Genomediff
Parses strings from files in the GenomeDiff format generated by the breseq variant caller for haploid microbial organisms.
Installation
$(node bin)/npm install genomediff
Note: It has only been tested with Node 5.
Usage
GenomeDiff strings are parsed using GenomeDiff.parse(<string>)
. The GenomeDiff object contains a metadata
dict with the meta data, as well as mutations
, evidence
and validation
lists, each containing records of that type. Records can be accessed through this list or by id using GenomeDiff.parse(<string>)[<id>]
. GenomeDiff is an iterable and iterating it will return all properties and records.
For accessing all the records you can use GenomeDiff.parse('<string>').values()
which returns an iterable but only with the Record
types.
For accessing the parents of a specific mutation you can use the parents
property available on each record:
let doc = GenomeDiff; // a genomediff stringlet someMutation = doc12; // mutation with id '12'someMutationparents // this will lookup all the parents of the record with id `12` and return as an array of Records
If you want to get an attribute from a parent record then you can use the .get(<attribute>)
method available on the record to do so:
let doc = GenomeDiff; // a genomediff stringlet someMutation = doc12; // mutation with id '12'someMutation // this will lookup all the parents of the record with id `12` and return the value of the attribute `coverage` if found on any of the parent records
If used with node, you can use the following:
var GenomeDiff = GenomeDiff;var fs = ;var file = fs; // path to your `.gd` filevar doc = GenomeDiff;
If used in a browser, use:
;var doc = GenomeDiff; // a genomediff string
Note: Keep in mind that this package requires an ES6 environment in order to work.
Running Tests
A full test suite can be run using npm test
. If you wish to run tests on file change, use jasmine-node dist/ --autotest --color --verbose
.
Development
When developing, use tsc --watch
to build the .ts
files on change. Alternatively, you can use npm run build
if you do not wish to run the build on file change.
Note: If you add new files or remove files, make sure to edit the "files"
field in tsconfig.json
:
"files": "./typings/typings.d.ts" // never remove this line // add more files after this line "./src/parser.ts" "./src/parser.spec.ts" "./src/records.ts" "./src/records.spec.ts" "./src/gd.ts" "./src/gd.spec.ts"