Looking for alternative of extractBetween function

close all

clear all

clc

name = 'Covid_strains';

file = strcat(name,'.fasta');

sequences = fastaread(file);

The code extract the sequences from the fasta file "Covid_strains". The file contains multiple sequences. The fastaread function create a structure containing Header and Sequences. Now I want to extract the some part of the header and store it in a table. The table will be the response variable for the predictor. I wanted to use extractbetween function for this. But since I am using older version of MATLAB, the function is not available to me. Please help.

[Rik]

You didn't enter your release when you posted your question, which makes it harder to help you.

I suspect the best choice would be to use regexp. With a regular expression you can capture the tokens.

[SUBHAJIT KAR]

I am using version 2016a. How can I extract 'B.1.2' from the the expression 'OK584715.1 |B.1.2' , using regexp ?

Answer 1

[Rik]

You need to come up with a regular expression that will exactly match what you want to extract. Below is my guess for what you want.

RE=['\|',... match a literal |
    '(.*)',... capture any character in a token
    '($|\n)'];% end of matched substring should be a newline or the end of the string
txt='OK584715.1 |B.1.2';
x=regexp(txt,RE,'tokens');x{1}

ans = 1×2 cell array
    {'B.1.2'}    {0×0 char}

[SUBHAJIT KAR]

Thanks a lot. But the command creating cell arrays under a cell array.

close all

clear all

clc

name = 'Covid_strains'

file = strcat(name,'.fasta')

seqs = fastaread(file)

T = {seqs.Header}'

T1 = cell2table(T,'VariableNames',{'Label'})

RE = ['\|','(.*)','($|\n)'];

x =regexp(T1.Label,RE,'tokens')

How can I get the output as a string insted of cell array?

[Steven Lord]

How can I get the output as a string insted[sic] of cell array?

With release R2016a? You don't.

According to the documentation page the string function was introduced in release R2016b.

[Rik]

Why did you remove all the semicolons as well as all documentation for the regular expression? And why are you closing all figures?

[SUBHAJIT KAR]

I actually forget to add those semicolons.