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@gmod/bed - npm Package Compare versions
Comparing version 1.0.4 to 2.0.0
@@ -0,1 +1,14 @@ | ||
| # [2.0.0](https://github.com/GMOD/bed-js/compare/v1.0.4...v2.0.0) (2019-04-15) | ||
| ### Major changes | ||
| - API now processes just text lines with the parseLine method | ||
| - Remove snake case of results | ||
| - Returned values match autoSql very faithfully and uses the naming from UCSC e.g. exact strings from autoSql {chrom, chromStart, chromEnd} | ||
| - Accepts a opts.uniqueId for the parseLine method which adds this to the featureData | ||
| - Parses the default BED schema with a defaultBedSchema.as autoSql definition instead of a separate method | ||
| ## [1.0.4](https://github.com/GMOD/bed-js/compare/v1.0.3...v1.0.4) (2019-04-14) | ||
@@ -2,0 +15,0 @@ |
| { | ||
| "name": "@gmod/bed", | ||
| "version": "1.0.4", | ||
| "version": "2.0.0", | ||
| "description": "A BED file format parser with autoSql support", | ||
@@ -5,0 +5,0 @@ "main": "dist/main.js", |
115
README.md
@@ -21,35 +21,14 @@ # bed-js | ||
| ### BED parser with default schema | ||
| The default instantiation of the parser with new BED() simply parses lines assuming the fields come from the standard BED schema. | ||
| ## API | ||
| ```js | ||
| const p = new BED() | ||
| const feature = p.parseLine('chr1\t0\t100') | ||
| ``` | ||
| ### Constructor | ||
| The default schema is the same 12 fields as UCSC | ||
| The BED constructor accepts an opts object with options | ||
| chrom | ||
| chromStart | ||
| chromEnd | ||
| name | ||
| score | ||
| strand | ||
| thickStart | ||
| thickEnd | ||
| itemRgb | ||
| blockCount | ||
| blockSizes | ||
| blockStarts | ||
| - opts.autoSql - a optional autoSql schema for parsing lines | ||
| - opts.type - a string representing one of a list of predefined types | ||
| If only a subset of those are used, it just parses up to that, e.g. your line can just contain chrom, chromStart, chromEnd, name, score. | ||
| The predefined types can include | ||
| ### BED parser with alternative schema | ||
| If you have a BED format that corresponds to a different schema, you can specify from a list of default built in alternate schemas or specify an autoSql as a string | ||
| The alternative types by default include | ||
| bigInteract | ||
@@ -65,5 +44,38 @@ bigMaf | ||
| Specify this in the type for the BED constructor | ||
| If neither autoSql or type is specified, the default BED schema is used (see [here](src/as/defaultBedSchema.as)) | ||
| ### parseLine(line, opts) | ||
| Parses a BED line according to the currently loaded schema | ||
| * line: string|Array<string> - is a tab delimited line with fields from the schema, or an array of fields with fields from the schema | ||
| * opts: Options - an options object | ||
| An Options object can contain | ||
| * opts.uniqueId - an indication of a uniqueId that is not encoded by the BED line itself | ||
| The default instantiation of the parser with new BED() simply parses lines assuming the fields come from the standard BED schema. | ||
| Your line can just contain just a subset of the fields e.g. `chrom, chromStart, chromEnd, name, score` | ||
| ## Examples | ||
| ### Parsing BED with default schema | ||
| ```js | ||
| const p = new BED() | ||
| p.parseLine('chr1\t0\t100') | ||
| // outputs { chrom: 'chr1', chromStart: 0, chromEnd: 100, strand: 0 } | ||
| ``` | ||
| ### Parsing BED with a built in schema e.g. bigGenePred | ||
| If you have a BED format that corresponds to a different schema, you can specify from the list of default built in schemas | ||
| Specify this in the opts.type for the BED constructor | ||
| ```js | ||
| const p = new BED({ type: 'bigGenePred' }) | ||
@@ -73,32 +85,36 @@ const line = 'chr1\t11868\t14409\tENST00000456328.2\t1000\t+\t11868\t11868\t255,128,0\t3\t359,109,1189,\t0,744,1352,\tDDX11L1\tnone\tnone\t-1,-1,-1,\tnone\tENST00000456328.2\tDDX11L1\tnone' | ||
| // above line outputs | ||
| { refID: 'chr1', | ||
| start: 11868, | ||
| end: 14409, | ||
| { chrom: 'chr1', | ||
| chromStart: 11868, | ||
| chromEnd: 14409, | ||
| name: 'ENST00000456328.2', | ||
| score: 1000, | ||
| strand: 1, | ||
| thick_start: 11868, | ||
| thick_end: 11868, | ||
| thickStart: 11868, | ||
| thickEnd: 11868, | ||
| reserved: '255,128,0', | ||
| block_count: 3, | ||
| block_sizes: [ 359, 109, 1189 ], | ||
| chrom_starts: [ 0, 744, 1352 ], | ||
| blockCount: 3, | ||
| blockSizes: [ 359, 109, 1189 ], | ||
| chromStarts: [ 0, 744, 1352 ], | ||
| name2: 'DDX11L1', | ||
| cds_start_stat: 'none', | ||
| cds_end_stat: 'none', | ||
| exon_frames: [ -1, -1, -1 ], | ||
| cdsStartStat: 'none', | ||
| cdsEndStat: 'none', | ||
| exonFrames: [ -1, -1, -1 ], | ||
| type: 'none', | ||
| gene_name: 'ENST00000456328.2', | ||
| gene_name2: 'DDX11L1', | ||
| gene_type: 'none' } | ||
| geneName: 'ENST00000456328.2', | ||
| geneName2: 'DDX11L1', | ||
| geneType: 'none' } | ||
| ``` | ||
| ### BED parser with autoSql | ||
| ### Parsing BED with a supplied autoSql | ||
| If you have a BED format with a custom alternative schema with autoSql, or if you are using a BigBed file that contains autoSql (e.g. with [@gmod/bbi](https://github.com/gmod/bbi-js) then you can get it from header.autoSql) | ||
| If you have a BED format with a custom alternative schema with autoSql, or if you are using a BigBed file that contains autoSql (e.g. with [@gmod/bbi](https://github.com/gmod/bbi-js) then you can get it from header.autoSql) then you initialize the schema in the constructor and then use parseLine as normal | ||
| ``` | ||
| const p = new BED({ autoSql: /* your autosql formatted string here */ }) | ||
| const {BigBed} = require('@gmod/bbi') | ||
| const bigbed = new BigBed({path: 'yourfile'}) | ||
| const {autoSql} = await bigbed.getHeader() | ||
| const p = new BED({ autoSql }) | ||
| p.parseLine(line) | ||
| // etc. | ||
| ``` | ||
@@ -110,6 +126,5 @@ | ||
| * Does not do any conversion of types beyond just converting known int/float values | ||
| * Does not convert blockStarts/blockEnds to gene features | ||
| * Does not parse header or track lines | ||
| * Does not handle files that use spaces instead of tabs even though this is allowed by UCSC | ||
| * Does not parse "browser" or "track" lines and will throw an error if parseLine receives one of these | ||
| * By default, parseLine parses only tab delimited text, if you want to use spaces as is allowed by UCSC then pass an array to `line` for parseLine | ||
| * Converts strand from {+,-,.} to {1,-1,0} and also sets strand 0 even if no strand is in the autoSql | ||
@@ -116,0 +131,0 @@ |
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