queryGeneCodex.m

function codexEntry = queryGeneCodex(Query,queryField,codexPath)
% codexEntry = queryGeneCodex(Query,queryField,codexPath)
% Searches the local geneCodex to see if data for a Query is
% available and returns [] if Query is not in codex otherwise returns the
% codex entry for the desired gene or genes, row 1 is the column headings and
% row 2+ is the codex information. Accepts a string or number search Query.
% * can be used to search partials (i.e. '*ORF*' will return ORF6 and C12ORF10)
% codexPath is an optional input indicating which codex to search, otherwise it searches the codex in the AtlasGeneDir
% queryField is an optional string input indicating which column of the codex to search for your query. If not included the search will look through Genes and Aliases
% if Query is empty '' this will return the title row of the codex

% geneCodex: [Gene,Aliases,Full_Name,Human_Locus,
%     Human_Entrez_ID,Mouse_Entrez_ID,Section_Dataset_IDs,geneDir,
%     geneCard,date_retreived]

% Load default codex
if ~exist('codexPath','var')
    load('AllenAPI_Paths.mat')
    codexPath = [AtlasGeneDir 'geneCodex.mat'];
end
load(codexPath)
codexEntry = [];

if isempty(Query)
    codexEntry = geneCodex(1,:);
    return;
end

% Search both Genes and Aliases
if ~exist('queryField','var')
    search1 = queryGeneCodex(Query,'Gene');
    search2 = queryGeneCodex(Query,'Aliases');
    if isempty(search1) && isempty(search2)
        return;
    elseif isempty(search1)
        codexEntry = search2;
    elseif isempty(search2)
        codexEntry = search1;
    else
        codexEntry = [search1;search2(2:end,:)];
        % keep unique entries
        [~,b] = unique(codexEntry(2:end,1));
        codexEntry = codexEntry([1;b+1],:);
    end
    return;
end
searchCol = find(strcmp(geneCodex(1,:),queryField));
if isempty(searchCol)
    error('Please search valid field of codex');
end

Query = ['^(' strrep(upper(Query),'*','\w*') ')$'];

if strcmp(queryField,'Aliases')
    search = find(cellfun(@(y) any(~cellfun(@isempty,regexp(strsplit(y,' '),Query))),upper(geneCodex(:,searchCol))));
elseif any(strcmp(queryField,{'Section_Dataset_IDs','Mouse_Entrez_ID','Human_Entrez_ID'}))
    search = find(cellfun(@(x) any(~cellfun(@isempty, regexp(cellstr(num2str(x)),Query))),geneCodex(:,searchCol)));
elseif ischar(geneCodex{2,searchCol})
    search = find(~cellfun(@isempty,regexp(upper(geneCodex(:,searchCol)),Query)));
else
    search = find([geneCodex{:,searchCol}]==Query);
end

if isempty(search)
    return;
elseif ~isrow(search)
    search = search';
end
codexEntry = geneCodex([1 search],:);

search = strcmp(upper(Query),geneCodex(:,1));
search1 = find(search);
if isempty(search1)
    search1 = find(cellfun(@(x) ~isempty(strfind([' ' x ' '],[' ' upper(Query) ' '])),geneCodex(:,2)));
end
if isempty(search1)
    out = -1;
else
    out = [geneCodex(1,:); geneCodex(search1,:)];
end