Untested Modules in BioPerl

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A list of modules with no tests (or if commented on, insufficient tests).

Contents

Bio::Tools::Profile

Bio::Tools::Prints

As noted by Torsten, the current output for FingerPRINTScanII ('Prints') may not parse correctly. Does it need to be updated or deprecated?

Bio::Tools::Fgenesh

Bio::Tools::Tmhmm

Re-wrote, documented and tested. --Torsten 18:32, 27 September 2006 (EDT)

Bio::Tools::Blat

Should probably use Bio::SearchIO::blast or Bio::SearchIO::psl (where appropriate) instead. --Chris Fields 12:41, 10 April 2007 (EDT)

Bio::Tools::Coil

Bio::Tools::ERPIN

Done. --Chris Fields 20:19, 27 September 2006 (EDT)

Bio::Tools::ESTScan

Bio::Tools::Eponine

Bio::Tools::Fgenesh

Bio::Tools::Grail

Bio::Tools::HMM

Tests explicitly require parts of Bioperl-ext and XS extensions; may not play well with some OS's. --Chris Fields 12:59, 10 April 2007 (EDT)

Bio::Tools::Hmmpfam

Not sure how well this is supported. Should probably use Bio::SearchIO::hmmer, Bio::SearchIO::hmmer_pull instead. --Chris Fields 13:03, 10 April 2007 (EDT)

Bio::Tools::Prints

Bio::Tools::Profile

Bio::Tools::PrositeScan

Bio::Tools::Seg

Rewritten, added docs and tests -- Torsten 23:48, 27 September 2006 (EDT)

Bio::Tools::Signalp

  • Torsten has taken this one.
  • Tests now added for parsing Signalp v.2 and v.3. More tests will likely be added when possible. --Chris Fields 12:51, 10 April 2007 (EDT)

Bio::Tools::WWW

Deprecated. No tests needed. --Chris Fields 12:44, 10 April 2007 (EDT)

Bio::Tools::WebBlat

Deprecated. No tests needed. --Chris Fields 12:44, 10 April 2007 (EDT)

Bio::Tools::dpAlign

Bio::Tools::isPcr

Bio::Tools::pSW

Tests explicitly require parts of Bioperl-ext and XS extensions; may not play well with some OS's. --Chris Fields 12:49, 10 April 2007 (EDT)

Bio::Tree::Draw::Cladogram

Bio::Tree::NodeNHX

Bio::Index::Abstract

Bio::Index::AbstractSeq

Bio::Index::Fastq

Bio::Index::Hmmer

Bio::SeqFeature::Gene::Intron

Bio::SeqFeature::Gene::NC_Feature

Bio::SeqFeature::Gene::Promoter

Bio::SeqFeature::PositionProxy

Bio::SeqFeature::SiRNA::Oligo

Bio::SeqFeature::SiRNA::Pair

Bio::SeqFeature::Similarity

Bio::Root::Vector

Removed from CVS. No need for tests. --Chris Fields 12:35, 10 April 2007 (EDT)

Bio::Restriction::IO::bairoch

Not sure what the progress on this is; the last I heard was that the implementation was being reworked... --Chris Fields 13:05, 10 April 2007 (EDT)

Bio::Tools::SiRNA::Ruleset::saigo

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