BAS is a collection of perl modules that facilitate the development of perl scripts for bio-informatics applications. This document is a tutorial for BAS. In order to take advantage of BAS, all you have to do is change a few setup.
Let's take an example. (1) Open the configuration file[BAS.conf]
$ emacs BAS.conf
* Following is contents of BAS
###############################################
# Bacteria Analysis System configuration file>#
###############################################
#$Id: BAS.conf,v 1.6 2001/09/09 11:53:20 s98982km Exp $
#scripted by Koya Mori(mory@g-language.org)
#This is a configuration of Bacteria Analysis System
package G::System::BAS_conf;
use strict("var");
sub BAS{
my $methods;
$methods= <<'CONF';
#####################################
# G instances #
#####################################
gb1 < /pub/dnadb/ncbi/genbank/genomes/bacteria/Ecoli/ecoli.gbk
#####################################
# CAI #
#####################################
>cai N
G-instance $gb
-output #[f or stdout] default:"stdout"
-w_output #[f or stdout] default:"stdout"
-w_filename
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(Abbreviation)
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We have 10 classes and 24 methods.
(2) choose an analysis data
Default data is Escherichia_coli_K12. If you want to use another data, you have to change [gb1]. Also you can add a variable (ex.[mgen]).
* Before
##################################### # G instances # ##################################### gb1 < /pub/dnadb/ncbi/genbank/genomes/bacteria/Ecoli/ecoli.gbk
* After
##################################### # G instances # ##################################### gb1 < /pub/dnadb/ncbi/genbank/genomes/bacteria/Ecoli/ecoli.gbk mgen < /pub/dnadb/ncbi/genbank/genomes/bacteria/Mgen/mgen.gbk # add
(3) Choose a method
This time we use [codon_usage](codon class),for example.
・How to use [codon_usage]
１、First, turn [N] to [Y](this means switch on) and choose the analysis data at [G-instance]. If you want to put a output data into a file, change output option to [f]. You can find the file in [mgen]directory. And if you want to output a graph data, change output option to [g] (the graph is saved into [mgen/graph]). Default option [show] means show all results including graph and standard output results automatically.
| -output | f | (put analysis data into a file) |
|---|---|---|
| g | (output a graph analysis data) | |
| show | (show all analysis data automatically) | |
| -filename | free | (using[-output] option, you can named filename) |
* Before
>codon_usage N G-instance $gb -CDSid -output show #[f or g or show] default:"show" -filename
* After
>codon_usage Y # switch on G-instance gb1 # choose data -CDSid -output g #[f or g or show] default:"show" -filename
1. save the file.
2. run the BAS
$./BAS
* Follwing is standard output results
__/__/__/__/__/__/__/__/__/__/__/__/__/
G-language System
Version: 1.0.0 gamma
Copyright (C) 2001 G-language Project
Institute of Advanced Biosciences,
Keio University, JAPAN
http://www.g-language.org/
__/__/__/__/__/__/__/__/__/__/__/__/__/
Length of Sequence : 816394
A Content : 249211 (30.53%)
T Content : 240560 (29.47%)
G Content : 163703 (20.05%)
C Content : 162920 (19.96%)
Others : 0 (0.00%)
AT Content : 59.99%
GC Content : 40.01%
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(Abbreviation)
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1. output the graph
$cd mgen/graph $ gimp codon_table.gif
$ cd mgen $ emacs codon_usage.csv
* Following is standard output results
/,taa,348,0.725
/,tag,132,0.275
A,gca,3759,0.386
A,gcc,730,0.075
A,gcg,462,0.047
A,gct,4799,0.492
C,tgc,295,0.203
C,tgt,1160,0.797
D,gac,1196,0.139
D,gat,7388,0.861
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(Abbreviation)
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There is difference between [Essential] and [option]. [option] has [-] before option name(ex. -CDSid ), but [Essential] hasn't. You must to put variable into [Essential], but [option] is not.
codon_usage Y
G-instance gb1 ## Essential ## -CDSid # option # -output f #[f or g or show] default:"show" # option # -filename # option #
Written 10 September 2001 - Ryo Hattori