peptide - npm Package Compare versions

Comparing version 1.1.0 to 1.2.0

src/digestSequence.js

+'use strict';
+
+var splitSequence=require('./splitSequence');
+
+function digestSequence(sequence, options) {
+    var options=options || {};
+
+    sequence=sequence.replace(/^H([^a-z])/,'$1').replace(/OH$/,'');
+
+    options.enzyme = options.enzyme || 'trypsin';
+    if (options.minMissed===undefined) options.minMissed=0;
+    if (options.maxMissed===undefined) options.maxMissed=0;
+    if (options.minResidue===undefined) options.minResidue=0;
+    if (options.maxResidue===undefined) options.maxResidue=Number.MAX_VALUE;
+    var regexp=getRegexp(options.enzyme);
+    var fragments=sequence.replace(regexp,"$1 ").split(/ /);
+    if (!fragments[fragments.length]) fragments=fragments.slice(0, fragments.length-1);
+
+    for (var i=0; i<fragments.length; i++) {
+        fragments[i]={
+            sequence:fragments[i],
+            nbResidue:splitSequence(fragments[i]).length
+        }
+    }
+
+    var results=[];
+
+    for (var i=0; i<fragments.length-options.minMissed; i++) {
+        for (var j=options.minMissed; j<=Math.min(options.maxMissed,fragments.length-i-1); j++) {
+            var fragment='';
+            var nbResidue=0;
+            for (var k=i; k<=(i+j); k++) {
+                fragment+=fragments[k].sequence;
+                nbResidue+=fragments[k].nbResidue
+            }
+            if (fragment && nbResidue>=options.minResidue && nbResidue<=options.maxResidue) {
+                results.push("H"+fragment+"OH");
+            }
+        }
+    }
+
+    return results;
+}
+
+
+function getRegexp(enzyme) {
+    switch (enzyme.toLowerCase().replace(/[^a-z0-9]/g,'')) {
+        case 'chymotrypsin':
+            return /(Phe|Tyr|Trp)(?!Pro)/g;
+        case 'trypsin':
+            return /(Lys|Arg)(?!Pro)/g;
+        case 'lysc':
+            return /(Lys)(?!Pro)/g;
+        case 'glucph4':
+            return /(Glu)(?!Pro|Glu)/g;
+        case 'glucph8':
+            return /(Asp|Glu)(?!Pro|Glu)/g;
+        case 'thermolysin':
+            return /(Leu|Ile|Met|Phe|Trp)/g;
+        case 'cyanogenbromide':
+            return /(Met)/g;
+    }
+    throw new Error('Digestion enzyme: '+enzyme+' is unknown');
+}
+
+module.exports = digestSequence;
+

src/splitSequence.js

+'use strict';
+
+function splitSequence(sequence) {
+    var aas=sequence.replace(/([A-Z])/g," $1").split(/ /);
+    var begin=0;
+    while (aas[begin]==='' || aas[begin]==='H') {
+        begin++;
+    }
+    var end=aas.length-1;
+    while (aas[end]==='O' || aas[end]==='H') {
+        end--;
+    }
+    aas=aas.slice(begin,end+1);
+    return aas;
+}
+
+
+module.exports = splitSequence;
+

bower.json

 {
   "name": "peptide",
-  "version": "1.1.0",
+  "version": "1.2.0",
   "description": "Peptide",
@@ -5,0 +5,0 @@ "keywords": [

package.json

 {
   "name": "peptide",
-  "version": "1.1.0",
+  "version": "1.2.0",
   "description": "Peptide",
@@ -5,0 +5,0 @@ "keywords": [

README.md

@@ -49,3 +49,4 @@ # peptide
 
-You can also specify internal fragments using the options 'ya' and 'yb' as well as the maximal length for internal fragments 'maxInternal'
+You can also specify internal fragments using the options 'ya' and 'yb' as well as the minimal length of internal fragments 'minInternal'
+and the maximal length of internal fragments 'maxInternal'
 
@@ -67,2 +68,31 @@ ## Isoelectric Point
 
+#### splitSequence(sequence)
+
+Split a 3 letter code sequence respecting uppercase, lowercase in an array of residu.
+
+__Arguments__
+
+* `sequence` - string with the amino acids sequence
+
+#### digestSequence(sequence, options)
+
+Allows to digest virtually a sequence
+
+__Arguments__
+
+* `sequence` - string with the amino acids sequence
+* `options`
+  * `minMissed` - minimal missed cleavage (default: 0)
+  * `maxMissed` - maximal missed cleavage (default: 0)
+  * `minResidue` - minimal number of residues (default: 0)
+  * `maxResidue` - maximal number of residues (default: infinity)
+  * `enzyme` - enzyme used for digestion
+    * chymotrypsin : (Phe|Tyr|Trp)(?!Pro)
+    * trypsin : (Lys|Arg)(?!Pro)
+    * lysc : (Lys)(?!Pro)
+    * glucph4 : (Glu)(?!Pro|Glu)
+    * glucph8 : (Asp|Glu)(?!Pro|Glu)
+    * thermolysin : (Leu|Ile|Met|Phe|Trp)
+    * cyanogenbromide : (Met)
+
 #### calculateIEP(sequence)
@@ -69,0 +99,0 @@

src/index.js

@@ -6,2 +6,4 @@ 'use strict';
 var chargePeptide = require('./chargePeptide');
+var splitSequence = require('./splitSequence');
+var digestSequence = require('./digestSequence');
 
@@ -14,5 +16,7 @@ exports.getInfo = function () {
 
+exports.splitSequence=splitSequence;
+exports.digestSequence=digestSequence;
+
 exports.calculateIEP = function (sequence) {
-    var aas=sequence.replace(/([A-Z])/g," $1").split(/ /);
-    aas=aas.slice(2,aas.length-2);
+    var aas=splitSequence(sequence);
     var result=IEP.calculateIEP(aas);
@@ -23,4 +27,3 @@ return result;
 exports.calculateIEPChart = function (sequence) {
-    var aas=sequence.replace(/([A-Z])/g," $1").split(/ /);
-    aas=aas.slice(2,aas.length-2);
+    var aas=splitSequence(sequence);
     var result=IEP.calculateChart(aas);
@@ -36,4 +39,3 @@ return result;
 exports.calculateCharge = function (sequence, ph) {
-    var aas=sequence.replace(/([A-Z])/g," $1").split(/ /);
-    aas=aas.slice(2,aas.length-2);
+    var aas=splitSequence(sequence);
     return IEP.calculateCharge(aas, ph);
@@ -57,2 +59,3 @@ }
     options.maxInternal = options.maxInternal || Number.MAX_VALUE;
+    options.minInternal = options.minInternal || 0;
 
@@ -75,6 +78,8 @@ var mfs = [];
                 var iTerm='';
-                for (var k=i; k<j; k++) {
-                    iTerm+=mfparts[k];
+                if ((j-i)>=options.minInternal){
+                    for (var k = i; k < j; k++) {
+                        iTerm += mfparts[k];
+                    }
+                    addITerm(mfs, iTerm, mfparts.length - i, j, options);
                 }
-                addITerm(mfs, iTerm, mfparts.length-i, j, options);
             }
@@ -81,0 +86,0 @@ }

No alert changes

Improved metrics

Total package byte prevSize

24087

17.47%

Number of package files

16

14.29%

Lines of code

666

12.5%

Number of lines in readme file

137

28.04%

No dependency changes