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getseqoptions.m
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getseqoptions.m
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function [attachment,cleanseq] = getseqoptions(inseq,mode)
% GETSEQOPTIONS: extract options and option values from IUPAC sequence,
% glycan or peptide.
%
% Syntax:
% attachment = getseqoptions(inseq,mode)
%
% Input:
% GLYseq: string, IUPAC condensed glycan/peptide sequence.
% mode: 'g' for glycan or 'p' for peptide.
%
% Output:
% attachment: structure, field names are option names, values are 1 x 2
% cell arrays, 1st element is option value, 2nd is which monosac. it is
% associated with
%
% Note:
% See document of GETGLYDRESSING and DRAWGLYCAN for available options.
% If there are any dashes inside quotation mark pairs, they will be
% recognized as options, therefore ruin the recognition result.
%
% Example:
% attachment = getseqoptions('Aa( -NR "x")Bb[Ff(-adduct "x34" -repeat -R)G]C[Hh(-anomer "xswe" -repeat -adduct "x25")Ii(-repeat)Jj]Dd()Ee')
%
% attachment =
%
% NR: {'"x"' [1]}
% R: {[] [3]}
% adduct: {2x2 cell}
% anomer: {'"xswe"' [6]}
% repeat: {3x2 cell}
%
% Children function:
% N/A
%
% DrawGlycan authors: Kai Cheng, Yusen Zhou, Sriram Neelamegham
%(c) 2019, Research Foundation for State University of New York. All rights reserved
cleanseq = inseq;
switch lower(mode)
case 'g'
[opttype,opttypestart,opttypeend] = regexp(inseq,DrawGlycanPara.regexp_option,'match','start','end');
[optcontent,optcontentstart,optcontentend] = regexp(inseq,DrawGlycanPara.regexp_optionvalue,'match','start','end');
[~,MonoIndex,~,~] = Split(inseq);
opttypemspos = zeros(size(opttypestart));
for i = 1:length(opttypestart)
opttypemspos(i) = find(opttypestart(i) > MonoIndex,1,'last');
end
allopt = [opttypestart,optcontentstart;opttypeend,optcontentend]; % matching options with contents
if ~isempty(allopt)
opttype = strrep(opttype,'-',''); % recognize option names by "-" prefix
alloptstr = [opttype,optcontent];
alloptind = [ones(size(opttypestart)),zeros(1,length(optcontent))];
[~,sortind] = sortrows(allopt',1);
alloptstr = alloptstr(sortind);
alloptind = alloptind(sortind);
whosoptind = find(alloptind);
ind = 1;
alloptgroup = zeros(length(opttype),2);
for i = 1:size(alloptgroup,1)
if whosoptind(i) < numel(alloptind)
if alloptind(whosoptind(i) + 1) == 0
alloptgroup(ind,:) = [whosoptind(i),whosoptind(i) + 1];
else
alloptgroup(ind,:) = [whosoptind(i),whosoptind(i)];
end
else
alloptgroup(ind,:) = [whosoptind(i),whosoptind(i)];
end
ind = ind + 1;
end
if ~isempty(opttype)
glymodinfo = [DrawGlycanPara.intglymodinfo,DrawGlycanPara.extglymodinfo,DrawGlycanPara.intglybondinfo,DrawGlycanPara.glyidentityinfo];
attachitemind = ismember(upper(opttype),glymodinfo);
if any(attachitemind)
extopttype = opttype(attachitemind);
extoptgroup = alloptgroup(attachitemind,:);
extopttypemspos = opttypemspos(attachitemind);
[uniattachtyp,~,attachtypeind] = unique(upper(extopttype));
for i = 1:max(attachtypeind)
optstrind = extoptgroup(attachtypeind == i,:);
attachcont = cell(size(optstrind,1),2);
tempopttypemspos = extopttypemspos(attachtypeind == i);
for j = 1:size(optstrind,1)
if diff(optstrind(j,:)) ~= 0
attachcont{j,1} = alloptstr{optstrind(j,2)};
attachcont{j,1} = attachcont{j,1}(2:end-1);
end
attachcont{j,2} = tempopttypemspos(j);
end
attachment.(upper((uniattachtyp{i}))) = attachcont;
end
else
attachment = [];
end
else
attachment = [];
end
for i = 1:length(optcontentstart)
cleanseq(optcontentstart(i):optcontentend(i)) = blanks(optcontentend(i)-optcontentstart(i)+1);
end
[mslinkagestart,mslinkageend] = regexp(cleanseq,DrawGlycanPara.regexp_monosaclinkage,'start','end'); % based on ()
for i = length(mslinkagestart):-1:1
if mslinkageend(i) - mslinkagestart(i) > 1
templinkageseq = cleanseq(mslinkagestart(i) + 1:mslinkageend(i) - 1);
localopt = allopt(:,allopt(1,:) > mslinkagestart(i) & allopt(2,:) < mslinkageend(i));
localopt = [min(localopt(1,:)),max(localopt(2,:))] - mslinkagestart(i);
if ~isempty(localopt)
templinkageseq(localopt(1):localopt(2)) = '';
end
templinkageseq = strtrim(templinkageseq);
cleanseq = [cleanseq(1:mslinkagestart(i)),templinkageseq,cleanseq(mslinkageend(i):end)];
end
end
else
attachment = [];
end
case 'p'
[optcontentstart,optcontentend,optcontent] = regexp(inseq,DrawGlycanPara.regexp_optionvalue,'start','end','match'); % clear " "
for i = 1:length(optcontentstart)
cleanseq(optcontentstart(i):optcontentend(i)) = blanks(optcontentend(i)-optcontentstart(i)+1);
end
[opttypestart,opttypeend,opttype] = regexp(cleanseq,DrawGlycanPara.regexp_option,'start','end','match');
[alltypestart,alltypeend,alltype] = regexp(cleanseq,DrawGlycanPara.regexp_monosaclinkage,'start','end','match');
for i = 1:length(alltypestart)
cleanseq(alltypestart(i):alltypeend(i)) = blanks(alltypeend(i)-alltypestart(i)+1);
end
[ngmodstart,ngmodend,ngmodtype] = regexp(cleanseq,'<(.*?)>','start','end','match');
for i = 1:length(ngmodstart)
cleanseq(ngmodstart(i):ngmodend(i)) = blanks(ngmodend(i)-ngmodstart(i)+1);
end
[aaIndex,aaend,aa] = regexp(cleanseq,DrawGlycanPara.regexp_AA,'start','end','match');
cleanseq(strfind(cleanseq,' ')) = ''; % here's the clean sequence
opttypemspos = zeros(size(opttypestart));
for i = 1:length(opttypestart)
opttypemspos(i) = find(opttypestart(i) > aaIndex,1,'last');
end
allopt = [opttypestart,optcontentstart;opttypeend,optcontentend]; % matching options with contents
if ~isempty(allopt)
opttype = strrep(opttype,'-','');
alloptstr = [opttype,optcontent];
alloptind = [ones(size(opttypestart)),zeros(1,length(optcontent))];
[~,sortind] = sortrows(allopt',1);
alloptstr = alloptstr(sortind);
alloptind = alloptind(sortind);
whosoptind = find(alloptind);
ind = 1;
alloptgroup = zeros(length(opttype),2);
for i = 1:size(alloptgroup,1)
if whosoptind(i) < numel(alloptind)
if alloptind(whosoptind(i) + 1) == 0
alloptgroup(ind,:) = [whosoptind(i),whosoptind(i) + 1];
else
alloptgroup(ind,:) = [whosoptind(i),whosoptind(i)];
end
else
alloptgroup(ind,:) = [whosoptind(i),whosoptind(i)];
end
ind = ind + 1;
end
if ~isempty(opttype)
attachitemind = ismember(upper(opttype),DrawGlycanPara.aamodinfo);
if any(attachitemind)
extopttype = opttype(attachitemind);
extoptgroup = alloptgroup(attachitemind,:);
extopttypemspos = opttypemspos(attachitemind);
[uniattachtyp,~,attachtypeind] = unique(extopttype);
for i = 1:max(attachtypeind)
optstrind = extoptgroup(attachtypeind == i,:);
attachcont = cell(size(optstrind,1),2);
tempopttypemspos = extopttypemspos(attachtypeind == i);
for j = 1:size(optstrind,1)
if diff(optstrind(j,:)) ~= 0
attachcont{j,1} = alloptstr{optstrind(j,2)};
attachcont{j,1} = attachcont{j,1}(2:end-1);
end
attachcont{j,2} = tempopttypemspos(j);
end
attachment.(uniattachtyp{i}) = attachcont;
end
else
attachment = [];
end
else
attachment = [];
end
else
attachment = [];
end
if ~isempty(ngmodstart)
attachcont = cell(length(ngmodstart),2);
for i = 1:length(ngmodstart)
ngmodmspos = find(ngmodstart(i) > aaIndex,1,'last');
attachcont(i,:) = {ngmodtype{i}(2:end-1),ngmodmspos};
end
attachment.NGMOD = attachcont;
end
end
end