seq_a = 'GAGAGATTTTCCAATTCGACG-------CGGGGTCAGG--GAAATTT'
seq_b = 'GAGAGATTGGCCTTAACTACCCAACCCACGGCCTGACCGAGGTCTTC'
G,A,C,T = Bases
- = INDEL
PYTHON - I am very new to programming and need some help, I would like to write a python program that will first find indels '-' in seq_a and then compare both sequences (seq_a and seq_b) downstream and upstream from the the indels counting the number of differences between the bases.
e.g.
seq_a - GG--GAAA
seq_b - CCGAGGTC
This example has 5 SNPS upstream and downstream from the the indel c-g, c-g, a-g, a-t, a-c
I was wondering if anyone could give me any pointers or ideas how I would start of this program?
Thanks :)
•
written
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will.duncan26 •
Assuming that you have your alignment in a file named "fasta.fas" this should get you started
from Bio import AlignIO
y=0
alignment = AlignIO.read("fasta.fas", "fasta")
for r in range(0,len(alignment[1].seq)):
if alignment[0,r] != alignment[1,r]:
if alignment[0,r] != "-" and alignment[1,r] != "-":
y=y+1
print r, alignment[0,r], alignment[1,r], y
else:
y=0
This returns position of SNP, nt in seq_A, nt in seq_B, running tally of the number of SNPs upstream of each indel
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Note that the easiest solution is to use biopython. It has some built-in facilities to perform alignment (e.g. the pairwise2 module) and can also just use command line alignment tools that tend to be faster.