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June 18, 2018 12:37
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import sys | |
from Bio import SeqIO | |
def mismatch(seq1, seq2): | |
index = [] | |
for i, (s1, s2) in enumerate(zip(seq1, seq2)): | |
if s1 != s2: | |
index.append(i) | |
return index | |
def get_effect(seq, pos, ref, mismatches): | |
effect = "." | |
if len(mismatches) > 1: | |
effect = "*" | |
elif pos in mismatches: | |
if seq.translate() == ref.translate(): | |
effect = "synonymous" | |
else: | |
effect = "non-synonymous" | |
return effect | |
sequences = SeqIO.index(sys.argv[1], "fasta") | |
result = [] | |
for i in range(0, len(sequences['species1'].seq), 3): | |
codon_s1 = sequences['species1'].seq[i:i+3] | |
codon_s2 = sequences['species2'].seq[i:i+3] | |
codon_s3 = sequences['species3'].seq[i:i+3] | |
if codon_s1 != codon_s2: | |
mismatches_s1 = mismatch(codon_s1, codon_s3) | |
mismatches_s2 = mismatch(codon_s2, codon_s3) | |
pos = set(mismatches_s1 + mismatches_s2) | |
for p in pos: | |
effect_s1 = get_effect(codon_s1, p, codon_s3, mismatches_s1) | |
effect_s2 = get_effect(codon_s2, p, codon_s3, mismatches_s2) | |
result.append(( | |
i+p+1, | |
codon_s3[p], | |
codon_s1[p], | |
effect_s1, | |
codon_s2[p], | |
effect_s2 | |
)) | |
print("#POS", "species3", "species1", "effect_s1", "species2", "effect_s2", sep="\t") | |
for row in result: | |
print("\t".join(map(str, row))) |
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Second answer on biostars question: https://www.biostars.org/p/320742