rscan - version: 0.1
=====================
Performs nucleotide scoring and color masking in multiple sequence alignments, to help in DNA signature search.
Runs within irb, in a terminal emulator with ANSI color support.
Requires gems: bio, rainbow.
Usage:
------
./rscan
Input:
------
Multiple DNA-sequence alignment fasta-formatted file. Groups definitions.
Default scoring formula = 1 - (ka/5)*(1-a) - (kb/10)*b
a: frequency of nt_base in the ingroup (consenus)
b: frequency of nt_base in the outgroup (aspecificity)
ka: consensus coefficient : 20 :strict, 10 :high (majority rule high), 3 :low (majority rule low)
kb: aspecificity tollerance coefficient : 0 :allow , 10 :penalty (allowed with penality), 20 :forbid (not allowed)
IRB user interface command list:
=================================
Alignment and groups
--------------------
open "filename"
open a fasta input file and create the working alignment
usage:
>> open "test.fasta"
labels?
print the sequences' index and label
usage:
>> labels?
groups?
print groups array
usage:
>> groups?
set_groups [arrays and/or ranges]
set the groups of sequences, expects an array of arrays or ranges
usage, with a 16 sequences alignemnt:
>> set_groups [0..4, 5..9, 10..15]
>> set_groups [0..4, [5,6,7], 8..14, [15]]
Set Consensus coefficient (ka)
------------------------------
con :preset_value
use a preset value for consensus coefficient ka
expects a symbol [:strict | :high | :low]
usage:
>> con :strict
ka numeric_value
setter for ka (consensus coefficient)
expects a numeric value
(standard values for default formula are: 20, 10, 3)
usage:
>> ka 10
Set Aspecificity-tollerance coefficient (kb)
--------------------------------------------
asp :preset_value
use a preset value for aspecificity tollerance coefficient kb
expects a symbol [:forbid | :penalty | :allow]
usage:
>> asp :allow
kb numeric_value
setter for kb (aspecificity tollerance coefficient)
expects an integer value
(standard values for default formula are: 20, 10, 0)
usage:
>> kb 10
Scan and Scores
---------------
scan
scan the alignment with the current parameters and print the score-masking color shading
usage:
>> scan
color_ranges [n1, n2, n3, n4]
defines the borders values of score ranges, for color masking
expects an array of 4 values, default is [0.5, 0.7, 0.8, 0.9]
ranges are defined as:
score < n1
n1 <= score < n2
n2 <= score < n3
n4 <= score < n4
score >= n4
usage:
>> color_ranges [0.3, 0.45, 0.6, 0.88]
set_formula "a function of a, b, @ka, @kb"
setter for the scoring formula
expects a string; variables and coefficient: a, @ka; b, @kb
usage:
>> setformula "1 - (a * @ka) - (b * @kb)"
formula?
print the scoring formula
usage:
>> formula?
Utilities
---------
clear
clear the console screen
usage:
>> clear
test
perform a test scan
usage:
>> test