bio 0.0.5

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bio #

Functions and command line tools for biological computation written in Dart.

CI Status Release Publish Pub Version

USAGE #

  • As a dart package

    • Add bio in pubspec.yaml
    • Run pub get
  • As a command line tool

    • Download binary from release. linux, mac and win are available.
    • Extract the binary file 7z e bio-xxx.7z
    • Run ./bio + subcommand

DOCUMENTATION #

eg, convert fastq into fasta, then subsamples 2 records and reverse complement the sequences.

bio seq --input ./data/seq.fq \
        --output ./data/seq_sampled.fa \
        --sample 2 --sample-seed 123 \
        --reverse-complement

BENCHMARK #

tooltest IO timetest RC time
biodart6.67815.533
seqkit (Golang)0.9960.879
seqtk (C)0.8490.854

0.0.5 #

  • add mdbook for cmd exaamples
  • write dartdoc for functions

0.0.4 #

  • support gz compression format

0.0.3 #

  • filter sequence by motif (--filter-motif)
  • filter sequence by name (--filter-names)
  • trim sequence at both end (--trim-start & --trim-end)

0.0.2 #

  • fix pub.dev warning
  • fix compatibility between --subset and --sample
  • support reverse complement the DNA sequence

0.0.1 #

  • support parsing multiline fasta format
  • format line length of fasta output
  • subset sequence by name list
  • random sample sequences

0.0.0 #

  • Initial version, just for testing

example/example.dart

//
// example.dart
// Copyright (C) 2020 Ye Chang <yech1990@gmail.com>
//
// Distributed under terms of the MIT license.
//

import 'package:bio/seq.dart' as seq;

void main() {
  seq.seqIO(
    inputFile: 'data/seq.fq',
    outputFile: 'data/seq.test',
    inputFormat: 'fq',
    outputFormat: 'fa',
    fastaLineLength: 20,
    filterNames: 'data/name.list',
    filterMotif: 'AAA',
    trimStart: 6,
    // sample: 2,
    //randomSeed: 123,
    trimEnd: 3,
    verbose: true,
    overwrite: true,
  );
}

Use this package as a library

1. Depend on it

Add this to your package's pubspec.yaml file:


dependencies:
  bio: ^0.0.5

2. Install it

You can install packages from the command line:

with pub:


$ pub get

with Flutter:


$ flutter pub get

Alternatively, your editor might support pub get or flutter pub get. Check the docs for your editor to learn more.

3. Import it

Now in your Dart code, you can use:


import 'package:bio/bio.dart';
  
Popularity:
Describes how popular the package is relative to other packages. [more]
7
Health:
Code health derived from static analysis. [more]
100
Maintenance:
Reflects how tidy and up-to-date the package is. [more]
90
Overall:
Weighted score of the above. [more]
51
Learn more about scoring.

We analyzed this package on May 26, 2020, and provided a score, details, and suggestions below. Analysis was completed with status completed using:

  • Dart: 2.8.1
  • pana: 0.13.8-dev

Maintenance suggestions

Package is pre-v0.1 release. (-10 points)

While nothing is inherently wrong with versions of 0.0.*, it might mean that the author is still experimenting with the general direction of the API.

Dependencies

Package Constraint Resolved Available
Direct dependencies
Dart SDK >=2.7.0 <3.0.0
args ^1.5.3 1.6.0
logging ^0.11.4 0.11.4
Dev dependencies
pedantic ^1.8.0
test ^1.6.0