analysis

from dgrec.example_data import get_example_data_dir

source

mut_rate

 mut_rate (gen_list:list, ran:tuple, ref_seq:str)

Computes the mutation rate per base within the specified range. The rate can be computed for specific bases using the base_restriction argument.

	Type	Details
gen_list	list	a genotype list with the number of molecules detected
ran	tuple	the position range in which to compute the mutation rate. If None the rate is computed for the full sequence.
ref_seq	str	reference sequence

data_path=get_example_data_dir()
gen_list=parse_genotypes(os.path.join(data_path,"sacB_genotypes.csv"))

read_ref_file="sacB_ref.fasta"
ref=next(SeqIO.parse(os.path.join(data_path,read_ref_file),"fasta"))
ref_seq=str(ref.seq)

#showing a few example lines
for g,n in gen_list[1:200:20]:
    print(n,"\t",g)

279      A91G
28   A68C
15   A72G,A79T,A91T
10   A61G,A72G
6    A61G,A68G
6    A68G,A76G,A91G
5    A61T,A79G
4    A86T
4    A72G,A76G,A86G,A91T
3    A61T,A76G,A91G

TR_range=(50,119)
before_TR_range=(5,50)
mut_rate_TR=mut_rate(gen_list,TR_range,ref_seq)
for b in mut_rate_TR:
    print(f"Mutation rate in VR at {b} positions: {mut_rate_TR[b]:.1e}")

mut_rate_outside_TR=mut_rate(gen_list,before_TR_range,ref_seq)
for b in mut_rate_outside_TR:
    print(f"Mutation rate outside VR at {b} positions: {mut_rate_outside_TR[b]:.1e}")

Mutation rate in VR at A positions: 1.9e-02
Mutation rate in VR at T positions: 9.9e-04
Mutation rate in VR at G positions: 1.1e-04
Mutation rate in VR at C positions: 2.2e-04
Mutation rate in VR at all positions: 2.9e-03
Mutation rate outside VR at A positions: 2.1e-05
Mutation rate outside VR at T positions: 4.8e-05
Mutation rate outside VR at G positions: 1.8e-04
Mutation rate outside VR at C positions: 5.9e-05
Mutation rate outside VR at all positions: 6.7e-05