Commit d07bf3d9 authored by Magali Ruffier's avatar Magali Ruffier
Browse files

fixed for Perl critic

parent 10eaf6bf
......@@ -167,7 +167,7 @@ sub new {
$self->driver($driver);
my $driver_class = 'Bio::EnsEMBL::DBSQL::Driver::' . $driver;
eval "require $driver_class";
eval "require $driver_class"; ## no critic
throw("Cannot load '$driver_class': $@") if $@;
my $driver_object = $driver_class->new($self);
$self->_driver_object($driver_object);
......
......@@ -1572,7 +1572,8 @@ sub finish_log {
$self->log($self->date_and_mem."\n\n");
}
if($self->param('joblog')) {
unless(open(JOB,'>',$self->param('joblog'))) {
my $fh;
unless(open($fh,'>',$self->param('joblog'))) {
$self->log_warning("Could not log job to '".$self->param('joblog').
"': $!");
return 1;
......@@ -1587,9 +1588,9 @@ sub finish_log {
push @keys,"END",time;
while(@keys) {
my ($k,$v) = splice(@keys,0,2);
print JOB "$k: $v\n";
print $fh "$k: $v\n";
}
close JOB;
close $fh;
}
return(1);
}
......@@ -2157,9 +2158,9 @@ sub save_seq {
my $self = shift;
my $content = shift ;
my $seq_file = $self->param('logpath') . '/SEQ_' . time() . int(rand()*100000000) . $$;
open (TMP,">$seq_file") or die("Cannot create working file.$!");
print TMP $content;
close TMP;
open (my $fh,">$seq_file", $seq_file) or die("Cannot create working file.$!");
print $fh $content;
close $fh;
return ($seq_file);
}
......@@ -2202,10 +2203,11 @@ sub get_alignment {
$out_file = $self->param('logpath').'/' . $out_file . '.out';
my $command;
my $fh;
if ($seq_type eq 'DNA') {
$command = sprintf $dnaAlignExe, $int_seq_file, $ext_seq_file, $out_file;
`$command`;
unless (open(OUT, "<$out_file")) {
unless (open($fh, "<", $out_file)) {
$command = sprintf $dnaAlignExe, $int_seq_file, $ext_seq_file, $out_file;
`$command`;
}
......@@ -2213,12 +2215,12 @@ sub get_alignment {
elsif ($seq_type eq 'PEP') {
$command = sprintf $pepAlignExe, $int_seq_file, $ext_seq_file, $label_width, $output_width, $out_file;
`$command`;
unless (open(OUT, "<$out_file")) {
unless (open($fh, "<", $out_file)) {
$self->log_warning("Cannot open alignment file\n");
}
}
my $alignment ;
while (<OUT>) {
while (<$fh>) {
next if $_ =~
/\#Report_file
|\#----.*
......
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