Added species db loading script to svn. This script will parse the fasta files and...

svn path=/; revision=50

diff --git a/interactome_scripts/load_species_db.pl b/interactome_scripts/load_species_db.pl
new file mode 100755 (executable)
index 0000000..e5aad70
--- /dev/null
+++ b/interactome_scripts/load_species_db.pl
@@ -0,0 +1,103 @@
+#!/usr/bin/perl
+
+###############################################################
+#  Written by Justin Elser 2/22/10                            #
+#                                                             #
+#  This program takes all fasta files in the current working  #
+#    directory and puts them in a database named protein      #
+#       sequences                                             #
+#                                                             #
+#  Initial version 0.1                                        #
+#     Shouldn't have to change much once this is done         #
+#         except to maybe add more species detection          #
+#         which is actually done in the pulled in subs        #
+#                                                             #
+###############################################################
+
+use strict;
+use warnings;
+
+use DBI;
+use Term::Screen::ReadLine;
+
+# pull in the find_species and find_gene common subroutines
+require "$ENV{HOME}/scripts/jaiswallab/interactome_scripts/find_species.pl";
+
+
+# define the database handle to be used 
+
+my $screen = Term::Screen::ReadLine->new();
+       # clear the screen
+       $screen->clrscr;
+       # ask for username
+       $screen->at(0,0)->puts("Username: ");
+       my $username = $screen->readline(ROW => 0, COL=>11);
+
+       # ask for password, replace character presses with stars
+       $screen->at(1,0)->puts("Password: ");
+       my $password = $screen->readline(ROW => 1, COL => 11, PASSWORD => 1);
+
+       $screen->at(2,0);
+       undef $screen;
+
+my $dbh = DBI->connect('DBI:mysql:protein_sequences;host=floret.cgrb.oregonstate.edu', $username, $password,
+       { RaiseError=> 1, AutoCommit=>1 }
+       ) or die "Failed to connect to database: $DBI::errstr";
+
+
+my @files = glob("*.fa");
+
+foreach my $file (@files) {
+       my $species = find_species($file);
+       print "on species $species\n";
+       
+       # create the database table
+       my $safe_table = $dbh->quote_identifier($species);
+       
+       $dbh->do("drop table if exists $safe_table");
+       $dbh->do("CREATE TABLE $safe_table (
+               `gene_id` VARCHAR( 255 ) NOT NULL ,
+               `gene_header` TEXT NOT NULL ,
+               `sequence` TEXT NOT NULL ,
+               UNIQUE ( `gene_id` )
+               ) TYPE = MYISAM");
+               
+       # and the statement handler to do the inserts
+       my $insert_sth = $dbh->prepare("insert into $safe_table (gene_id, gene_header, sequence) values (?,?,?)");
+       
+       # create the variables
+       my %seq_hash; # keys is $gene, values are $seq and $gene_header
+       my $gene;
+       my $seq;
+       
+       open(in_file,$file);
+       
+       while(<in_file>) {
+               my $gene_header;
+               my $line = $_;
+               chomp $line;
+               if($line =~ /^\>/) {
+                       if(defined($gene)) {
+                               $seq_hash{$gene}->{'sequence'} = $seq;
+                               $seq_hash{$gene}->{'gene_header'} = $gene_header;
+                       }
+                       $gene_header = $line;
+                       $gene = find_gene($gene_header,$species);
+                       $gene =~ s/^\>//;
+                       $seq = "";
+               }else{
+                       $seq = "$seq"."$line";
+               }
+       }
+       
+       # add the last gene to the hash
+       $seq_hash{$gene}->{'sequence'} = $seq;
+       $seq_hash{$gene}->{'gene_header'} = $gene_header;
+
+       foreach my $key (keys %seq_hash) {
+               $insert_sth->execute($key,$seq_hash{$key}->{'gene_header'},$seq_hash{$key}->{'sequence'});
+       }
+}
+
+
+