====== Overview ======


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.

====== How to change a 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 
     . 
     . 
     . 
    (Abbreviation) 
     . 
     . 
     .
 
We have 10 classes and 24 methods.

  *CAI
    *cai
  *Codon
    *codon_counter
    *amino_counter
    *codon_usage
  *Consensus
    *base_counter
    *base_information_content
    *base_z_value
    *base_entropy
    *base_relative_entropy
    *base_individual_information_matrix
  *GCskew
    *view_cds
    *find_ori_ter
    *gcskew
    *genomicskew
    *cum_gcskew
    *gcwin
  *Free Energy
    *foreach_RNAfold
  *Markov
    *over_lapping_finder
  *Over Lapping Gene
    *over_lapping_finder
  *Pat Search
    *palindrome
  *Tandem Repeat
    *foreach_tandem
    *graphical_LTR_search
  *Util
    *seq2gif
    *genome_map

(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% 
                               . 
                               . 
                           (Abbreviation) 
                               . 
                               . 

1. output the graph
  $ cd mgen/graph 
  $ gimp codon_table.gif 



  *If you want to put analysis data into a file.
  *change output option to [f].
  *save the file
  *run the BAS.
  *output the file

  $ 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 
      . 
      . 
      . 
   (Abbreviation) 
      . 
      . 
      . 


====== Notes ======


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