Fasta_Header_Rename

A simple matlab code to rename the headers in fasta file. Self-explanatory variable names.

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%Author = Arun Prasanna
%Rename the headers in fasta file to desired choice
%For example: The input fasta file used here had header in >num_name format
%strtok is used to strip and extract the required format
clear; clc;
tic;
Path = 'Drive\Path\ToReadFile';%
FileList = dir(Path);
[rFL, cFL] = size(FileList); 
for i = 3:rFL %i of 1 & 2 are . & .. respectively
    Fas_Fname{i-2,1} = FileList(i).name; %FileList is a structure
end
[rFas,cFas] = size(Fas_Fname);

for i = 1:rFas
    clear Header Seq ProtID Sp new_Header
    OpenFile = cell2mat(strcat(Path,Fas_Fname(i)));
    [Header, Seq] = fastaread(OpenFile);[rH,cH] = size(Header);
    for j = 1:cH
        [ProtID, Sp] = strtok(Header(1,j),'_'); %First Sp = _name
        [Sp, rm] = strtok(Sp,'_'); %Second SP = name ! which we need
        new_Header(1,j) = Sp;
    end
    New_Path = 'Drive\Path\ToStore';
    outFname = cell2mat(strcat(New_Path,Fas_Fname(i)));
    fastawrite(outFname, new_Header,Seq);
    fprintf('Finished %d\t of ', i);
    fprintf('%d\n',rFas);
end
toc;
 

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