# Commands to make the MySQL tables

mysql -h webdbsrv -P 3306 -u spogrw -pspogex S_pombe_SPOG_1 < drop_yogy.sql
mysql -h webdbsrv -P 3306 -u spogrw -pspogex S_pombe_SPOG_1 < create_yogy.sql
mysql -h webdbsrv -P 3306 -u spogrw -pspogex S_pombe_SPOG_1 < truncate_yogy.sql

# In the following scripts, it is necessary to download certain
#   database files from the internet - the locations of these
#   files are given in the relevant script or in this script.


# Files to download in perl script.

./yogy_populate.pl


# Selected files to download from:
#   http://inparanoid.cgb.ki.se/download/current/sqltables/

foreach file (longsqltable.*)
  echo $file
  ./yogy_add_inp_terms.pl $file
end


# http://orthomcl.cbil.upenn.edu/OrthoMCL_DB_Data/all_orthomcl.out

./yogy_add_orthomcl_cluster.pl all_orthomcl.out

# http://orthomcl.cbil.upenn.edu/OrthoMCL_DB_Data/BAE_geneid_anno

./yogy_add_orthomcl_lookup.pl BAE_geneid_anno


# File to download in perl script.

./yogy_add_go_terms.pl

# Selected files to download from:
#   http://www.geneontology.org/GO.current.annotations.shtml

foreach file (gene_association.*)
  echo $file
  ./yogy_add_go_assocs.pl $file
end

# Same location, renamed file, so that it doesn't get loaded
#   with the previous loop!

./yogy_add_go_assocs_uni.pl big_file_gene_association.goa_uniprot


# Files to download in perl script.
# This script may fail during running, so some of it may need to be re-run.

./yogy_add_new_orgs.pl


# Selected xrefs files to download from:
#   ftp://ftp.ebi.ac.uk/pub/databases/IPI/current/

foreach file (ipi.[ABCHMR]*.xrefs)
  echo $file
  ./yogy_add_ipi_lookup.pl $file
end


# ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/gene2accession.gz

./yogy_add_gi_lookup.pl gene2accession


# ftp://ftp.ebi.ac.uk/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_sprot.dat.gz

uni_parse/uni_parse.pl uni_parse/uniprot_sprot.dat >! uni_parse/uniprot_sprot.txt

./yogy_add_uniprot_lookup.pl uni_parse/uniprot_sprot.txt


# ftp://ftp.ebi.ac.uk/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_trembl.dat.gz

uni_parse/uni_parse.pl uni_parse/uniprot_trembl.dat >! uni_parse/uniprot_trembl.txt

./yogy_add_uniprot_lookup.pl uni_parse/uniprot_trembl.txt


# Takes a couple of days to run this script!
# It speeeds up the on-the-fly searching for UniProt IDs from GI numbers.

./yogy_find_uniprot_ids.pl