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Perl script that retrieves a list of all the fully sequenced species that are in the TreeFam database, and stores them in a Perl pickle
#!/usr/local/bin/perl
#
# Perl script store_treefam_species.pl
# Written by Avril Coghlan (a.coghlan@ucc.ie)
# 3-Apr-09.
#
# For the TreeFam project.
#
# This perl script connects to the TreeFam database and stores
# a list of fully sequenced species in a pickle.
#
# The command-line format is:
# % perl <store_treefam_species.pl> version
# where version is the version of the TreeFam database to use.
#
#------------------------------------------------------------------#
# CHECK IF THERE ARE THE CORRECT NUMBER OF COMMAND-LINE ARGUMENTS:
$num_args = $#ARGV + 1;
if ($num_args != 1)
{
print "Usage of store_treefam_species.pl\n\n";
print "perl store_treefam_species.pl <version>\n";
print "where <version> is the version of the TreeFam database to use.\n";
print "For example, >perl -w store_treefam_species.pl 7\n";
exit;
}
# FIND THE RELEASE OF TREEFAM TO USE:
$version = $ARGV[0];
# READ IN MY PERL MODULES:
use Avril_modules;
use Treefam::DBConnection;
use DBI;
use Storable;
$VERBOSE = 0;
#------------------------------------------------------------------#
# GET A LIST OF ALL FULLY SEQUENCED TREEFAM SPECIES:
$database = 'treefam_'.$version;
%SEQUENCED = ();
%TAXID = ();
$num = 0;
$dbh = DBI->connect("dbi:mysql:$database:db.treefam.org:3308", 'anonymous', '') || return;
$table_w = 'species';
$st = "SELECT TAXNAME, SWCODE, TAX_ID from $table_w WHERE FLAG=\"1\"";
$sth = $dbh->prepare($st) or die "Cannot prepare $st: $dbh->errstr\n";
$rv = $sth->execute or die "Cannot execute the query: $sth->errstr";
if ($rv >= 1)
{
while ((@array) = $sth->fetchrow_array)
{
$num++;
$TAXNAME = $array[0];
$swcode = $array[1]; # eg. CAEEL
$taxid = $array[2];
if ($VERBOSE == 1) { print "$num: species $TAXNAME ($swcode), taxid $taxid\n";}
$SEQUENCED{$swcode} = 1;
$TAXID{$swcode} = $taxid;
}
}
$rc = $dbh->disconnect();
$rc = "";
print STDERR "Read in fully sequenced species...\n";
# STORE THE HASH TABLES %SEQUENCED AND %TAXID IN A PICKLE:
$output1 = "treefam.".$version."_sequenced";
store \%SEQUENCED,$output1;
$output2 = "treefam.".$version."_taxid";
store \%TAXID,$output2;
#------------------------------------------------------------------#
print STDERR "FINISHED.\n";
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