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|
#!/usr/bin/perl
use strict;
use warnings;
BEGIN {
if (not exists $ENV{'ARBHOME'}) { die "Environment variable \$ARBHOME has to be defined"; }
my $arbhome = $ENV{'ARBHOME'};
push @INC, "$arbhome/lib";
push @INC, "$arbhome/PERL_SCRIPTS/GENOME";
1;
}
use ARB;
use GI;
# -----------------------
# configure here:
my $create_ORFs = 0; # 0 -> error if ORF not found; 1 -> auto-create gene
my $verbose = 0; # 0 -> be quiet; 1 -> be noisy
my $overwrite = 0; # 0 -> if entry exists -> error; 1 -> silently overwrite entry
# -----------------------
my $importfilename;
{
my $argcount = $#ARGV + 1;
if ($argcount == 1) {
$importfilename = $ARGV[0];
}
else {
print "\nUsage: import_proteomdata.pl datafile\n";
print "Imports a proteom datafile in CSV format.\n";
GI::show_csv_info();
print "The columns in datafile should contain:\n";
print '"ORF-Name","Substrat","Ausstiche","Mittelw Score","Stabw Score","best hit","x","y"'.
"\n\n";
exit(1);
}
}
GI::connectDB();
GI::define_tokenizer_columns(8); # datafile is expected to contain 8 columns
GI::message("Reading '$importfilename'..");
open(IMPORT,"<$importfilename") || GI::error("Can't read '$importfilename'");
my $lineno = 1;
my @head = GI::tokenize_columns(<IMPORT>,"$lineno of $importfilename");
my ($gb_genome,$genome_name) = GI::findCurrentGenome();
my $gb_gene_data = ARB::search($gb_genome, "gene_data", "CONTAINER");
if (!$gb_gene_data) {
my $reason = ARB::await_error();
GI::error("Couldn't find or create container 'gene_data' for organism '$genome_name' ($reason)");
}
GI::unmarkGenesOfGenome($gb_genome);
GI::message("Importing data to organism '$genome_name' ..");
my $gene_count = 0;
ORF: foreach (<IMPORT>) { # loop over all lines from inputfile
$lineno++;
my @elems = GI::tokenize_columns($_,"$lineno of $importfilename");
my ($orf,$substrate,$spots,$mean_score,$sd_score,$best_hit,$coordx,$coordy) = @elems;
# find (or create) the orf gene:
my ($gb_orf, $error) = GI::findORF($gb_gene_data,$genome_name,$orf,$create_ORFs,$verbose);
if (!$error) {
my $substrate_field = "proteome/$substrate";
my $gb_substrate = ARB::search($gb_orf, $substrate_field, "NONE");
if (!$gb_substrate) {
$gb_substrate = ARB::search($gb_orf, $substrate_field, "CONTAINER");
}
if (!$gb_substrate) {
my $reason = ARB::await_error();
$error = "Could not create container '$substrate_field' ($reason)";
}
else {
$error = GI::write_entry($gb_substrate, "spots", "STRING", $spots, $overwrite, $verbose);
if (!$error) { $error = GI::write_entry($gb_substrate, "score", "INT", $mean_score, $overwrite, $verbose); }
if (!$error) { $error = GI::write_entry($gb_substrate, "sd", "INT", $sd_score, $overwrite, $verbose); }
if (!$error) { $error = GI::write_entry($gb_substrate, "id", "STRING", $best_hit, $overwrite, $verbose); }
if (!$error) { $error = GI::write_entry($gb_substrate, "coordx","INT", $coordx, $overwrite, $verbose); }
if (!$error) { $error = GI::write_entry($gb_substrate, "coordy","INT", $coordy, $overwrite, $verbose); }
if (!$error) {
my $marked = ARB::read_flag($gb_orf);
if ($marked == 0) {
ARB::write_flag($gb_orf,1); # mark changed genes
$gene_count++;
}
}
}
}
if ($error) { GI::error("$error (while parsing $lineno of $importfilename)"); }
}
close IMPORT;
GI::message("$gene_count genes modified and marked.");
GI::disconnectDB();
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