popgen_python

This is a suite of program to perform basic task on fasta sequences. Program are written in python3.

This include :

• heterozygosity.py : compute heterozygosity from a fasta file with two sequences corresponding to the two chromosomes.

• cleanAlignment.py : exclude site with missing data "N" from a alignment

Author: Benoit Nabholz

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heterozygosity.py

Usage:

heterozygosity.py -f fasta_seq.fasta -w window_size

• f : name of the fasta file
• w : size of the window in base pair

Output

• name : name window
• Position : Position in the alignment
• Ts : Number of transition
• Ts/Tv : ratio of transition over transversion in the window
• S : number of SNP
• Num_site: number of site in the window that are not "-" or "N"
• Het : Heterozygosity = S / N_site

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cleanAlignment.py

Usage:

cleanAlignment.py fasta_seq.fasta