keith/sequence
Nucleotide sequence comparison service
  API.md
# StdLib DNA Sequence Alignment - MapReduce Example This is a [StdLib](https://stdlib.com) service to perform exhaustive, ungapped DNA sequence alignment in a massively parallel fashion. It makes use of the [NtSeq](https://github.com/keithwhor/NtSeq) Node.js package to perform alignment and derive results. You can find this service on [StdLib: keith/sequence](https://stdlib.com/services/keith/sequence), or [GitHub: keithwhor/stdlib-sequence](https://github.com/keithwhor/stdlib-sequence). ## Example Query You can provide any genome sequence you want with the `seq` parameter, though by default the sequence is the first 1,000,000 nucleotides of the E. coli K12 Genome. ```javascript f('keith/sequence')({q: 'GATTACACAT', count: 2}, (err, result) => { // do something with result }); ``` Also available at https://keith.stdlib.com/sequence?q=GATTACACAT&count=2 Returns; ```json { "results": [ { "position": 474308, "sequence": "GATTACGCAT", "mask": "GATTAC-CAT", "cover": "GATTACRCAT" }, { "position": 965004, "sequence": "GATTGCACAT", "mask": "GATT-CACAT", "cover": "GATTRCACAT" } ] } ``` ## Usage You can use this service via HTTPS: ``` https://keith.stdlib.com/sequence?q=ATGC ``` Via the [StdLib CLI "f" command](https://github.com/poly/stdlib): ``` $ npm install lib -g $ f keith/sequence --q ATGC ``` Or in a Node.js / Browser-based project using [the "f" package](https://github.com/poly/f): ```javascript const f = require('f'); f('keith/sequence')({q: 'ATGC'}, (err, result) => { // handle result }); ``` ## Service Parameters This service accepts a few parameters; `q`: Query sequence for alignment (what you're searching for) `seq`: Genome sequence to search through `count`: Number of results to return (default 1) `repeat`: Repeats of query sequence (repeat query sequence this many times) `stats`: Show search statistics ## Example Response https://keith.stdlib.com/sequence?q=GATTACACAT&count=1&stats ```json { "results": [ { "position": 474308, "sequence": "GATTACGCAT", "mask": "GATTAC-CAT", "cover": "GATTACRCAT" } ], "stats": { "length": { "q": 10, "seq": 1000000 }, "workers": 0, "time": { "total": 1791, "prepare": 83, "map": 722, "reduce": 0, "sort": 986 } } } ``` `results` is an Array of results, order by number of matches. `result.position` is the position of the matching sequence in the target genome. `result.sequence` is the sequence of the match, beginning at `result.position`. `result.mask` is the "sequence mask" from [NtSeq](https://github.com/keithwhor/NtSeq), i.e. the "pessimistic" sequence that represents the intersection of both query and target sequences. `result.cover` is the "sequence cover" from [NtSeq](https://github.com/keithwhor/NtSeq), i.e. the "optimistic" sequence that represents the union of both query and target sequences. `stats` is an Object showing general query statistics, will only be provided if the `stats` query parameter is set. `stats.length` shows the total function input length. `stats.workers` shows the parallelization amount (0 means no workers were dispatched) `stats.time` shows a breakdown of time (in ms) spent in each step ## MapReduce To see an example of [StdLib](https://stdlib.com) MapReduce in action, simply specify inputs that cause parallelization to occur (more than 1,000,000,000 nt²). ``` $ f keith/sequence --q A --repeat 10000 --count 0 --stats ``` https://keith.stdlib.com/sequence?q=A&repeat=10000&count=0&stats ```json { "results": [], "stats": { "length": { "q": 10000, "seq": 1000000 }, "workers": 10, "time": { "total": 6497, "prepare": 47, "map": 5504, "reduce": 46, "sort": 900 } } } ``` ## Deploy to StdLib, Build Your Own MapReduce Service If you'd like to deploy a copy of this service on StdLib, use the [StdLib CLI tools](https://github.com/poly/stdlib); ``` $ npm install lib -g $ lib init $ lib up ``` Make sure to change `{"stdlib": {"name": "keith/sequence"}}` in `package.json` to match your username and desired service name. ## That's it! Thanks for checking this service out. I look forward to seeing other people build out MapReduce example on StdLib. :) You can [sign up for StdLib here](https://stdlib.com). Check out [StdLib on GitHub](https://github.com/poly/stdlib). Follow us on Twitter, [@polybit](https://twitter.com/polybit). Or follow me specifically, [@keithwhor](https://twitter.com/keithwhor). Happy Building!
  Published by keith on Jan 18th 2017, 9:56 AM
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