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Commit 64fa7058 authored by Leo Gordon's avatar Leo Gordon
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some readability changes

parent 32789a98
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......@@ -205,11 +205,11 @@ sub job_creation {
my $starttime = time();
my $count = 0;
if (defined($self->{'hashed_a'}) and defined($self->{'hashed_b'})) {
while ($self->{resolved_input_id} = $self->resolve_suffix()) {
print STDERR " ", $self->{resolved_input_id}, "\n" if ($self->{debug});
$self->create_resolved_input_id_job() unless ($self->{debug});
while (my $resolved_input_id = $self->resolve_suffix()) {
print STDERR " $resolved_input_id\n" if ($self->{debug});
$self->create_resolved_input_id_job($resolved_input_id) unless ($self->{debug});
if(++$count % 100 == 0) {
print "", $self->{resolved_input_id}, " at ",(time()-$starttime)," secs\n";
print "$resolved_input_id at ",(time()-$starttime)," secs\n";
}
}
} elsif (defined($self->{'inputfile'})) {
......@@ -217,10 +217,9 @@ sub job_creation {
while (<FILE>) {
chomp $_;
my $id = $_;
my $input_id = $self->{'input_id'};
$input_id =~ s/\$inputfile/$id/;
$self->{resolved_input_id} = $input_id;
$self->create_resolved_input_id_job();
my $resolved_input_id = $self->{'input_id'};
$resolved_input_id =~ s/\$inputfile/$id/;
$self->create_resolved_input_id_job($resolved_input_id);
print "Job ", $count, " at ",(time()-$starttime)," secs\n" if(++$count % 50 == 0);
}
close FILE;
......@@ -235,16 +234,16 @@ sub job_creation {
$to = shift @full_list;
}
# expanding tags here (now you can substitute $suffix, $suffix2, $suffixn and if you really need it, $tag):
$self->{resolved_input_id} = $self->{'input_id'};
$self->{resolved_input_id} =~ s/\$suffixn/$batch_cnt/g; # the order of substitutions is important!
$self->{resolved_input_id} =~ s/\$suffix2/$to/g;
$self->{resolved_input_id} =~ s/\$suffix/$from/g;
$self->{resolved_input_id} =~ s/\$tag/$tag/g;
my $resolved_input_id = $self->{'input_id'};
$resolved_input_id =~ s/\$suffixn/$batch_cnt/g; # the order of substitutions is important!
$resolved_input_id =~ s/\$suffix2/$to/g;
$resolved_input_id =~ s/\$suffix/$from/g;
$resolved_input_id =~ s/\$tag/$tag/g;
if(++$count % 100 == 0) {
print "", $self->{resolved_input_id}, " at ",(time()-$starttime)," secs\n";
print "$resolved_input_id at ",(time()-$starttime)," secs\n";
}
$self->create_resolved_input_id_job();
$self->create_resolved_input_id_job($resolved_input_id);
}
}
my $total_time = (time()-$starttime);
......@@ -253,10 +252,11 @@ sub job_creation {
}
sub create_resolved_input_id_job {
my $self = shift;
my ($self, $resolved_input_id) = @_;
Bio::EnsEMBL::Hive::DBSQL::AnalysisJobAdaptor->CreateNewJob
(
-input_id => $self->{resolved_input_id},
-input_id => $resolved_input_id,
-analysis => $self->{_analysis},
-input_job_id => 0,
) unless ($self->{'debug'});
......
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