Command line tools to (ANSI) colorize DNA sequences, columns, or numbers found within text files. Useful for bioinformatics or data analysis.
| Tool | Version | Use |
|---|---|---|
| color_cols.pl | V0.7 | Color specific columns within text |
| color_nums.pl | V0.4 | Color numbers within text |
| color_seq.pl | V0.7 | Colors DNA sequence characters within text |
- 5/27/14 RTK
- 1/15/15 RTK (update; Renamed from comline color seq num)
- 3/31/15 RTK (update color cols.pl)
- 4/8/16 RTK; Update color_seq to support lowercase and not (inverse)
- 4/23/16 RTK; Update color_seq: Add -cran to restrict columns; Fix off-by-one bug with -bran
- 10/7/17 RTK; Update all three scripts and use doc too.
- 12/13/17 RTK; Update color_cols 0.54 to 0.55; add -ic
- 12/20/19 RTK; Update; Remove (local) includes; /usr/bin/env perl -w
- 2023-01-28 RTK; Remove Readonly.pm dependence from all color scripts.
The color scripts are simple command line filters intended to colorize specific value-associated “words” contained within simple ASCII text. This is useful to highlight specific values for quick value identification and pattern visualization. The tools take text from a file or standard input then output this with ANSI escape sequences interjected to color specific characters in a terminal display. All tools also accept various command line options to allow user control over character or token selection and color choice.
Use is described in the document comline_color_seq_num_use.pdf. This also describes options and shows colored screenshots corresponding to example usage of all scripts.
Example test-case files include a fasta format sequence file ("examp.fas") and several number-containing files (*.mat)
These perl modules are required:
| Module | Use |
|---|---|
| Term::ANSIColor | For color encoding |
| Getopt::Long | For command line processing |
| Readonly | For constants |
| Carp |
To install above modules, try this:
cpan install ANSIColor Getopt Readonly Carp
Or you may need to use sudo:
sudo cpan install ANSIColor Getopt Readonly Carp
General
Cook up some test case / example case scripts.
color_seq.pl
Lines are considered independently; Windows of base type cannot wrap for multi-line sequence formats like fasta.
color_nums.pl
Would be nice to have more than three colors (though given the ASNI pallete, what can one expect!)