Unrecognized function or variable 'ApOPs'.

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Rahul
Rahul on 23 Nov 2022
Answered: Rahul on 26 Nov 2022
I am trying to make Oligopaint library (OligoLego-Github based) using intersected oligprobes generated from OligoMiner for bacteril genome contig.Please suggest me what should i edit in the program commands
I encountered one error- Unrecognized function or variable 'ApOPs'.)
The appendting text was
(%% Call AppToMSBS
LoadRegionsFolder='C:\MATLAB\';
LoadBarcodesFolder='C:\MATLAB\StreetsLatest\';
SaveFolder=LoadRegionsFolder;
ApOPs('MS',[LoadRegionsFolder,'5_MS_Output.bed'],'BS'...
,[LoadRegionsFolder,'5_BS_Output.bed'],'Toes'...
,[LoadBarcodesFolder,'Toes_V1.txt'],...
'Streets',[LoadBarcodesFolder,'Streets_V1.txt'],...
'PTable',[LoadBarcodesFolder,'PenaltyTable_V1.txt'],...
'SavePath',SaveFolder,'MaxAvoid','0')%,'SameUniversal',[LoadRegionsFolder,'Universal.txt']);

Answers (3)

Image Analyst
Image Analyst on 23 Nov 2022
You don't have ApOPs on the search path. What folder does it live in? Let's say it's 'C:\MATLAB\Oligopaint' Then add this to the beginning of your code
addpath(genpath('C:\MATLAB\Oligopaint'));
savepath;
  3 Comments
Walter Roberson
Walter Roberson on 23 Nov 2022
No, readtextfile() is on the path. But the file name in MSPath cannot be found (at least not under that name). It appears you are providing 'MS' as the complete file name.
[LoadRegionsFolder,'5_BS_Output.bed'],
We recommend that you use
fullfile(LoadRegionsFolder,'5_BS_Output.bed'),

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Rahul
Rahul on 26 Nov 2022
Thank you for the suggestions friends.
MS.bed and BS.bed are renamed isected/output files as mentioned earlier. Do i need to make folders with names of LoadRegionsFolder, LoadBarcodesFolder,SaveFolder, ApOPs before starting the appending.m file in MATLAB R2020b.
the .txt files are saved in StreetsLatest folder.
Do I need to rearrange these files in folders where they are saved now.
I tried the above suggestions but still i get this error:
Unrecognized function or variable 'MSPath'.
Error in ApOPs (line 92)
AppToMSBS(MSPath,BSPath,StreetsPath,PTablePath,ToesPath,MaxAvoid,SavePath);
Appending program was:
Call AppToMSBS
LoadRegionsFolder='C:/Program Files/MATLAB/';
LoadBarcodesFolder='C:/Program Files/MATLAB/StreetsLatest/';
SaveFolder=LoadRegionsFolder;
%addpath('genpath'['C:/Program Files/MATLAB']);
savepath;
ApOPs('fullfile',[LoadRegionsFolder,'MS.bed'],'BS'...
,[LoadRegionsFolder,'BS.bed'],'Toes'...
,[LoadBarcodesFolder,'Toes_V1.txt'],...
'Streets',[LoadBarcodesFolder,'Streets_V1.txt'],...
'PTable',[LoadBarcodesFolder,'PenaltyTable_V1.txt'],...
'SavePath',SaveFolder,'MaxAvoid','0')%,'SameUniversal',[LoadRegionsFolder,'Universal.txt']);

Rahul
Rahul on 26 Nov 2022
The details of ApOPs is given below as found from MATLAB R2020b. Please have a look
ApOPs.m
Documentation
This function appends streets/toes to Oligopaints probes.
Required input:
1. 'MS' - MainStreet intersected text (*.txt) file, which is the
output of bedtools intersect -wa -wb -a ROI.bed -b probes.bed
When intersecting, please add a 4th column for your ROI file, which
is the names of each region (user-defined)
2. Streets - A text file, which is a list of mainstreets/backstreets.
This file can be created using 'MakingStreets.m'.
3. PairsMatrix text file, which can be created using 'MakingStreets.m'.
4. Maximum street number to avoid, which is the number of the highest
previous Street used for appending, in case would like to avoid using
same streets, when running the script multiple times.
4. SavePath - The path where you want to save the outputs of this
function.
Optional input:
5. 'BS' - BackStreet intersected text (*.txt) file (same format as the
MainStreet)
6. In ase would like to make library compatible with toeholds, so the RC
of the toehold will become the mainstreet/backstreet.
Output:
1. Oligopaints.txt - a text file which has all the oligopaints (OPs) of the
library. Each line is a different OP.
2. MS_IDs.txt - a list with the Forward primers, bridges and toeholds (if
asked to) sequences.
3. BS_IDs.txt - if a backstreet list was given as an input as well, will
have the same for backstreet.
4. MSDensity.txt - Density of rgions
5. BSDensity.txt - if a backstreet list was given as an input as well, will
have the same for backstreet.
6. Universal.txt - forward and reverse primer sequence for universals.

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