#!/bin/sh

########### CODE DESCRIPTION ################################################################
#  1. loads EnsemblSNP gff3 files using Bio::DB::GFF schema into the GFFSNP mysql database. #
#  2. generates histogram for that chromosomal region. calls it snp_density_chr*.gff        #
#  3. loads the chromosome region gff3 file(one line) into the GFFSNP database              #
#  4. loads the gff3 data and the snp_density_chr*.gff data back into the GFFSNP database   #
#############################################################################################
 
####  this code is undertaken presuming that you are in the folder which contains all the folders with ensemblSNP gff3 files. currently as of 7th July 2010, this code is in "/usr/local/gbrowse2/databases/SeqFeatScrew/EnsemblSNP" folder on Hastings(the development server). inside thsi folder, are multiple folders names chr1..chr20 and chrX, each of which, have ensembl SNP data in gff3 format. This also presumes that the EntrezgeneGff3 is in the path "/usr/local/gbrowse2/databases/SeqFeatScrew/" thsi should have the chromosome_rn_ref_*.gff3 data. 
####

bp_load_gff.pl -adaptor dbi::mysql -dsn "dbi:mysql:database=GFFSNP;host=hastings.hmgc.mcw.edu" -user gbrowser -pass gbr12ws4h -c -upgrade -gff3_munge chr20/*.gff3;

bp_generate_histogram.pl -merge -d "dbi:mysql:database=GFFSNP;host=hastings.hmgc.mcw.edu" -u gbrowser -p gbr12ws4h -bin 10000 SNP > chr20/snp_density_chr20.gff;


for var in 1 2 3 4 5 6 7 8 9 X;
do
bp_load_gff.pl -adaptor dbi::mysql -dsn "dbi:mysql:database=GFFSNP;host=hastings.hmgc.mcw.edu" -user gbrowser -pass gbr12ws4h -c -upgrade -gff3_munge chr$var/*.gff3;

bp_generate_histogram.pl -merge -d "dbi:mysql:database=GFFSNP;host=hastings.hmgc.mcw.edu" -u gbrowser -p gbr12ws4h -bin 10000 SNP > chr$var/snp_density_chr$var.gff;
done;

for var in 0 1 2 3 4 5 6 7 8 9 X;
do
bp_load_gff.pl -adaptor dbi::mysql -dsn "dbi:mysql:database=GFFSNP;host=hastings.hmgc.mcw.edu" -user gbrowser -pass gbr12ws4h -c -upgrade -gff3_munge chr1$var/*.gff3;

bp_generate_histogram.pl -merge -d "dbi:mysql:database=GFFSNP;host=hastings.hmgc.mcw.edu" -u gbrowser -p gbr12ws4h -bin 10000 SNP > chr1$var/snp_density_chr1$var.gff;
done;



####loading finall data into database####
bp_load_gff.pl -adaptor dbi::mysql -dsn "dbi:mysql:database=GFFSNP;host=hastings.hmgc.mcw.edu" -user gbrowser -pass gbr12ws4h -c -upgrade -gff3_munge ../EntrezGeneGff3/chromosome_rn_ref_chr20.gbk.gff3;
 
bp_load_gff.pl -adaptor dbi::mysql -dsn "dbi:mysql:database=GFFSNP;host=hastings.hmgc.mcw.edu" -user gbrowser -pass gbr12ws4h -upgrade -gff3_munge chr20/*;

for var in 1 2 3 4 5 6 7 8 9 X;
do
bp_load_gff.pl -adaptor dbi::mysql -dsn "dbi:mysql:database=GFFSNP;host=hastings.hmgc.mcw.edu" -user gbrowser -pass gbr12ws4h -upgrade -gff3_munge ../EntrezGeneGff3/chromosome_rn_ref_chr$var.gbk.gff3;
 
bp_load_gff.pl -adaptor dbi::mysql -dsn "dbi:mysql:database=GFFSNP;host=hastings.hmgc.mcw.edu" -user gbrowser -pass gbr12ws4h -upgrade -gff3_munge chr$var/*;
done;


for var in 0 1 2 3 4 5 6 7 8 9 X;
do
bp_load_gff.pl -adaptor dbi::mysql -dsn "dbi:mysql:database=GFFSNP;host=hastings.hmgc.mcw.edu" -user gbrowser -pass gbr12ws4h -upgrade -gff3_munge ../EntrezGeneGff3/chromosome_rn_ref_chr1$var.gbk.gff3;
 
bp_load_gff.pl -adaptor dbi::mysql -dsn "dbi:mysql:database=GFFSNP;host=hastings.hmgc.mcw.edu" -user gbrowser -pass gbr12ws4h -upgrade -gff3_munge chr1$var/*;
done;