04-21-2009
Hi John,
Please find the answers as below:
Please describe exactly what the script needs to do.
This script splits the data from Detail files (i.e which are the input files for the shell script in .txt format) . In this case the detal file located at ${m_recv_dir}/${m_glb_d92_nm}${m_glb_file_seq} . which is the starting portion of the code which i posted.
This script reads the data line by line from the text file and prepare output .DAT file.
Once the .DAT file is created it puts '*/' end of file character at the bottom of the output file generated. Once the .DAT output file is generated another shell script loads data from this .DAT files to work tables of the database using SQL Loader.
What files does it use for input? What is the format of those files?
The format of the input file is .txt
What is the format of the output?
The output format is .DAT
Please do let me know what else information you need so you can help me on this..
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LEARN ABOUT DEBIAN
bp_process_wormbase
BP_PROCESS_WORMBASE(1p) User Contributed Perl Documentation BP_PROCESS_WORMBASE(1p)
NAME
process_wormbase.pl - Massage WormBase GFF files into a version suitable for the Generic Genome Browser
SYNOPSIS
% process_wormbase.pl ./WS61 > wormbase.gff
DESCRIPTION
This script massages the Wormbase GFF files located at ftp://www.wormbase.org/pub/wormbase/GENE_DUMPS into a version of the GFF format
suitable for display by the generic genome browser. It mainly adds comments to the annotations and designates certain well-spaced genetic
loci as framework landmarks.
This script requires the AcePerl distribution, which is available on CPAN (look for the "Ace" module).
To use this script, get the WormBase GFF files from the FTP site listed above and place them in a directory. It might be a good idea to
name the directory after the current release, such as WS61. You do not need to uncompress the files.
Then give that directory as the argument to this script and capture the script's output to a file:
% process_wormbase.pl ./WS61 > wormbase.gff
It may take a while before you see output from this script, since it must first fetch gene and protein database from the remote AceDB
running at www.wormbase.org. The wormbase.gff file can then be loaded into a Bio::DB::GFF database using the following command:
% bulk_load_gff.pl -d <databasename> wormbase.gff
SEE ALSO
Bio::DB::GFF, bulk_load_gff.pl, load_gff.pl
AUTHOR
Lincoln Stein <lstein@cshl.org>
Copyright (c) 2002 Cold Spring Harbor Laboratory
This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself. See DISCLAIMER.txt for
disclaimers of warranty.
perl v5.14.2 2012-03-02 BP_PROCESS_WORMBASE(1p)