sql2html.pl

#!/bin/perl
# 1st Feb 2011
# Generate an HTML documentation page from an SQL file.
#
# It needs to have a "javascript like" documentation above each table. e.g.:
####################################################################################
#/**
#@table variation

#@desc This is the schema's generic representation of a variation.

#@column variation_id				Primary key, internal identifier.
#@column source_id					Foreign key references to the @link source table.
#@column name								Name of the variation. e.g. "rs1333049".
#@column validation_status	Variant discovery method and validation from dbSNP.
#@column ancestral_allele		Taken from dbSNP to show ancestral allele for the variation.
#@column flipped						This is set to 1 if the variant is flipped.
#@column class_so_id				Class of the variation, based on the Sequence Ontology.

#@see variation_synonym
#@see flanking_sequence
#@see failed_variation
#@see variation_feature
#@see variation_group_variation
#@see allele
#@see allele_group_allele
#@see individual_genotype_multiple_bp
#*/
#
#
#create table variation (
#		variation_id int(10) unsigned not null auto_increment, # PK
#		source_id int(10) unsigned not null, 
#		name varchar(255),
#		validation_status SET('cluster','freq','submitter','doublehit','hapmap','1000Genome','failed','precious'),
#		ancestral_allele text,
#		flipped tinyint(1) unsigned NULL DEFAULT NULL,
#		class_so_id ENUM('SO:0001483','SO:1000002','SO:0000667') DEFAULT 'SO:0001059', # default to sequence_alteration
#
#		primary key( variation_id ),
#		unique ( name ),
#		key source_idx (source_id)
#);
########################################################################################
# Tags description:
# /** and */ : begin and end of the document block
# @header    : tag to create a group of tables
# @table     : name of the sql table
# @desc      : description of the role/content of the table, set or info tags
# @column    : column_name [tab(s)] Column description. Note: 1 ligne = 1 column
# @see       : tables names linked to the described table
# @link      : Internal link to an other table description. The format is ... @link table_name ...
# @info      : tag to describe additional information about a table or a set of tables


use strict;
use POSIX;
use Getopt::Long;

###############
### Options ###
###############
my ($sql_file,$html_file,$db_team,$header_flag,$sort_headers,$sort_tables,$help);

usage() if (!scalar(@ARGV));
 
GetOptions(
    'i=s' => \$sql_file,
    'o=s' => \$html_file,
		'd=s' => \$db_team,