Data format

You should prepare set.data, orf.data and clone.data(optional)
before you run Make_Files.csh.

If you have  Sybase SQL Server System 10 or 11, follow 1( 1-1, 1-2, 1-3 )
                                         if not, follow 1( 1-1 ), 2, 3


1. SET data format ( set.data )

   set vars

1-1. Set vars for CircleMap and OrfMaP

CircleMap  circular map

e.g. http://www.kazusa.or.jp/cyanobase/map/java/cmap_small/cmap_sm.html

 OrfMap

e.g.  http://www.kazusa.or.jp/cyanobase/map/java/orf_small/orf_sm1.html


  totalsize ->   bp
  scalebase -> length in Kbp / line (only 10 kbp or 15kbp can be permitted)
  cloneflg  -> use (on ) don't use(off)
     If you want to show  cosmid/phage/plasmid clones in OrfMap, 
     set clone flg on, if not off.

  cgidir    -> path for cgi-bin files
  httpdir   -> path for html document files


# the Sybase value that stands for the direction of ORF

  direct_f  -> forward 
  direct_r  -> reverse

e.g.
----------------------------------------------
totalsize  3573470
scalebase  15
cloneflg   on

cgidir     /usr/local/etc/cern-httpd/cgi-bin
htmldir    /usr/local/etc/cern-httpd/htdocs

direct_f   direct
direct_r   complement
----------------------------------------------

1-2. SYBASE  environments

  SYBASE   -> $SYBASEpath   ($SYBASE)
  DSQUERY  -> dsquery       ($DSQUERY)
  usr      -> user name     (sybase login name)
  passwd    password        (sybase password)
  dbase    -> database name (sybase dbname)


e.g.
------------------------------
SYBASE     /usr/sybase/tool
DSQUERY    SYBASE
usr        cyano
passwd     abcdef
dbase      cyanodb
------------------------------

1-3. Set the Sybase table and column name 

    If you want to show  cosmid/phage/plasmid clones in OrfMap, 
    follow A, B

    if not, you need to follow A only.

    All data types are described in SybaseTable.doc.

(A) ORF Tables and Columns

  (a) Table

    ORF_ID_Table    -> ORF ID and name
    ORF_Data_Table  -> ORF data table
    ORF_Color_Table -> ORF color table

  (b) Column

    ORF_ID          -> ORF ID
    ORF_Name        -> ORF name
    ORF_Begin       -> ORF begin
    ORF_End         -> ORF end
    ORF_length      -> ORF length
    ORF_direction   -> ORF direction
    ORF_classify    -> classification of ORF 
    ORF_color       -> ORF color 


e.g.
----------------------------------
ORF_ID_Table       id_vs_name_orf
ORF_Data_Table     orfdata
ORF_Color_Table    color

ORF_ID             orf_id
ORF_Name           orf_name
ORF_Begin          begin
ORF_End            end
ORF_length         aa_length
ORF_direction      direction
ORF_classify       classify
ORF_color          color_rgb
----------------------------------


(B) Clone Tables and Columns

  (a) Table

    CLONE_ID_Table    -> CLONE ID and name
    CLONE_Data_Table  -> CLONE data table

  (b) Column

    CLONE_ID          -> CLONE ID
    CLONE_Name        -> CLONE name
    CLONE_Pos_Begin   -> CLONE begin
    CLONE_Pos_End     -> CLONE end
    CLONE_Seq_Begin   -> Sequenced region begin 
    CLONE_Seq_End     -> Sequenced region end
    CLONE_length      -> Sequenced length


e.g.
----------------------------------
CLONE_ID_Table      id_vs_name_cl
CLONE_Data_Table    clonedata

CLONE_ID            clone_id
CLONE_Name          clone_name
CLONE_Pos_Begin     pos_begin
CLONE_Pos_End       pos_end
CLONE_Seq_Begin     seq_begin
CLONE_Seq_End       seq_end
CLONE_length        length
----------------------------------


2. ORF data format ( orf.data )

format:

ORF_Name ORF_Begin  ORF_End  ORF_length ORF_direction ORF_color 

e.g.
-----------------------------------------------------
slr0612         937       185 direct     119,136,153
slr0613        1577       173 direct     255,255,255
sll0558        2172       233 complement 119,136,153
sll1214        3192       358 complement 0,0,0
sll1213        4451       312 complement 119,136,153
-----------------------------------------------------


3. CLONE data format ( clone.data )

format:
CLONE_Name  CLONE_Pos_Begin  CLONE_Pos_End
CLONE_Seq_Begin  CLONE_Seq_End  CLONE_length

e.g.
-----------------------------------------------------------------------
cs0079   20918   59110   25608   59876   34269
cs0483   59877   98941   59877   97839   37963
cs0329   97840   140346   97840   135132   37293
-----------------------------------------------------------------------