeanRSites /= len(sexList)
refSeq = seqDict[sexList[0]]
outSeq = seqDict[outList[0]]
outCodons = codonDict[outList[0]]
sex_sum2PQ_S = 0
sex_sum2PQ_N = 0
sex_sum2PQ_C1 = 0
sex_sum2PQ_C2 = 0
sex_sum2PQ_C3 = 0
sex_sum2PQ_C4 = 0
sex_sum2PQ_C5 = 0
sex_sum2PQ_C6 = 0
sex_sum2PQ_C7 = 0
sex_sum2PQ_R1 = 0
sex_sum2PQ_R2 = 0
sex_sum2PQ_R3 = 0
sex_sum2PQ_R4 = 0
sex_sum2PQ_R5 = 0
sex_sum2PQ_R6 = 0
sex_sum2PQ_R7 = 0
sex_sum2PQ_meanC = 0
sex_sum2PQ_meanR = 0
sex_synS = 0
sex_nsynS = 0
sex_con1S = 0
sex_con2S = 0
sex_con3S = 0
sex_con4S = 0
sex_con5S = 0
sex_con6S = 0
sex_con7S = 0
sex_meanConS = 0
sex_rad1S = 0
sex_rad2S = 0
sex_rad3S = 0
sex_rad4S = 0
sex_rad5S = 0
sex_rad6S = 0
sex_rad7S = 0
sex_meanRadS = 0
i = 0
while i < len(codonDict[seqList[0]]):
outCodon = outCodons[i]
gene = False
for locus in positionDict:
start = locus[0]
stop = locus[1]
if i*3 >= start and i*3 <= stop:
gene = positionDict[locus]
currAlleleDict = {}
currAlleleList = []
currAADict = {}
for seq in sexList:
currCodons = codonDict[seq]
currCodon = currCodons[i]
if currCodon not in currAlleleDict and 'N' not in currCodon and '-' not in currCodon:
currAlleleDict[currCodon] = 1
currAlleleList.append(currCodon)
elif 'N' not in currCodon and '-' not in currCodon:
currValue = currAlleleDict[currCodon]
currValue += 1
currAlleleDict[currCodon] = currValue
if len(currAlleleDict) > 1:
totalIndividuals = 0
site1 = []
site2 = []
site3 = []
for codon in currAlleleList:
totalIndividuals += currAlleleDict[codon]
if codon[0] not in site1:
site1.append(codon[0])
if codon[1] not in site2:
site2.append(codon[1])
if codon[2] not in site3:
site3.append(codon[2])
currFreqDict = {}
totalChanges = (len(site1) - 1) + (len(site2) - 1) + (len(site3) - 1)
variableSites = []
if len(site1) > 1:
variableSites.append(i*3)
if len(site2) > 1:
variableSites.append((i*3) + 1)
if len(site3) > 1:
variableSites.append((i*3) + 1)
aaList = []
twoPQ = 2
for codon in currAlleleDict:
freq = float(currAlleleDict[codon])/totalIndividuals
currFreqDict[codon] = freq
if i == 0 and codon in startCodons:
aa = 'M'
else:
aa = geneticCode[codon]
currAADict[codon] = aa
if aa not in aaList:
aaList.append(aa)
if totalChanges == 1:
for codon in currAlleleDict:
freq = float(currAlleleDict[codon])/totalIndividuals
currFreqDict[codon] = freq
twoPQ *= freq
if len(aaList) == 1:
sex_synS += 1
sex_sum2PQ_S += twoPQ
else:
sex_nsynS += 1
sex_sum2PQ_N += twoPQ
mutType = CRI(aaList) #[1,2,3,4,5,6,7,cri]
if mutType[0] == 0:
sex_con1S += 1
sex_sum2PQ_C1 += twoPQ
else:
sex_rad1S += 1
sex_sum2PQ_R1 += twoPQ
if mutType[1] == 0:
sex_con2S += 1
sex_sum2PQ_C2 += twoPQ
else:
sex_rad2S += 1
sex_sum2PQ_R2 += twoPQ
if mutType[2] == 0:
sex_con3S += 1
sex_sum2PQ_C3 += twoPQ
else:
sex_rad3S += 1
sex_sum2PQ_R3 += twoPQ
if mutType[3] == 0:
sex_con4S += 1
sex_sum2PQ_C4 += twoPQ
else:
sex_rad4S += 1
sex_sum2PQ_R4 += twoPQ
if mutType[4] == 0:
sex_con5S += 1
sex_sum2PQ_C5 += twoPQ
else:
sex_rad5S += 1
sex_sum2PQ_R5 += twoPQ
if mutType[5] == 0:
sex_con6S += 1
sex_sum2PQ_C6 += twoPQ
else:
sex_rad6S += 1
sex_sum2PQ_R6 += twoPQ
if mutType[6] == 0:
sex_con7S += 1
sex_sum2PQ_C7 += twoPQ
else:
sex_rad7S += 1
sex_sum2PQ_R7 += twoPQ
if mutType[7] <= 0.5:
sex_meanConS += 1
sex_sum2PQ_meanC += twoPQ
else:
sex_meanRadS += 1
sex_sum2PQ_meanR += twoPQ
elif totalChanges == 2:
if len(currAlleleDict) == 3:
ab = 0
ac = 0
bc = 0
codonA = currAlleleList[0]
codonB = currAlleleList[1]
codonC = currAlleleList[2]
if codonA[0] != codonB[0]:
ab += 1
if codonA[1] != codonB[1]:
ab += 1
if codonA[2] != codonB[2]:
ab += 1
if codonA[0] != codonC[0]:
ac += 1
if codonA[1] != codonC[1]:
ac += 1
if codonA[2] != codonC[2]:
ac += 1
if codonC[0] != codonB[0]:
bc += 1
if codonC[1] != codonB[1]:
bc += 1
if codonC[2] != codonB[2]:
bc += 1
if ab == ac and ac == bc:
if 'N' not in outCodon and '-' not in outCodon:
if outCodon == codonA:
aaList1 = [currAADict[codonA],currAADict[codonB]]
aaList2 = [currAADict[codonA],currAADict[codonC]]
codonList1 = [codonA,codonB]
codonList2 = [codonA,codonC]
if aaList1[0] == aaList1[1]:
if aaList2[0] == aaList2[1]:
sex_synS += 2
twoPQ = 4
for allele in currFreqDict:
twoPQ *= currFreqDict[allele]
sex_sum2PQ_S += twoPQ
else:
twoPQ1 = 2*currFreqDict[codonList1[1]]*(1-currFreqDict[codonList1[1]]) #syn
twoPQ2 = 2*currFreqDict[codonList2[1]]*(1-currFreqDict[codonList2[1]]) #nsyn
sex_sum2PQ_S += twoPQ1
sex_sum2PQ_N += twoPQ2
sex_synS += 1
sex_nsynS += 1
mutType = CRI(aaList2) #[1,2,3,4,5,6,7,cri]
if mutType[0] == 0:
sex_con1S += 1
sex_sum2PQ_C1 += twoPQ2
else:
sex_rad1S += 1
sex_sum2PQ_R1 += twoPQ2
if mutType[1] == 0:
sex_con2S += 1
sex_sum2PQ_C2 += twoPQ2
else:
sex_rad2S += 1
sex_sum2PQ_R2 += twoPQ2
if mutType[2] == 0:
sex_con3S += 1
sex_sum2PQ_C3 += twoPQ2
else:
sex_rad3S += 1
sex_sum2PQ_R3 += twoPQ2
if mutType[3] == 0:
sex_con4S += 1
sex_sum2PQ_C4 += twoPQ2
else:
sex_rad4S += 1
sex_sum2PQ_R4 += twoPQ2
if mutType[4] == 0:
sex_con5S += 1
sex_sum2PQ_C5 += twoPQ2
else:
sex_rad5S += 1
sex_sum2PQ_R5 += twoPQ2
if mutType[5] == 0:
sex_con6S += 1
sex_sum2PQ_C6 += twoPQ2
else:
sex_rad6S += 1
sex_sum2PQ_R6 += twoPQ2
if mutType[6] == 0:
sex_con7S += 1
sex_sum2PQ_C7 += twoPQ2
else:
sex_rad7S += 1
sex_sum2PQ_R7 += twoPQ2
if mutType[7] <= 0.5:
sex_meanConS += 1
sex_sum2PQ_meanC += twoPQ2
else:
sex_meanRadS += 1
sex_sum2PQ_meanR += twoPQ2
elif aaList2[0] == aaList2[1]:
sex_nsynS += 1
sex_synS += 1
twoPQ1 = 2*currFreqDict[codonList1[1]]*(1-currFreqDict[codonList1[1]]) #nsyn
twoPQ2 = 2*currFreqDict[codonList2[1]]*(1-currFreqDict[codonList2[1]]) #syn
sex_sum2PQ_S += twoPQ2
sex_sum2PQ_N += twoPQ1
mutType = CRI(aaList1) #[1,2,3,4,5,6,7,cri]
if mutType[0] == 0:
sex_con1S += 1
sex_sum2PQ_C1 += twoPQ1
else:
sex_rad1S += 1
sex_sum2PQ_R1 += twoPQ1
if mutType[1] == 0:
sex_con2S += 1
sex_sum2PQ_C2 += twoPQ1
else:
sex_rad2S += 1
sex_sum2PQ_R2 += twoPQ1
if mutType[2] == 0:
sex_con3S += 1
sex_sum2PQ_C3 += twoPQ1
else:
sex_rad3S += 1
sex_sum2PQ_R3 += twoPQ1
if mutType[3] == 0:
sex_con4S += 1
sex_sum2PQ_C4 += twoPQ1
else:
sex_rad4S += 1
sex_sum2PQ_R4 += twoPQ1
if mutType[4] == 0:
sex_con5S += 1
sex_sum2PQ_C5 += twoPQ1
else:
sex_rad5S += 1
sex_sum2PQ_R5 += twoPQ1
if mutType[5] == 0:
sex_con6S += 1
sex_sum2PQ_C6 += twoPQ1
else:
sex_rad6S += 1
sex_sum2PQ_R6 += twoPQ1
if mutType[6] == 0:
sex_con7S += 1
sex_sum2PQ_C7 += twoPQ1
else:
sex_rad7S += 1
sex_sum2PQ_R7 += twoPQ1
if mutType[7] <= 0.5:
sex_meanConS += 1
sex_sum2PQ_meanC += twoPQ1
else:
sex_meanRadS += 1
sex_sum2PQ_meanR += twoPQ1
else:
sex_nsynS += 2
twoPQ1 = 2*currFreqDict[codonList1[1]]*(1-currFreqDict[codonList1[1]]) #nsyn
twoPQ2 = 2*currFreqDict[codonList2[1]]*(1-currFreqDict[codonList2[1]]) #nsyn
sex_sum2PQ_N += twoPQ1 + twoPQ2
mutType = CRI(aaList1) #[1,2,3,4,5,6,7,cri]
if mutType[0] == 0:
sex_con1S += 1
sex_sum2PQ_C1 += twoPQ1
else:
sex_rad1S += 1
sex_sum2PQ_R1 += twoPQ1
if mutType[1] == 0:
sex_con2S += 1
sex_sum2PQ_C2 += twoPQ1
else:
sex_rad2S += 1
sex_sum2PQ_R2 += twoPQ1
if mutType[2] == 0:
sex_con3S += 1
sex_sum2PQ_C3 += twoPQ1
else:
sex_rad3S += 1
sex_sum2PQ_R3 += twoPQ1
if mutType[3] == 0:
sex_con4S += 1
sex_sum2PQ_C4 += twoPQ1
else:
sex_rad4S += 1
sex_sum2PQ_R4 += twoPQ1
if mutType[4] == 0:
sex_con5S += 1
sex_sum2PQ_C5 += twoPQ1
else:
sex_rad5S += 1
sex_sum2PQ_R5 += twoPQ1
if mutType[5] == 0:
sex_con6S += 1
sex_sum2PQ_C6 += twoPQ1
else:
sex_rad6S += 1
sex_sum2PQ_R6 += twoPQ1
if mutType[6] == 0:
sex_con7S += 1
sex_sum2PQ_C7 += twoPQ1
else:
sex_rad7S += 1
sex_sum2PQ_R7 += twoPQ1
if mutType[7] <= 0.5:
sex_meanConS += 1
sex_sum2PQ_meanC += twoPQ1
else:
sex_meanRadS += 1
sex_sum2PQ_meanR += twoPQ1
mutType = CRI(aaList2) #[1,2,3,4,5,6,7,cri]
if mutType[0] == 0:
sex_con1S += 1
sex_sum2PQ_C1 += twoPQ2
else:
sex_rad1S += 1
sex_sum2PQ_R1 += twoPQ2
if mutType[1] == 0:
sex_con2S += 1
sex_sum2PQ_C2 += twoPQ2
else:
sex_rad2S += 1
sex_sum2PQ_R2 += twoPQ2
if mutType[2] == 0:
sex_con3S += 1
sex_sum2PQ_C3 += twoPQ2
else:
sex_rad3S += 1
sex_sum2PQ_R3 += twoPQ2
if mutType[3] == 0:
sex_con4S += 1
sex_sum2PQ_C4 += twoPQ2
else:
sex_rad4S += 1
sex_sum2PQ_R4 += twoPQ2
if mutType[4] == 0:
sex_con5S += 1
sex_sum2PQ_C5 += twoPQ2
else:
sex_rad5S += 1
sex_sum2PQ_R5 += twoPQ2
if mutType[5] == 0:
sex_con6S += 1
sex_sum2PQ_C6 += twoPQ2
else:
sex_rad6S += 1
sex_sum2PQ_R6 += twoPQ2
if mutType[6] == 0:
sex_con7S += 1
sex_sum2PQ_C7 += twoPQ2
else:
sex_rad7S += 1
sex_sum2PQ_R7 += twoPQ2
if mutType[7] <= 0.5:
sex_meanConS += 1
sex_sum2PQ_meanC += twoPQ2
else:
sex_meanRadS += 1
sex_sum2PQ_meanR += twoPQ2
elif outCodon == codonB:
aaList1 = [currAADict[codonB],currAADict[codonA]]
aaList2 = [currAADict[codonB],currAADict[codonC]]
codonList1 = [codonB,codonA]
codonList2 = [codonB,codonC]
if aaList1[0] == aaList1[1]:
if aaList2[0] == aaList2[1]:
sex_synS += 2
twoPQ = 4
for allele in currFreqDict:
twoPQ *= currFreqDict[allele]
sex_sum2PQ_S += twoPQ
else:
twoPQ1 = 2*currFreqDict[codonList1[1]]*(1-currFreqDict[codonList1[1]]) #syn
twoPQ2 = 2*currFreqDict[codonList2[1]]*(1-currFreqDict[codonList2[1]]) #nsyn
sex_sum2PQ_S += twoPQ1
sex_sum2PQ_N += twoPQ2
sex_synS += 1
sex_nsynS += 1
mutType = CRI(aaList2) #[1,2,3,4,5,6,7,cri]
if mutType[0] == 0:
sex_con1S += 1
sex_sum2PQ_C1 += twoPQ2
else:
sex_rad1S += 1
sex_sum2PQ_R1 += twoPQ2
if mutType[1] == 0:
sex_con2S += 1
sex_sum2PQ_C2 += twoPQ2
else:
sex_rad2S += 1
sex_sum2PQ_R2 += twoPQ2
if mutType[2] == 0:
sex_con3S += 1
sex_sum2PQ_C3 += twoPQ2
else:
sex_rad3S += 1
sex_sum2PQ_R3 += twoPQ2
if mutType[3] == 0:
sex_con4S += 1
sex_sum2PQ_C4 += twoPQ2
else:
sex_rad4S += 1
sex_sum2PQ_R4 += twoPQ2
if mutType[4] == 0:
sex_con5S += 1
sex_sum2PQ_C5 += twoPQ2
else:
sex_rad5S += 1
sex_sum2PQ_R5 += twoPQ2
if mutType[5] == 0:
sex_con6S += 1
sex_sum2PQ_C6 += twoPQ2
else:
sex_rad6S += 1
sex_sum2PQ_R6 += twoPQ2
if mutType[6] == 0:
sex_con7S += 1
sex_sum2PQ_C7 += twoPQ2
else:
sex_rad7S += 1
sex_sum2PQ_R7 += twoPQ2
if mutType[7] <= 0.5:
sex_meanConS += 1
sex_sum2PQ_meanC += twoPQ2
else:
sex_meanRadS += 1
sex_sum2PQ_meanR += twoPQ2
elif aaList2[0] == aaList2[1]:
sex_nsynS += 1
sex_synS += 1
twoPQ1 = 2*currFreqDict[codonList1[1]]*(1-currFreqDict[codonList1[1]]) #nsyn
twoPQ2 = 2*currFreqDict[codonList2[1]]*(1-currFreqDict[codonList2[1]]) #syn
sex_sum2PQ_S += twoPQ2
sex_sum2PQ_N += twoPQ1
mutType = CRI(aaList1) #[1,2,3,4,5,6,7,cri]
if mutType[0] == 0:
sex_con1S += 1
sex_sum2PQ_C1 += twoPQ1
else:
sex_rad1S += 1
sex_sum2PQ_R1 += twoPQ1
if mutType[1] == 0:
sex_con2S += 1
sex_sum2PQ_C2 += twoPQ1
else:
sex_rad2S += 1
sex_sum2PQ_R2 += twoPQ1
if mutType[2] == 0:
sex_con3S += 1
sex_sum2PQ_C3 += twoPQ1
else:
sex_rad3S += 1
sex_sum2PQ_R3 += twoPQ1
if mutType[3] == 0:
sex_con4S += 1
sex_sum2PQ_C4 += twoPQ1
else:
sex_rad4S += 1
sex_sum2PQ_R4 += twoPQ1
if mutType[4] == 0:
sex_con5S += 1
sex_sum2PQ_C5 += twoPQ1
else:
sex_rad5S += 1
sex_sum2PQ_R5 += twoPQ1
if mutType[5] == 0:
sex_con6S += 1
sex_sum2PQ_C6 += twoPQ1
else:
sex_rad6S += 1
sex_sum2PQ_R6 += twoPQ1
if mutType[6] == 0:
sex_con7S += 1
sex_sum2PQ_C7 += twoPQ1
else:
sex_rad7S += 1
sex_sum2PQ_R7 += twoPQ1
if mutType[7] <= 0.5:
sex_meanConS += 1
sex_sum2PQ_meanC += twoPQ1
else:
sex_meanRadS += 1
sex_sum2PQ_meanR += twoPQ1
else:
sex_nsynS += 2
twoPQ1 = 2*currFreqDict[codonList1[1]]*(1-currFreqDict[codonList1[1]]) #nsyn
twoPQ2 = 2*currFreqDict[codonList2[1]]*(1-currFreqDict[codonList2[1]]) #nsyn
sex_sum2PQ_N += twoPQ1 + twoPQ2
mutType = CRI(aaList1) #[1,2,3,4,5,6,7,cri]
if mutType[0] == 0:
sex_con1S += 1
sex_sum2PQ_C1 += twoPQ1
else:
sex_rad1S += 1
sex_sum2PQ_R1 += twoPQ1
if mutType[1] == 0:
sex_con2S += 1
sex_sum2PQ_C2 += twoPQ1
else:
sex_rad2S += 1
sex_sum2PQ_R2 += twoPQ1
if mutType[2] == 0:
sex_con3S += 1
sex_sum2PQ_C3 += twoPQ1
else:
sex_rad3S += 1
sex_sum2PQ_R3 += twoPQ1
if mutType[3] == 0:
sex_con4S += 1
sex_sum2PQ_C4 += twoPQ1
else:
sex_rad4S += 1
sex_sum2PQ_R4 += twoPQ1
if mutType[4] == 0:
sex_con5S += 1
sex_sum2PQ_C5 += twoPQ1
else:
sex_rad5S += 1
sex_sum2PQ_R5 += twoPQ1
if mutType[5] == 0:
sex_con6S += 1
sex_sum2PQ_C6 += twoPQ1
else:
sex_rad6S += 1
sex_sum2PQ_R6 += twoPQ1
if mutType[6] == 0:
sex_con7S += 1
sex_sum2PQ_C7 += twoPQ1
else:
sex_rad7S += 1
sex_sum2PQ_R7 += twoPQ1
if mutType[7] <= 0.5:
sex_meanConS += 1
sex_sum2PQ_meanC += twoPQ1
else:
sex_meanRadS += 1
sex_sum2PQ_meanR += twoPQ1
mutType = CRI(aaList2) #[1,2,3,4,5,6,7,cri]
if mutType[0] == 0:
sex_con1S += 1
sex_sum2PQ_C1 += twoPQ2
else:
sex_rad1S += 1
sex_sum2PQ_R1 += twoPQ2
if mutType[1] == 0:
sex_con2S += 1
sex_sum2PQ_C2 += twoPQ2
else:
sex_rad2S += 1
sex_sum2PQ_R2 += twoPQ2
if mutType[2] == 0:
sex_con3S += 1
sex_sum2PQ_C3 += twoPQ2
else:
sex_rad3S += 1
sex_sum2PQ_R3 += twoPQ2
if mutType[3] == 0:
sex_con4S += 1
sex_sum2PQ_C4 += twoPQ2
else:
sex_rad4S += 1
sex_sum2PQ_R4 += twoPQ2
if mutType[4] == 0:
sex_con5S += 1
sex_sum2PQ_C5 += twoPQ2
else:
sex_rad5S += 1
sex_sum2PQ_R5 += twoPQ2
if mutType[5] == 0:
sex_con6S += 1
sex_sum2PQ_C6 += twoPQ2
else:
sex_rad6S += 1
sex_sum2PQ_R6 += twoPQ2
if mutType[6] == 0:
sex_con7S += 1
sex_sum2PQ_C7 += twoPQ2
else:
sex_rad7S += 1
sex_sum2PQ_R7 += twoPQ2
if mutType[7] <= 0.5:
sex_meanConS += 1
sex_sum2PQ_meanC += twoPQ2
else:
sex_meanRadS += 1
sex_sum2PQ_meanR += twoPQ2
elif outCodon == codonC:
aaList1 = [currAADict[codonC],currAADict[codonA]]
aaList2 = [currAADict[codonC],currAADict[codonB]]
codonList1 = [codonA,codonB]
codonList2 = [codonA,codonC]
if aaList1[0] == aaList1[1]:
if aaList2[0] == aaList2[1]:
sex_synS += 2
twoPQ = 4
for allele in currFreqDict:
twoPQ *= currFreqDict[allele]
sex_sum2PQ_S += twoPQ
else:
twoPQ1 = 2*currFreqDict[codonList1[1]]*(1-currFreqDict[codonList1[1]]) #syn
twoPQ2 = 2*currFreqDict[codonList2[1]]*(1-currFreqDict[codonList2[1]]) #nsyn
sex_sum2PQ_S += twoPQ1
sex_sum2PQ_N += twoPQ2
sex_synS += 1
sex_nsynS += 1
mutType = CRI(aaList2) #[1,2,3,4,5,6,7,cri]
if mutType[0] == 0:
sex_con1S += 1
sex_sum2PQ_C1 += twoPQ2
else:
sex_rad1S += 1
sex_sum2PQ_R1 += twoPQ2
if mutType[1] == 0:
sex_con2S += 1
sex_sum2PQ_C2 += twoPQ2
else:
sex_rad2S += 1
sex_sum2PQ_R2 += twoPQ2
if mutType[2] == 0:
sex_con3S += 1
sex_sum2PQ_C3 += twoPQ2
else:
sex_rad3S += 1
sex_sum2PQ_R3 += twoPQ2
if mutType[3] == 0:
sex_con4S += 1
sex_sum2PQ_C4 += twoPQ2
else:
sex_rad4S += 1
sex_sum2PQ_R4 += twoPQ2
if mutType[4] == 0:
sex_con5S += 1
sex_sum2PQ_C5 += twoPQ2
else:
sex_rad5S += 1
sex_sum2PQ_R5 += twoPQ2
if mutType[5] == 0:
sex_con6S += 1
sex_sum2PQ_C6 += twoPQ2
else:
sex_rad6S += 1
sex_sum2PQ_R6 += twoPQ2
if mutType[6] == 0:
sex_con7S += 1
sex_sum2PQ_C7 += twoPQ2
else:
sex_rad7S += 1
sex_sum2PQ_R7 += twoPQ2
if mutType[7] <= 0.5:
sex_meanConS += 1
sex_sum2PQ_meanC += twoPQ2
else:
sex_meanRadS += 1
sex_sum2PQ_meanR += twoPQ2
elif aaList2[0] == aaList2[1]:
sex_nsynS += 1
sex_synS += 1
twoPQ1 = 2*currFreqDict[codonList1[1]]*(1-currFreqDict[codonList1[1]]) #nsyn
twoPQ2 = 2*currFreqDict[codonList2[1]]*(1-currFreqDict[codonList2[1]]) #syn
sex_sum2PQ_S += twoPQ2
sex_sum2PQ_N += twoPQ1
mutType = CRI(aaList1) #[1,2,3,4,5,6,7,cri]
if mutType[0] == 0:
sex_con1S += 1
sex_sum2PQ_C1 += twoPQ1
else:
sex_rad1S += 1
sex_sum2PQ_R1 += twoPQ1
if mutType[1] == 0:
sex_con2S += 1
sex_sum2PQ_C2 += twoPQ1
else:
sex_rad2S += 1
sex_sum2PQ_R2 += twoPQ1
if mutType[2] == 0:
sex_con3S += 1
sex_sum2PQ_C3 += twoPQ1
else:
sex_rad3S += 1
sex_sum2PQ_R3 += twoPQ1
if mutType[3] == 0:
sex_con4S += 1
sex_sum2PQ_C4 += twoPQ1
else:
sex_rad4S += 1
sex_sum2PQ_R4 += twoPQ1
if mutType[4] == 0:
sex_con5S += 1
sex_sum2PQ_C5 += twoPQ1
else:
sex_rad5S += 1
sex_sum2PQ_R5 += twoPQ1
if mutType[5] == 0:
sex_con6S += 1
sex_sum2PQ_C6 += twoPQ1
else:
sex_rad6S += 1
sex_sum2PQ_R6 += twoPQ1
if mutType[6] == 0:
sex_con7S += 1
sex_sum2PQ_C7 += twoPQ1
else:
sex_rad7S += 1
sex_sum2PQ_R7 += twoPQ1
if mutType[7] <= 0.5:
sex_meanConS += 1
sex_sum2PQ_meanC += twoPQ1
else:
sex_meanRadS += 1
sex_sum2PQ_meanR += twoPQ1
else:
sex_nsynS += 2
twoPQ1 = 2*currFreqDict[codonList1[1]]*(1-currFreqDict[codonList1[1]]) #nsyn
twoPQ2 = 2*currFreqDict[codonList2[1]]*(1-currFreqDict[codonList2[1]]) #nsyn
sex_sum2PQ_N += twoPQ1 + twoPQ2
mutType = CRI(aaList1) #[1,2,3,4,5,6,7,cri]
if mutType[0] == 0:
sex_con1S += 1
sex_sum2PQ_C1 += twoPQ1
else:
sex_rad1S += 1
sex_sum2PQ_R1 += twoPQ1
if mutType[1] == 0:
sex_con2S += 1
sex_sum2PQ_C2 += twoPQ1
else:
sex_rad2S += 1
sex_sum2PQ_R2 += twoPQ1
if mutType[2] == 0:
sex_con3S += 1
sex_sum2PQ_C3 += twoPQ1
else:
sex_rad3S += 1
sex_sum2PQ_R3 += twoPQ1
if mutType[3] == 0:
sex_con4S += 1
sex_sum2PQ_C4 += twoPQ1
else:
sex_rad4S += 1
sex_sum2PQ_R4 += twoPQ1
if mutType[4] == 0:
sex_con5S += 1
sex_sum2PQ_C5 += twoPQ1
else:
sex_rad5S += 1
sex_sum2PQ_R5 += twoPQ1
if mutType[5] == 0:
sex_con6S += 1
sex_sum2PQ_C6 += twoPQ1
else:
sex_rad6S += 1
sex_sum2PQ_R6 += twoPQ1
if mutType[6] == 0:
sex_con7S += 1
sex_sum2PQ_C7 += twoPQ1
else:
sex_rad7S += 1
sex_sum2PQ_R7 += twoPQ1
if mutType[7] <= 0.5:
sex_meanConS += 1
sex_sum2PQ_meanC += twoPQ1
else:
sex_meanRadS += 1
sex_sum2PQ_meanR += twoPQ1
mutType = CRI(aaList2) #[1,2,3,4,5,6,7,cri]
if mutType[0] == 0:
sex_con1S += 1
sex_sum2PQ_C1 += twoPQ2
else:
sex_rad1S += 1
sex_sum2PQ_R1 += twoPQ2
if mutType[1] == 0:
sex_con2S += 1
sex_sum2PQ_C2 += twoPQ2
else:
sex_rad2S += 1
sex_sum2PQ_R2 += twoPQ2
if mutType[2] == 0:
sex_con3S += 1
sex_sum2PQ_C3 += twoPQ2