mergeDlkcatAndFuzzyKcats
Merges the results from DLKcat and fuzzy matching to BRENDA database.
Order of preference:
1: BRENDA match with correct E.C. number, with origin (see below) not
lower than the specified topOriginLimit
2: DLKcat match
3: BRENDA match with correct E.C. number, with origin below
topOriginLimit but not lower than the bottomOriginLimit
4: BRENDA match with wildcards in the E.C. number, with not more
wildcards than wildcardLimit, and origin not lower than the
bottomOriginLimit
Input:
kcatListDLKcat kcatList derived from readDLKcatOutput
kcatListFuzzy kcatList derived from fuzzyKcatMatching
topOriginLimit origin limit for prioritized BRENDA matches. Origin
is explained in more detail below. (Optional,
default 6)
bottomOriginLimit origin limit for low priority BRENDA matches.
Origin is explained in more detail below.
(Optional, default 6)
wildcardLimit maximum number of wildcards in E.C. number of
BRENDA matches (Optional, default 3)
Output:
mergedKcatList merged list of kcats
The origin parameter:
1: correct organism, correct substrate, kcat
2: any organism, correct substrate, kcat
3: correct organism, any substrate, kcat
4: any organism, any substrate, kcat
5: correct organism, specific activity
6: any organism, specific activity
Example of wildcards in E.C. number:
0: 1.1.1.3 glycerol-3-phosphate dehydrogenase (NAD+)
1: 1.1.1.- oxidoreductase, acting on the CH-OH group of donors,
with NAD+ or NADP+ as acceptor
2: 1.1.-.- oxidoreductase, acting on the CH-OH group of donors
3: 1.-.-.- oxidoreductase
Usage:
mergedKcatList = mergeDLKcatAndFuzzyKcats(kcatListDLKcat, kcatListFuzzy, topOriginLimit, bottomOriginLimit, wildcardLimit)0001 function mergedKcatList = mergeDLKcatAndFuzzyKcats(kcatListDLKcat, kcatListFuzzy, topOriginLimit, bottomOriginLimit, wildcardLimit) 0002 % mergeDlkcatAndFuzzyKcats 0003 % Merges the results from DLKcat and fuzzy matching to BRENDA database. 0004 % Order of preference: 0005 % 1: BRENDA match with correct E.C. number, with origin (see below) not 0006 % lower than the specified topOriginLimit 0007 % 2: DLKcat match 0008 % 3: BRENDA match with correct E.C. number, with origin below 0009 % topOriginLimit but not lower than the bottomOriginLimit 0010 % 4: BRENDA match with wildcards in the E.C. number, with not more 0011 % wildcards than wildcardLimit, and origin not lower than the 0012 % bottomOriginLimit 0013 % 0014 % Input: 0015 % kcatListDLKcat kcatList derived from readDLKcatOutput 0016 % kcatListFuzzy kcatList derived from fuzzyKcatMatching 0017 % topOriginLimit origin limit for prioritized BRENDA matches. Origin 0018 % is explained in more detail below. (Optional, 0019 % default 6) 0020 % bottomOriginLimit origin limit for low priority BRENDA matches. 0021 % Origin is explained in more detail below. 0022 % (Optional, default 6) 0023 % wildcardLimit maximum number of wildcards in E.C. number of 0024 % BRENDA matches (Optional, default 3) 0025 % 0026 % Output: 0027 % mergedKcatList merged list of kcats 0028 % 0029 % The origin parameter: 0030 % 1: correct organism, correct substrate, kcat 0031 % 2: any organism, correct substrate, kcat 0032 % 3: correct organism, any substrate, kcat 0033 % 4: any organism, any substrate, kcat 0034 % 5: correct organism, specific activity 0035 % 6: any organism, specific activity 0036 % 0037 % Example of wildcards in E.C. number: 0038 % 0: 1.1.1.3 glycerol-3-phosphate dehydrogenase (NAD+) 0039 % 1: 1.1.1.- oxidoreductase, acting on the CH-OH group of donors, 0040 % with NAD+ or NADP+ as acceptor 0041 % 2: 1.1.-.- oxidoreductase, acting on the CH-OH group of donors 0042 % 3: 1.-.-.- oxidoreductase 0043 % 0044 % Usage: 0045 % mergedKcatList = mergeDLKcatAndFuzzyKcats(kcatListDLKcat, kcatListFuzzy, topOriginLimit, bottomOriginLimit, wildcardLimit) 0046 0047 if nargin < 5 0048 wildcardLimit = 3; 0049 end 0050 0051 if nargin < 4 0052 bottomOriginLimit = 6; 0053 end 0054 0055 if nargin < 3 0056 topOriginLimit = 6; 0057 end 0058 0059 if (topOriginLimit < 1) || (topOriginLimit > 6) 0060 error('topPrioOriginLimit should be between 1 and 6.'); 0061 end 0062 0063 if (bottomOriginLimit < 1) || (bottomOriginLimit > 6) 0064 error('originCutLevel should be between 1 and 6.'); 0065 end 0066 0067 if (wildcardLimit < 0) || (wildcardLimit > 3) 0068 error('wildcardCutLevel should be between 0 and 3.'); 0069 end 0070 0071 wc = kcatListFuzzy.wildcardLvl; 0072 wc(isnan(wc)) = 1000; %large wildcard 0073 0074 origin = kcatListFuzzy.origin; 0075 origin(isnan(origin)) = 1000; %large origin 0076 0077 prio1 = (wc == 0) & (origin <= topOriginLimit); 0078 0079 rxnsWithPrio1 = unique(kcatListFuzzy.rxns(prio1)); 0080 0081 %Things get a bit complicated since not all reactions are in the kcatLists and 0082 %some reactions may appear multiple times 0083 prio2 = true(length(kcatListDLKcat.rxns),1); 0084 prio2(ismember(kcatListDLKcat.rxns, rxnsWithPrio1)) = false; 0085 prio2Rxns = unique(kcatListDLKcat.rxns(prio2)); 0086 0087 %The prioritization between wildcards and origin is already done in fuzzy matching, 0088 %so we can join them here 0089 prio3 = ((wc == 0) & (origin > topOriginLimit) & (origin <= bottomOriginLimit)) | ... 0090 ((wc > 0) & (wc <= wildcardLimit) & (origin <= bottomOriginLimit)); 0091 prio3(ismember(kcatListFuzzy.rxns, prio2Rxns)) = false; 0092 0093 fuzzyRxns = prio1 | prio3; 0094 0095 %Now build the merged list, fuzzy followed by dlkcat 0096 %The order of the reactions is therefore not preserved. 0097 mergedKcatList = struct(); 0098 mergedKcatList.source = 'Merged DLKcat and fuzzy'; 0099 [fuzzySrc{1:sum(fuzzyRxns)}] = deal(kcatListFuzzy.source); 0100 [dlkcatSrc{1:sum(prio2)}] = deal(kcatListDLKcat.source); 0101 mergedKcatList.kcatSource = [fuzzySrc.';dlkcatSrc.']; 0102 mergedKcatList.rxns = [kcatListFuzzy.rxns(fuzzyRxns);kcatListDLKcat.rxns(prio2)]; 0103 mergedKcatList.genes = [cell(sum(fuzzyRxns),1);kcatListDLKcat.genes(prio2)]; 0104 mergedKcatList.substrates = [kcatListFuzzy.substrates(fuzzyRxns);kcatListDLKcat.substrates(prio2)]; 0105 mergedKcatList.kcats = [kcatListFuzzy.kcats(fuzzyRxns);kcatListDLKcat.kcats(prio2)]; 0106 mergedKcatList.eccodes = [kcatListFuzzy.eccodes(fuzzyRxns);cell(sum(prio2),1)]; 0107 mergedKcatList.wildcardLvl = [kcatListFuzzy.wildcardLvl(fuzzyRxns);nan(sum(prio2),1)]; 0108 mergedKcatList.origin = [kcatListFuzzy.origin(fuzzyRxns);nan(sum(prio2),1)]; 0109 end