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bionode-gff
Advanced tools
bionode-gff - npm Package Compare versions
Comparing version 1.0.0 to 2.0.0
| var fs = require('fs'); | ||
| var readline = require('readline'); | ||
| var stream = require('stream'); | ||
| /** | ||
| * | ||
| * @type {{read: Function}} | ||
| */ | ||
| var GFF3 = { | ||
| /** | ||
| * | ||
| * @param path | ||
| * @param onFeature | ||
| * @param onEnd | ||
| */ | ||
| read: function (path, onFeature, onEnd) { | ||
| var events = require('events'); | ||
| var gff = new events.EventEmitter(); | ||
| gff.read = function (path) { | ||
| var instream = fs.createReadStream(path); | ||
@@ -22,54 +17,47 @@ var outstream = new stream(); | ||
| rl.on('line', function (line) { | ||
| if (line.indexOf('#') != 0) { | ||
| //its not a comment, ill process it | ||
| if (line.indexOf('#') != 0) { | ||
| //its not a comment, ill process it | ||
| var parts = line.split('\t'); | ||
| var parts = line.split('\t'); | ||
| if (parts.length !== 9) { | ||
| //the file might use spaces instead of tabs | ||
| //ill try to split it by spaces | ||
| parts = line.trim().split(/\s+/); | ||
| } | ||
| if (parts.length !== 9) { | ||
| //the file might use spaces instead of tabs | ||
| //ill try to split it by spaces | ||
| parts = line.trim().split(/\s+/); | ||
| } | ||
| if (parts.length == 9) { | ||
| var attParts = parts[8].split(';'); | ||
| var arrayObject = {}; | ||
| for (var i = 0; i < attParts.length; ++i) { | ||
| var pair = attParts[i].split("="); | ||
| arrayObject[pair[0]] = pair[1]; | ||
| } | ||
| if (parts.length == 9) { | ||
| var attParts = parts[8].split(';'); | ||
| var arrayObject = {}; | ||
| for (var i = 0; i < attParts.length; ++i) { | ||
| var pair = attParts[i].split("="); | ||
| arrayObject[pair[0]] = pair[1]; | ||
| } | ||
| var feature = { | ||
| seqid: parts[0], | ||
| source: parts[1], | ||
| type: parts[2], | ||
| start: parts[3], | ||
| end: parts[4], | ||
| score: parts[5], | ||
| strand: parts[6], | ||
| phase: parts[7], | ||
| attributes: arrayObject | ||
| }; | ||
| onFeature(feature); | ||
| } else { | ||
| console.log(parts); | ||
| error(new Error('9 parts of feature not found')); | ||
| var feature = { | ||
| seqid: parts[0], | ||
| source: parts[1], | ||
| type: parts[2], | ||
| start: parts[3], | ||
| end: parts[4], | ||
| score: parts[5], | ||
| strand: parts[6], | ||
| phase: parts[7], | ||
| attributes: arrayObject | ||
| }; | ||
| gff.emit('data', feature); | ||
| } else { | ||
| var err = new Error('9 parts of feature not found'); | ||
| gff.emit('error', err); | ||
| } | ||
| } | ||
| } | ||
| }); | ||
| rl.on('close', function () { | ||
| onEnd(); | ||
| gff.emit('end'); | ||
| }); | ||
| } | ||
| return this; | ||
| }; | ||
| /** | ||
| * | ||
| * @param err | ||
| */ | ||
| function error(err) { | ||
| console.error(err); | ||
| throw err; | ||
| } | ||
| module.exports = GFF3; | ||
| module.exports = gff; |
| { | ||
| "name": "bionode-gff", | ||
| "version": "1.0.0", | ||
| "version": "2.0.0", | ||
| "description": "gff parser for nodejs", | ||
@@ -5,0 +5,0 @@ "main": "index.js", |
@@ -11,2 +11,5 @@ <p align="center"> | ||
| [](https://nodei.co/npm/bionode-gff/) | ||
| [](https://travis-ci.org/bionode/bionode-gff) | ||
@@ -30,3 +33,3 @@ | ||
| var ncbi = require('bionode-gff') | ||
| GFF.read(filePath, onFeature, done); | ||
| GFF.read(filePath).on('data',onFeatures).on('end', done); | ||
@@ -33,0 +36,0 @@ function onFeature(feature){ |
559
test/test.js
@@ -10,238 +10,32 @@ var GFF = require('../index'); | ||
| describe('GFF', function () { | ||
| describe('.read', function () { | ||
| it('should read without error', function (done) { | ||
| describe('.read', function () { | ||
| it('should read without error', function (done) { | ||
| function onFeature(seq) { | ||
| allFeatures.push(seq); | ||
| //console.log(seq.seqid); | ||
| //console.log(seq.source); | ||
| //console.log(seq.type); | ||
| //console.log(seq.start); | ||
| //console.log(seq.end); | ||
| //console.log(seq.score || '.'); | ||
| //console.log(seq.strand || '?'); | ||
| //console.log(seq.phase || '.'); | ||
| //console.log(seq.attributes); | ||
| } | ||
| function onFeature(seq) { | ||
| allFeatures.push(seq); | ||
| //console.log(seq.seqid); | ||
| //console.log(seq.source); | ||
| //console.log(seq.type); | ||
| //console.log(seq.start); | ||
| //console.log(seq.end); | ||
| //console.log(seq.score || '.'); | ||
| //console.log(seq.strand || '?'); | ||
| //console.log(seq.phase || '.'); | ||
| //console.log(seq.attributes); | ||
| } | ||
| GFF.read(filePath, onFeature, done); | ||
| }); | ||
| it('should look like a valid output', function () { | ||
| assert.notStrictEqual(allFeatures, validOutput); | ||
| GFF.read(filePath).on('data', onFeature).on('end', done); | ||
| //GFF.read(filePath, onFeature, done); | ||
| }); | ||
| it('should look like a valid output', function () { | ||
| assert.notStrictEqual(allFeatures, validOutput); | ||
| }) | ||
| }) | ||
| }) | ||
| }); | ||
| var validOutput = [{ | ||
| seqid: 'human15.1', | ||
| source: '.', | ||
| type: 'gene', | ||
| start: '214301', | ||
| end: '215772', | ||
| score: '.', | ||
| strand: '+', | ||
| phase: '.', | ||
| attributes: {ID: 'HsG8283'} | ||
| }, | ||
| { | ||
| seqid: 'human15.1', | ||
| source: '.', | ||
| type: 'mRNA', | ||
| start: '214360', | ||
| end: '215771', | ||
| score: '.', | ||
| strand: '+', | ||
| phase: '.', | ||
| attributes: { | ||
| Comments: 'fixed+one+splice+junction', | ||
| Parent: 'HsG8283', | ||
| Evidence: '7000000069743825', | ||
| Transcript_type: 'Novel_Transcript', | ||
| Name: 'Novel+Transcript%2C+variant+%28partial%29', | ||
| ID: 'HsT20206' | ||
| } | ||
| }, | ||
| { | ||
| seqid: 'human15.1', | ||
| source: '.', | ||
| type: 'CDS', | ||
| start: '214360', | ||
| end: '214441', | ||
| score: '.', | ||
| strand: '+', | ||
| phase: '.', | ||
| attributes: {Parent: 'HsT20206'} | ||
| }, | ||
| { | ||
| seqid: 'human15.1', | ||
| source: '.', | ||
| type: 'CDS', | ||
| start: '215299', | ||
| end: '215444', | ||
| score: '.', | ||
| strand: '+', | ||
| phase: '.', | ||
| attributes: {Parent: 'HsT20206'} | ||
| }, | ||
| { | ||
| seqid: 'human15.1', | ||
| source: '.', | ||
| type: 'CDS', | ||
| start: '215641', | ||
| end: '215766', | ||
| score: '.', | ||
| strand: '+', | ||
| phase: '.', | ||
| attributes: {Parent: 'HsT20206'} | ||
| }, | ||
| { | ||
| seqid: 'human15.1', | ||
| source: '.', | ||
| type: 'three_prime_UT', | ||
| start: '215767', | ||
| end: '215771', | ||
| score: '.', | ||
| strand: '+', | ||
| phase: '.', | ||
| attributes: {Parent: 'HsT20206'} | ||
| }, | ||
| { | ||
| seqid: 'human15.1', | ||
| source: '.', | ||
| type: 'mRNA', | ||
| start: '214590', | ||
| end: '215772', | ||
| score: '.', | ||
| strand: '+', | ||
| phase: '.', | ||
| attributes: { | ||
| Comments: 'fixed+one+splice+site%0A', | ||
| Parent: 'HsG8283', | ||
| Evidence: '7000000069600840', | ||
| Transcript_type: 'Novel_Transcript', | ||
| Name: 'Novel+Transcript%2C+variant+%28partial%29', | ||
| ID: 'HsT20207' | ||
| } | ||
| }, | ||
| { | ||
| seqid: 'human15.1', | ||
| source: '.', | ||
| type: 'five_prime_UTR', | ||
| start: '214590', | ||
| end: '214590', | ||
| score: '.', | ||
| strand: '+', | ||
| phase: '.', | ||
| attributes: {Parent: 'HsT20207'} | ||
| }, | ||
| { | ||
| seqid: 'human15.1', | ||
| source: '.', | ||
| type: 'CDS', | ||
| start: '214591', | ||
| end: '214660', | ||
| score: '.', | ||
| strand: '+', | ||
| phase: '.', | ||
| attributes: {Parent: 'HsT20207'} | ||
| }, | ||
| { | ||
| seqid: 'human15.1', | ||
| source: '.', | ||
| type: 'CDS', | ||
| start: '215299', | ||
| end: '215444', | ||
| score: '.', | ||
| strand: '+', | ||
| phase: '.', | ||
| attributes: {Parent: 'HsT20207'} | ||
| }, | ||
| { | ||
| seqid: 'human15.1', | ||
| source: '.', | ||
| type: 'CDS', | ||
| start: '215641', | ||
| end: '215769', | ||
| score: '.', | ||
| strand: '+', | ||
| phase: '.', | ||
| attributes: {Parent: 'HsT20207'} | ||
| }, | ||
| { | ||
| seqid: 'human15.1', | ||
| source: '.', | ||
| type: 'three_prime_UT', | ||
| start: '215770', | ||
| end: '215772', | ||
| score: '.', | ||
| strand: '+', | ||
| phase: '.', | ||
| attributes: {Parent: 'HsT20207'} | ||
| }, | ||
| { | ||
| seqid: 'human15.1', | ||
| source: '.', | ||
| type: 'mRNA', | ||
| type: 'gene', | ||
| start: '214301', | ||
| end: '215769', | ||
| score: '.', | ||
| strand: '+', | ||
| phase: '.', | ||
| attributes: { | ||
| Parent: 'HsG8283', | ||
| Evidence: '7000000069974357', | ||
| Transcript_type: 'Candidates+for+Deletion', | ||
| Name: 'Novel+Transcript+%28partial%29', | ||
| ID: 'HsT16028' | ||
| } | ||
| }, | ||
| { | ||
| seqid: 'human15.1', | ||
| source: '.', | ||
| type: 'five_prime_UTR', | ||
| start: '214301', | ||
| end: '214302', | ||
| score: '.', | ||
| strand: '+', | ||
| phase: '.', | ||
| attributes: {Parent: 'HsT16028'} | ||
| }, | ||
| { | ||
| seqid: 'human15.1', | ||
| source: '.', | ||
| type: 'CDS', | ||
| start: '214303', | ||
| end: '214460', | ||
| score: '.', | ||
| strand: '+', | ||
| phase: '.', | ||
| attributes: {Parent: 'HsT16028'} | ||
| }, | ||
| { | ||
| seqid: 'human15.1', | ||
| source: '.', | ||
| type: 'CDS', | ||
| start: '215299', | ||
| end: '215467', | ||
| score: '.', | ||
| strand: '+', | ||
| phase: '.', | ||
| attributes: {Parent: 'HsT16028'} | ||
| }, | ||
| { | ||
| seqid: 'human15.1', | ||
| source: '.', | ||
| type: 'three_prime_UT', | ||
| start: '215468', | ||
| end: '215769', | ||
| score: '.', | ||
| strand: '+', | ||
| phase: '.', | ||
| attributes: {Parent: 'HsT16028'} | ||
| }, | ||
| { | ||
| seqid: 'human15.1', | ||
| source: '.', | ||
| type: 'mRNA', | ||
| start: '215218', | ||
| end: '215772', | ||
@@ -251,56 +45,263 @@ score: '.', | ||
| phase: '.', | ||
| attributes: { | ||
| Parent: 'HsG8283', | ||
| Evidence: '7000000069512231', | ||
| Transcript_type: 'Novel_Transcript', | ||
| Name: 'Novel+Transcript%2C+variant', | ||
| ID: 'HsT16029' | ||
| } | ||
| }, | ||
| { | ||
| seqid: 'human15.1', | ||
| source: '.', | ||
| type: 'five_prime_UTR', | ||
| start: '215218', | ||
| end: '215233', | ||
| score: '.', | ||
| strand: '+', | ||
| phase: '.', | ||
| attributes: {Parent: 'HsT16029'} | ||
| }, | ||
| { | ||
| seqid: 'human15.1', | ||
| source: '.', | ||
| type: 'CDS', | ||
| start: '215234', | ||
| end: '215444', | ||
| score: '.', | ||
| strand: '+', | ||
| phase: '.', | ||
| attributes: {Parent: 'HsT16029'} | ||
| }, | ||
| { | ||
| seqid: 'human15.1', | ||
| source: '.', | ||
| type: 'CDS', | ||
| start: '215641', | ||
| end: '215735', | ||
| score: '.', | ||
| strand: '+', | ||
| phase: '.', | ||
| attributes: {Parent: 'HsT16029'} | ||
| }, | ||
| { | ||
| seqid: 'human15.1', | ||
| source: '.', | ||
| type: 'three_prime_UT', | ||
| start: '215736', | ||
| end: '215772', | ||
| score: '.', | ||
| strand: '+', | ||
| phase: '.', | ||
| attributes: {Parent: 'HsT16029'} | ||
| }]; | ||
| attributes: {ID: 'HsG8283'} | ||
| }, | ||
| { | ||
| seqid: 'human15.1', | ||
| source: '.', | ||
| type: 'mRNA', | ||
| start: '214360', | ||
| end: '215771', | ||
| score: '.', | ||
| strand: '+', | ||
| phase: '.', | ||
| attributes: { | ||
| Comments: 'fixed+one+splice+junction', | ||
| Parent: 'HsG8283', | ||
| Evidence: '7000000069743825', | ||
| Transcript_type: 'Novel_Transcript', | ||
| Name: 'Novel+Transcript%2C+variant+%28partial%29', | ||
| ID: 'HsT20206' | ||
| } | ||
| }, | ||
| { | ||
| seqid: 'human15.1', | ||
| source: '.', | ||
| type: 'CDS', | ||
| start: '214360', | ||
| end: '214441', | ||
| score: '.', | ||
| strand: '+', | ||
| phase: '.', | ||
| attributes: {Parent: 'HsT20206'} | ||
| }, | ||
| { | ||
| seqid: 'human15.1', | ||
| source: '.', | ||
| type: 'CDS', | ||
| start: '215299', | ||
| end: '215444', | ||
| score: '.', | ||
| strand: '+', | ||
| phase: '.', | ||
| attributes: {Parent: 'HsT20206'} | ||
| }, | ||
| { | ||
| seqid: 'human15.1', | ||
| source: '.', | ||
| type: 'CDS', | ||
| start: '215641', | ||
| end: '215766', | ||
| score: '.', | ||
| strand: '+', | ||
| phase: '.', | ||
| attributes: {Parent: 'HsT20206'} | ||
| }, | ||
| { | ||
| seqid: 'human15.1', | ||
| source: '.', | ||
| type: 'three_prime_UT', | ||
| start: '215767', | ||
| end: '215771', | ||
| score: '.', | ||
| strand: '+', | ||
| phase: '.', | ||
| attributes: {Parent: 'HsT20206'} | ||
| }, | ||
| { | ||
| seqid: 'human15.1', | ||
| source: '.', | ||
| type: 'mRNA', | ||
| start: '214590', | ||
| end: '215772', | ||
| score: '.', | ||
| strand: '+', | ||
| phase: '.', | ||
| attributes: { | ||
| Comments: 'fixed+one+splice+site%0A', | ||
| Parent: 'HsG8283', | ||
| Evidence: '7000000069600840', | ||
| Transcript_type: 'Novel_Transcript', | ||
| Name: 'Novel+Transcript%2C+variant+%28partial%29', | ||
| ID: 'HsT20207' | ||
| } | ||
| }, | ||
| { | ||
| seqid: 'human15.1', | ||
| source: '.', | ||
| type: 'five_prime_UTR', | ||
| start: '214590', | ||
| end: '214590', | ||
| score: '.', | ||
| strand: '+', | ||
| phase: '.', | ||
| attributes: {Parent: 'HsT20207'} | ||
| }, | ||
| { | ||
| seqid: 'human15.1', | ||
| source: '.', | ||
| type: 'CDS', | ||
| start: '214591', | ||
| end: '214660', | ||
| score: '.', | ||
| strand: '+', | ||
| phase: '.', | ||
| attributes: {Parent: 'HsT20207'} | ||
| }, | ||
| { | ||
| seqid: 'human15.1', | ||
| source: '.', | ||
| type: 'CDS', | ||
| start: '215299', | ||
| end: '215444', | ||
| score: '.', | ||
| strand: '+', | ||
| phase: '.', | ||
| attributes: {Parent: 'HsT20207'} | ||
| }, | ||
| { | ||
| seqid: 'human15.1', | ||
| source: '.', | ||
| type: 'CDS', | ||
| start: '215641', | ||
| end: '215769', | ||
| score: '.', | ||
| strand: '+', | ||
| phase: '.', | ||
| attributes: {Parent: 'HsT20207'} | ||
| }, | ||
| { | ||
| seqid: 'human15.1', | ||
| source: '.', | ||
| type: 'three_prime_UT', | ||
| start: '215770', | ||
| end: '215772', | ||
| score: '.', | ||
| strand: '+', | ||
| phase: '.', | ||
| attributes: {Parent: 'HsT20207'} | ||
| }, | ||
| { | ||
| seqid: 'human15.1', | ||
| source: '.', | ||
| type: 'mRNA', | ||
| start: '214301', | ||
| end: '215769', | ||
| score: '.', | ||
| strand: '+', | ||
| phase: '.', | ||
| attributes: { | ||
| Parent: 'HsG8283', | ||
| Evidence: '7000000069974357', | ||
| Transcript_type: 'Candidates+for+Deletion', | ||
| Name: 'Novel+Transcript+%28partial%29', | ||
| ID: 'HsT16028' | ||
| } | ||
| }, | ||
| { | ||
| seqid: 'human15.1', | ||
| source: '.', | ||
| type: 'five_prime_UTR', | ||
| start: '214301', | ||
| end: '214302', | ||
| score: '.', | ||
| strand: '+', | ||
| phase: '.', | ||
| attributes: {Parent: 'HsT16028'} | ||
| }, | ||
| { | ||
| seqid: 'human15.1', | ||
| source: '.', | ||
| type: 'CDS', | ||
| start: '214303', | ||
| end: '214460', | ||
| score: '.', | ||
| strand: '+', | ||
| phase: '.', | ||
| attributes: {Parent: 'HsT16028'} | ||
| }, | ||
| { | ||
| seqid: 'human15.1', | ||
| source: '.', | ||
| type: 'CDS', | ||
| start: '215299', | ||
| end: '215467', | ||
| score: '.', | ||
| strand: '+', | ||
| phase: '.', | ||
| attributes: {Parent: 'HsT16028'} | ||
| }, | ||
| { | ||
| seqid: 'human15.1', | ||
| source: '.', | ||
| type: 'three_prime_UT', | ||
| start: '215468', | ||
| end: '215769', | ||
| score: '.', | ||
| strand: '+', | ||
| phase: '.', | ||
| attributes: {Parent: 'HsT16028'} | ||
| }, | ||
| { | ||
| seqid: 'human15.1', | ||
| source: '.', | ||
| type: 'mRNA', | ||
| start: '215218', | ||
| end: '215772', | ||
| score: '.', | ||
| strand: '+', | ||
| phase: '.', | ||
| attributes: { | ||
| Parent: 'HsG8283', | ||
| Evidence: '7000000069512231', | ||
| Transcript_type: 'Novel_Transcript', | ||
| Name: 'Novel+Transcript%2C+variant', | ||
| ID: 'HsT16029' | ||
| } | ||
| }, | ||
| { | ||
| seqid: 'human15.1', | ||
| source: '.', | ||
| type: 'five_prime_UTR', | ||
| start: '215218', | ||
| end: '215233', | ||
| score: '.', | ||
| strand: '+', | ||
| phase: '.', | ||
| attributes: {Parent: 'HsT16029'} | ||
| }, | ||
| { | ||
| seqid: 'human15.1', | ||
| source: '.', | ||
| type: 'CDS', | ||
| start: '215234', | ||
| end: '215444', | ||
| score: '.', | ||
| strand: '+', | ||
| phase: '.', | ||
| attributes: {Parent: 'HsT16029'} | ||
| }, | ||
| { | ||
| seqid: 'human15.1', | ||
| source: '.', | ||
| type: 'CDS', | ||
| start: '215641', | ||
| end: '215735', | ||
| score: '.', | ||
| strand: '+', | ||
| phase: '.', | ||
| attributes: {Parent: 'HsT16029'} | ||
| }, | ||
| { | ||
| seqid: 'human15.1', | ||
| source: '.', | ||
| type: 'three_prime_UT', | ||
| start: '215736', | ||
| end: '215772', | ||
| score: '.', | ||
| strand: '+', | ||
| phase: '.', | ||
| attributes: {Parent: 'HsT16029'} | ||
| }]; | ||
New alerts
License Policy Violation
LicenseThis package is not allowed per your license policy. Review the package's license to ensure compliance.
Found 1 instance in 1 package
Fixed alerts
License Policy Violation
LicenseThis package is not allowed per your license policy. Review the package's license to ensure compliance.
Found 1 instance in 1 package
Improved metrics
- Total package byte prevSize
- increased by12.46%
12897
- Number of lines in readme file
- increased by6.52%
49
Worsened metrics
- Lines of code
- decreased by-4.17%
345
No dependency changes