[Bioperl-l] bioperl-live: audit of FIXME/???/TODO/etc and undef/die

[Sendu Bala]

Torsten Seemann wrote:
>
> "return undef;" => "return;"  # return undef intentional?
> 
> Bio/DB/Biblio/pdf.pm:    return undef;
> Bio/DB/Biblio/pdf.pm:    return undef unless $link;
> Bio/DB/Biblio/pdf.pm:  return undef;
> Bio/DB/Biblio/eutils.pm:  return undef;
> Bio/DB/WebDBSeqI.pm:    return undef if ( !defined $self->ua || !defin
> Bio/Tools/Run/RemoteBlast.pm:    return undef if ( !defined $self->ua
> Bio/FeatureIO/gff.pm:  return undef if $self->fasta_mode();
> Bio/FeatureIO/gff.pm:  # be graceful about empty lines or comments, an
> Bio/FeatureIO/gff.pm:will return undef if not all features in the stre
> Bio/Root/IOManager.pm:    return undef unless -e $file;
> Bio/Root/Object.pm:    return undef unless defined $self->{'_err'};

I've changed all those; none of them seemed intentional.


> "die" => "$self->throw" # use Bio::Perl exception handling
> 
> Bio/Variation/IO.pm:    $format2 = shift || die "Usage: reformat forma
> Bio/Phenotype/OMIM/OMIMparser.pm:    if ( ! defined( $description ) )
> Bio/Phenotype/OMIM/OMIMparser.pm:    if ( ! defined( $mutation ) )   {
> Bio/LiveSeq/Chain.pm:    die "_praepostinsert_array: Something went ve
> Bio/Tools/isPcr.pm:    my $seq = $seqio->next_seq || die("cannot get a
> Bio/Tools/Analysis/DNA/ESEfinder.pm:  die "Could not get a result"
> Bio/Tools/Analysis/Protein/NetPhos.pm:  die "Could not get a result" u
> Bio/Tools/Analysis/Protein/Mitoprot.pm:  die "Could not get a result"
> Bio/Tools/Analysis/Protein/Scansite.pm:  die "Could not get a result"
> Bio/Tools/dpAlign.pm:        die("\nThe C-compiled engine for Smith Wa
> Bio/Tools/ipcress.pm:    my $seq = $seqio->next_seq || die("cannot get
> Bio/Tools/EPCR.pm:    my $seq = $seqio->next_seq || die("cannot get a
> Bio/Tools/HMM.pm:        die("\nThe C-compiled engine for Hidden Marko
> Bio/Seq/PrimedSeq.pm:      my $file = shift || die "need a file to rea
> Bio/Seq/PrimedSeq.pm:     my $file = shift || die "$0 <file>";

Of these, only Variation/IO.pm and Phenotype/OMIM/OMIMparser.pm needed 
changing (most are in the POD). I haven't investigated Lincoln's modules:

 > Bio/DB/SeqFeature/Store/DBI/mysql.pm:  $db->store($feature) or die "Co
 > Bio/DB/SeqFeature/Store/berkeleydb.pm:  $db->store($feature) or die
 > Bio/DB/SeqFeature/Store.pm:  $db->store($feature) or die "Couldn't sto
 > Bio/Graphics/Glyph.pm:  my $feature = $arg{-feature} or die "No featur
 > Bio/Graphics/Glyph/image.pm:    open F,$path or die "Can't open $path:
 > Bio/Graphics/Panel.pm:  open (F,">$imagefile") || die("Can't open imag