[Bioperl-l] bioperl-live: audit of FIXME/???/TODO/etc and undef/die
Lincoln Stein
lstein at cshl.edu
Tue Sep 19 17:38:31 UTC 2006
Torsten,
Thanks for doing this audit. I'll take care of my modules.
Lincoln
On 9/19/06, Torsten Seemann <torsten.seemann at infotech.monash.edu.au> wrote:
>
> Developers,
>
> Given the pending RC1 release, I decided to do a quick audit of
> bioperl-live, see below. Hopefully no much POD text may got through.
> Hope it is useful anyway.
>
> --Torsten
>
>
> "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 $self->{'_err'};
>
> "die" => "$self->throw" # use Bio::Perl exception handling
>
> Bio/Variation/IO.pm: $format2 = shift || die "Usage: reformat forma
> 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
> 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>";
>
> "FIXME"
>
> Bio/AlignIO/po.pm
> Bio/DB/Expression/geo.pm
> Bio/FeatureIO/gff.pm
> Bio/Ontology/RelationshipType.pm
> Bio/SeqIO/kegg.pm
> Bio/SeqIO/swiss.pm
> Bio/Tools/ESTScan.pm
> Bio/Tools/Est2Genome.pm
> Bio/Tools/GuessSeqFormat.pm
> Bio/Tools/HMMER/Results.pm
>
> "???"
>
> Bio/Variation/VariantI.pm: $self->allele_mut($value); #????
> Bio/DB/Biblio/soap.pm:use Bio::Biblio; # TBD: ?? WHY SHOULD I DO THIS
> Bio/DB/GFF/Adaptor/dbi/oracleace.pm: # then generate a bogus Homolo
> Bio/DB/GFF/Adaptor/dbi/mysqlace.pm: # then generate a bogus Homolog
> Bio/SeqFeature/Annotated.pm: Args : ???
> Bio/SeqFeature/Tools/Unflattener.pm: # what should w
> Bio/SeqFeature/Tools/IDHandler.pm: # warn??
> Bio/Root/IO.pm: $ROOTDIR = ""; # what is reasonable??
> Bio/LiveSeq/Chain.pm:# *??* create hash2dchain ???? (with hashkeys use
> Bio/LiveSeq/Chain.pm:# **????** how about using array of arrays instea
> Bio/LiveSeq/Chain.pm:# in verbose $string assignment around line 721 ?
>
> "TODO"
>
> Bio/Root/Root.pm: # TODO: Fix the MSG: line of the re-thrown err
> Bio/Root/Storable.pm: # TODO: add cleanup and unlink methods. For n
> Bio/Seq/EncodedSeq.pm: #TODO: finish all this
> Bio/SeqFeature/Tools/Unflattener.pm: # TODO - we ignore this
> Bio/SeqFeature/Tools/Unflattener.pm: # TODO - allow more
> Bio/SeqFeature/Tools/Unflattener.pm: ## features. TODO: P
> Bio/SeqIO/game/gameWriter.pm:#TODO: can't sequences also have database
> Bio/SeqIO/chaos.pm: # TODO
> Bio/SeqIO/pir.pm: # TODO - not processing SFS data
> Bio/SeqIO/strider.pm: # TODO: determine 'DNA Degenerate
> Bio/Search/BlastUtils.pm: # TODO: Account for strand/frame issue!
>
> "***"
>
> Bio/Map/Physical.pm: #*** why doesn't it call Bio::Map::Clone->new
> Bio/Map/Physical.pm: #*** why doesn't it call Bio::Map::FPCMarker->
> Bio/Map/Physical.pm: #*** why doesn't it call Bio::Map::Contig->new
> Bio/Map/PositionI.pm:#*** should this be overridden from RangeI?
> Bio/Matrix/PSM/SiteMatrix.pm: #*** IUPACp values not actually u
> Bio/Tree/TreeFunctionsI.pm: #*** the algorithm here hasn't really b
> Bio/SeqIO/agave.pm:***NOTE*** At the moment, not all of the tags are
> Bio/LiveSeq/Chain.pm:# **** performance concerns
> Bio/Map/LinkageMap.pm:#*** what is this? what calls it? note that it s
> Bio/Map/Marker.pm: *** does not actually add this marker to the
> Bio/Map/SimpleMap.pm: *** does not actually add the element to th
> Bio/Map/FPCMarker.pm: *** This has nothing to do with an actual
> Bio/Map/PositionI.pm:#*** should this be overridden from RangeI?
>
> "Why?"
>
> Bio/Search/Hit/PullHitI.pm: # why does this method even exist?!
> Bio/Search/Hit/PullHitI.pm: # why does this method even exist?!
> Bio/DB/Biblio/soap.pm:use Bio::Biblio; # TBD: ?? WHY SHOULD I DO THIS
> Bio/Graphics/Glyph/dot.pm: # The can() method fails with GD::SVG. Why
> Bio/SeqIO/bsml.pm: # Need to kill object for following code to work...
> Bio/SeqIO/tinyseq.pm: foreach my $subatt(@$seqatt) { # why are there t
> Bio/SeqIO/tinyseq.pm: # NCBI puts refseq ids in TSeq_sid, others in
> Bio/SeqIO/game/featHandler.pm: # Why is CDS coordinate info saved a
> Bio/SeqIO/swiss.pm: # Um, why would this be anything else but PRT?
> Bio/Taxonomy.pm: # taxonomy - why would you be doing things this
> Bio/Seq.pm: # I can't remember why not delegating was ever deemed
> Bio/Cluster/UniGene.pm: # why does NCBI prepend a 'g' to its own
> Bio/LiveSeq/IO/BioPerl.pm:# why array from each_tag_value($qual) ? Whe
> Bio/SearchIO/Writer/HSPTableWriter.pm:# Don't know why this
> Bio/SearchIO/Writer/ResultTableWriter.pm:# Don't know why t
> Bio/Tools/Alignment/Consed.pm:Why was this developed like this? I was
> Bio/Tools/Alignment/Consed.pm: # if there is a member array (why woul
> io/Map/Physical.pm: #*** why doesn't it call Bio::Map::Clone->new ?
> Bio/Map/Physical.pm: #*** why doesn't it call Bio::Map::FPCMarker->
> Bio/Map/Physical.pm: #*** why doesn't it call Bio::Map::Contig->new
> Bio/SeqFeature/Primer.pm: off from those of the idtdna web
> Bio/SeqFeature/Primer.pm: as primer3 does. Don't ask why, I never f
> Bio/Seq/PrimaryQual.pm: Returns : 1 for a valid sequence (WHY? Shouldn
> Bio/Seq/PrimaryQual.pm: Args : a scalar (any scalar, why PrimarySeq
>
> "hack"
>
> Bio/DB/Flat/BinarySearch.pm:# is an awful hack - in reality Michele's
> Bio/DB/WebDBSeqI.pm:# sorry, but this is hacked in because of BioFetch
> Bio/DB/SeqFeature/Store/GFF3Loader.pm: # TEMPORARY HACKS TO SIMPLIFY
> Bio/AlignIO/phylip.pm: #if you use a version of phylip (hacked) tha
> Bio/SearchIO/blast.pm: # bl2seq hackiness... Not sure I lik
> Bio/Tools/Sigcleave.pm:## a quick hack to make sure that we get the sc
> Bio/Tools/Blast/HTML.pm: # This is fine for yeast but not worm. This
> Bio/Tools/Geneid.pm: # then need to perform the hack of extract
> Bio/Root/Utilities.pm: # this is a quick hack to check for availabili
> Bio/Root/Err.pm:objects more eval/die-savvy (but the current strategy
>
>
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>
--
Lincoln D. Stein
Cold Spring Harbor Laboratory
1 Bungtown Road
Cold Spring Harbor, NY 11724
(516) 367-8380 (voice)
(516) 367-8389 (fax)
FOR URGENT MESSAGES & SCHEDULING,
PLEASE CONTACT MY ASSISTANT,
SANDRA MICHELSEN, AT michelse at cshl.edu
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