Biotools

These are just trivial bioinformatics tools that are convenient to have available on the command line.

Installation: cargo install biotools

Build: git clone git@github.com:jimrybarski/biotools.git && cd biotools && cargo build --release

You can add --help after any subcommand for subcommand-specific options.

Simple bioinformatics tools for sequence analysis and manipulation

Usage: biotools <COMMAND>

Subcommands:
  reverse-complement   Converts a nucleic acid sequence to its reverse complement.
  length               Computes the length of a sequence.
  gc-content           Computes the GC content of a nucleic acid sequence.
  pairwise-local       Performs a local pairwise alignment of two sequences.
  pairwise-semiglobal  Performs a semiglobal pairwise alignment of two sequences.
  pairwise-global      Performs a global pairwise alignment of two sequences.
  help                 Print this message or the help of the given subcommand(s)

Options:
  -h, --help     Print help
  -V, --version  Print version

Reverse complement

There are no options. Spaces and dashes are allowed to permit usage with gap-containing pairwise alignments.

$ biotools reverse-complement GATTACA
TGTAATC
$ biotools reverse-complement GATT ACA-TTGA
TCAA-TGT AATC

Length

There are no options. Spaces and dashes are allowed to permit usage with gap-containing pairwise alignments.

$ biotools length GATTACA
7
$ biotools length GAT  C   TACA
8
$ biotools length GAT-CTACA
8

GC content

There are no options. Spaces and dashes are allowed to permit usage with gap-containing pairwise alignments.

$ biotools gc-content GGG GAA-TA
0.5000000000000000

Pairwise alignment

There are three pairwise alignment commands, for local, semiglobal and global alignments. We use the aligner from rust-bio, which ultimately uses an implementation of Smith-Waterman.

$ biotools pairwise-local ACAGT ACGT
3 GT 5
  ||
2 GT 4

$ biotools pairwise-semiglobal ACAGT ACGT
0 ACAGT 5
  || ||
0 AC-GT 4

$ biotools pairwise-global GGGGCCCCGGGGACAGT ACGT
0 GGGGCCCCGGGGACAGT 17
              || ||
0 ------------AC-GT  4

Coordinates can be disabled:

biotools pairwise-semiglobal ACAGT ACGT --hide-coords
ACAGT
|| ||
AC-GT

You can have biotools try both the forward sequence and reverse complement and then pick the one with the best alignment score. The text RC will be displayed the right of the first sequence if the reverse complement was better. The coordinates are of the reverse complemented sequence in this case, not the original.

$ biotools pairwise-semiglobal TGTAATC GGCGATTACAATGACA
0 TGTAATC  7
  |..|||.
6 TACAATG 13

$ biotools pairwise-semiglobal TGTAATC GGCGATTACAATGACA --try-rc
0 GATTACA  7 RC
  |||||||
3 GATTACA 10

You can adjust the gap penalties (substitutions are always penalized a value of 1). These are given as positive numbers. Defaults: gap open penalty: 2, gap extend penalty: 1.

$ biotools pairwise-semiglobal ACGT ACAAAAGT --gap-open 5 --gap-extend 5
0 ACGT 4
  |.||
4 AAGT 8

$ biotools pairwise-semiglobal ACGT ACAAAAGT --gap-open 0 --gap-extend 0
0 AC----GT 4
  ||    ||
0 ACAAAAGT 8

Suggested aliases

The subcommands are deliberately verbose to give clarity to new users. You may prefer aliases such as these:

alias rc='biotools reverse-complement'
alias len='biotools length'
alias gc='biotools gc-content'
alias pw='biotools pairwise-semiglobal --try-rc'
alias pwl='biotools pairwise-local --try-rc'
alias pwg='biotools pairwise-global --try-rc'