bio 0.0.4

Some useful command line utils written in Dart. For parsing and manipulating sequence records in various formats...

bio

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

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

seq (Seq)

seqIO

• convert fastq into fasta

  bio seq --input ./data/seq.fq --output ./data/seq.fa
  

• format fasta with max number of characters per line

  bio seq --input ./data/seq.fq --output ./data/seq_formated.fa --fasta-line-length 20
  

• subset records with list of names

  bio seq --input ./data/seq.fq --output ./data/seq_subset.fa --filter-names ./data/name.list
  

• subsamples N records

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

• trim DNA records

  bio seq --input ./data/seq.fq --output ./data/seq_sample.fa --trim-start 6 --trim-end 3
  

alignIO

phylo (Phylo)

treeIO

popgen

BENCHMARK

tool	test IO time	test RC time
biodart	6.678	15.533
seqkit (Golang)	0.996	0.879
seqtk (C)	0.849	0.854