Unrecognized function or variable 'ApOPs'.

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']);

Answer 1

[Image Analyst]

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;

[Rahul]

Thank you for suggestion

I run again and found few errors.

Error using readtextfile (line 15)

could not open file

Error in AppToMSBS (line 9)

Main = readtextfile(MSPath);

Error in ApOPs (line 92)

AppToMSBS(MSPath,BSPath,StreetsPath,PTablePath,ToesPath,MaxAvoid,SavePath);

How can i rectify them, pls suggest

[Image Analyst]

Again, the function readtextfile() is not on the search path. Find it and add it to the path.

[Walter Roberson]

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'),

Answer 2

[Rahul]

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']);

Answer 3

[Rahul]

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.