Skip to content

A0c_AccessoryGenome.m rename recipsize -> dictsize #8

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
ACCakut wants to merge 1 commit into
base: main
Choose a base branch
from
Open

A0c_AccessoryGenome.m rename recipsize -> dictsize #8

Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
9 changes: 6 additions & 3 deletions 1_Detection/A0c_AccessoryGenome.m
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -9,8 +9,11 @@
path = "/home/isabel/Documents/Doktorarbeit_Mai2022/1_kleinesPaper_BigData/Donor2Bs166/";
fileName = "Bmoj_2NCe";
fileSuffix = "_bcf.vcf";

% genome size of the .dict that .vcf was mapped to = number of letters in .fasta file
dictsize = 4215607; % B.sub Bs166
%dictsize = 4027680; % B.spiz W23 WT

recipsize = 4215607;
maxDP = 50; % Everything covered >= maxDP, is not included in the
% accessory genome
minLength = 0; % Only regions longer minLength bps are considered
Expand Down Expand Up @@ -49,7 +52,7 @@
% 2. Find positions with no entry in the bcf - no read mapped, position
% with no cover --> posMissingMask == 1

posRecip = [1 : recipsize];
posRecip = [1 : dictsize];
posMissingMask = ~ismember(posRecip, posAll);

% include 1.: set all pos where DP < 50: posMissingMask == 1
Expand Down Expand Up @@ -82,5 +85,5 @@
save(savePath + saveName + "_allBP.mat","accList")

%
accessoryFraction = sum(totalLengthFilt)/recipsize;
accessoryFraction = sum(totalLengthFilt)/dictsize;
disp("For " + fileName + ", "+ num2str(accessoryFraction*100, "%0.1f")+ " % of the genome is accessory.");