Run 0 1.1.0 delta

These are detailed notes on changes made between 0 and bioperl-release-1-1-0.

Bio::Tools::Run::Alignment::Clustalw

Migrated code that runs tools to Bio::Tools::Run

Renaming packages for new dir structure

Fixed to PROPER usage of tempfile

More intelligent detection of installed modules (File::Spec) and cleanup of .dnd files

Quoted unquoted string literals used as hash keys.

Migrated to new Bio::Root::RootI chained new

Changed to adopt Bio::Root::IO.

Properly removing tempfiles

Io was not initialized, meaning tempfiles were not cleaned up

Intitialize io -- facilitate tempfile cleanup

The module was requiring input sequences to eq Bio::Seq, changed that to isa->Bio::PrimarySeqI. Clustalw chrashes if the the sequence does not have id() set, undef id() now throws an error.

Checks that seq is a Bio::PrimarySeq and seq->id() is set

Enabled BPbl2seq to read multiple HSPs. Also various documentation fixes.

The code for setting the path to binary was in BEGIN block making it impossible to change from a calling perl script. Moved it into new(). $ENV{CLUSTALDIR} = '/path/to/clustalwdir/'; now works.

The code for setting the path to binary was in BEGIN block making it impossible to change from a calling perl script. Moved it into new(). $ENV{CLUSTALDIR} = '/path/to/clustalwdir/'; now works.

Changed exists_clustal() to use new Bio::Root::IO->exists_exe().

Sweeping change: Bio::Root::RootI is now a pure abstract interface and cannot be inherited from unless you implement several of its abstract methods. Most people will want to inherit from Bio::Root::Root. This change was necessary in order to support Bioperl objects that were not based on hashrefs.

More quiet warning so tests are less chatty

Check to insure defined object before calling ISA

Use the updated PROGRAM exe location information to set the PROGRAM variable

Added method version() $self->isa('Bio::Factory::ApplicationFactoryI')

Debug message now uses the debug method

Verbosity=-1 is same as quiet()

Params should be appended not overwriting

No need for the dir variable

Now can take a program path as arg on the new method, aboids need for ENV variable (ENV still in not to break other people's scripts,etc)

Tweak to clustalw test for falling over correctly

Turn of clustalw debugging

Slightly more intelligent checking for clustalw exe

Merged exe checking from branch

Minor documentation fixes

Bio::Tools::Run::Alignment::DBA

Wrapper object for Ewan Birney's Dna Block Aligner

Changed to use PAML template for find executable insated of ClustalW way

Fixed tempdir, inherit from wrapperbase

Doh left out tempdir bug

Bio::Tools::Run::Alignment::TCoffee

Migrated code that runs tools to Bio::Tools::Run

Renaming packages for new dir structure

Fixed to PROPER usage of tempfile

Extra documentation

More intelligent detection of installed modules (File::Spec) and cleanup of .dnd files

Quoted unquoted string literals used as hash keys.

Migrated to new Bio::Root::RootI chained new

Fixed several doc format bugs.

Correct authors + email for consistency

Changed to adopt Bio::Root::IO.

Fixed TCoffee changes to properly output seqs to temp file when passing in array of seqs

Io was not initialized, meaning tempfiles were not cleaned up

Intitialize io -- facilitate tempfile cleanup

Checks that seq is a Bio::PrimarySeq and seq->id() is set

Enabled BPbl2seq to read multiple HSPs. Also various documentation fixes.

The code for setting the path to binary was in BEGIN block making it impossible to change from a calling perl script. Moved it into new(). $ENV{TCOFFEEDIR} = '/path/to/clustalwdir/'; now works.

The code for setting the path to binary was in BEGIN block making it impossible to change from a calling perl script. Moved it into new(). $ENV{TCOFFEEDIR} = '/path/to/clustalwdir/'; now works.

Changed exists_tcoffee() to use new Bio::Root::IO->exists_exe().

Sweeping change: Bio::Root::RootI is now a pure abstract interface and cannot be inherited from unless you implement several of its abstract methods. Most people will want to inherit from Bio::Root::Root. This change was necessary in order to support Bioperl objects that were not based on hashrefs.

StandAloneBlast now checks for ecoli.nt (is this right?) and TCoffee is a little more verbose

Use the updated PROGRAM exe location information to set the PROGRAM variable

Added version() Implementaion might print an annoying string "FATAL error..." on non-UNIX platforms. Post 1.37 versions of t_coffee will have an explicit -version argument.

Verbosity=-1 is same as quiet()

Version determining regexp protected

Bio::Tools::Run::EMBOSSApplication

Classes for wrapping EMBOSS suite

Claning. Needs code to compare input and ACD options

EMBOSS more runnable and w/ tests

Sweeping change: Bio::Root::RootI is now a pure abstract interface and cannot be inherited from unless you implement several of its abstract methods. Most people will want to inherit from Bio::Root::Root. This change was necessary in order to support Bioperl objects that were not based on hashrefs.

Handle cmd line arguments pointing to a Bio::PrimarySeqI object or array or Bio::PrimarySeqI

Added ability to dump alignments as well as sequences when running an EMBOSS application

Cleanup before each run of an application

Merged changes from trunk to branch

Handle some weird boundary cases

Added ACD parsing and modified EMBOSS modules to check parameters if verbose() is set over zero

Explicitly closing some filehandles appears to do a better job freeing resources

Bio::Tools::Run::EMBOSSacd

Added ACD parsing and modified EMBOSS modules to check parameters if verbose() is set over zero

Bio::Tools::Run::Eponine

wrapper for Eponine.. fixed bug

Inherit from WrapperBase

Cleanup of tempfiles works

Bio::Tools::Run::Genscan

Wrapper for Genscan executable

POX fixes

Fixing wrapper to be in line with ProtML + WrapperBase

Dumb print statement cuzing failed test

Bio::Tools::Run::Phylo::Molphy::ProtML

Added ProtML wrapper - part of Molphy packager for ML tree building

Codeml->protml doc fixes

Code formatting

Cleanup of tempfiles works

Bio::Tools::Run::Phylo::PAML::Codeml

PAML package -- codeml wrapper and test committed

Small doc tweaks and added runnable synopsis

POX fixes

Little fixes: catdir -> catfile, better error matching regexp

Migrate from PAMLBase to WrapperBase

Fix internal parameter name

Copy+paste error

Added additions of .exe for on windows, allow alignment to be specified as a file as well as Bio::Align::AlignI object

API changed a little bit with new parser

Cleanup of tempfiles works

Whoops,one more time, cleanup tempfiles and dirs

Cosmetic code fix

Bio::Tools::Run::Phylo::PAML::PAMLBase

PAML package -- codeml wrapper and test committed

Migrate from PAMLBase to WrapperBase

Bio::Tools::Run::Phylo::PAML::Yn00

Yn00 wrapper for PAML

Return the values as hash of hashes as they are all pairwise calculations - nei and yang results are returned as 2 separate arrays- this is all going to be improved when we abstract the parsing to a separate parser class

POX fixes

Remove debug copyfile

Migrate from PAMLBase to WrapperBase

Handle windows exes

Bio::Tools::Run::Phylo::Phylip::Neighbor

Added Neighbor-Joining wrapper

Fix warnings

Update some of the docs

Move towards wrapperbase type wrappers

Bio::Tools::Run::Phylo::Phylip::ProtDist

Wrapper for phylip program protdist which calculates a distance matrix based on amino acid substitution

Removed superfluous variables

Update some of the docs

Doc fix

Brought in line with WrapperBase

Move towards wrapperbase type wrappers

Doh left out tempdir bug

Bio::Tools::Run::Phylo::Phylip::ProtPars

New wrapper for the phylip program protpars for creating of phylogenetic trees from a multiple alignment

Removed superfluous variables

Move towards wrapperbase type wrappers

Doh left out tempdir bug

Bio::Tools::Run::PiseApplication

Source code for Pise Factory and Application classes. Bio/Factory/Pise.pm: factory Bio/Tools/Run/PiseApplication.pm: base class for all programs Bio/Tools/Run/PiseJob.pm: class for a launched job Bio/Tools/Run/PiseJobParser.pm: XML parser for a job result page

Bio::Tools::Run::PiseApplication::CSR

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::Puzzle

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::abiview

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::addquart

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::align2model

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::alistat

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::antigenic

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::assp

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::backtranseq

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::bambe

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::banana

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::bionj

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::biosed

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::bl2seq

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::blast2

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::blimps

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::blimps_block

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::blimps_matrix

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::boxshade

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::btwisted

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::cai

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::cap

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::cds

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::chaos

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::charge

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::checktrans

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::chips

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::cirdna

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::clique

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::clustalw

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::clustalw_convert

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::codcmp

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::coderet

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::codnocod

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::codontree

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::codonw

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::comalign

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::combat

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::compseq

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::con_filter

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::confmat

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::cons

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::consense

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::consensus

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::cpgplot

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::cpgreport

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::cusp

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::cutseq

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::dan

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::dca

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::decorate

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::degapseq

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::descseq

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::dialign2

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::diffseq

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::digest

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::distmat

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::distquart

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::dnadist

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::dnapars

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::dollop

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::domainer

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::dotmatcher

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::dotpath

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::dottup

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::drawgram

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::drawpyr

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::drawtree

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::dreg

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::druid

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::dsc

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::dssp

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::einverted

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::emma

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::emowse

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::environ

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::eprimer3

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::equicktandem

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::est2genome

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::etandem

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::extractfeat

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::extractseq

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::fasta

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::fastdnaml

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::fastrna

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::filtersites

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::findkm

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::fitch

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::fmtseq

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::freak

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::fuzznuc

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::fuzzpro

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::fuzztran

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::gb2xml

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::geecee

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::genscan

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::getblock

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::getorf

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::gff2ps

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::gibbs

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::gibbs_scan

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::golden

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::grailclnt

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::gruppi

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::helixturnhelix

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::hmmalign

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::hmmbuild

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::hmmcalibrate

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::hmmconvert

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::hmmemit

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::hmmer2sam

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::hmmfetch

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::hmmpfam

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::hmmscore

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::hmmsearch

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::hmoment

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::homology

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::html4blast

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::iep

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::infoalign

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::infoseq

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::interface

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::isochore

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::kitsch

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::lassap

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::lgicsearch

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::lindna

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::listor

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::loadseq

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::lvb

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::makehist

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::map

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::marscan

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::maskfeat

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::maskseq

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::matcher

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::megamerger

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::melting

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::merger

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::mfold

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::mix

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::modelfromalign

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::most

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::mreps

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::msa

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::msbar

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::mspcrunch

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::mview_alig

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::mview_blast

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::mwfilter

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::needle

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::neighbor

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::newcpgreport

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::newcpgseek

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::newseq

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::njdist

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::nnssp

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::notseq

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::nrscope

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::nthseq

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::octanol

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::oddcomp

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::palindrome

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::pam

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::parciquart

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::pars

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::pasteseq

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::patmatdb

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::patmatmotifs

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::patser

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::pepcoil

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::pepinfo

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::pepnet

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::pepstats

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::pepwheel

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::pepwindow

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::pepwindowall

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::pestfind

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::pftools

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::phiblast

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::pima

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::plotcon

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::plotorf

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::plsearch

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::polydot

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::pratt

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::predator

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::preg

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::prettyalign

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::prettyplot

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::prettyseq

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::primersearch

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::primo

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::prodom

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::profit

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::prophecy

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::prophet

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::prose

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::prot_nucml

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::protal2dna

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::protdist

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::protpars

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::pscan

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::psiblast

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::psort2

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::pyramids

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::pyreval

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::qstar

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::readnexus

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::readseq

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::recoder

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::redata

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::remap

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::repeats

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::restover

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::restrict

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::revseq

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::rnadistance

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::rnaeval

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::rnafold

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::rnaga

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::rnaheat

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::rnainverse

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::rnapdist

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::rnasubopt

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::sam2hmmer

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::sampleseqs

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::saps

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::satellites

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::scan_for_matches

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::scope

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::scopparse

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::seqboot

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::seqgen

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::seqmatchall

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::seqsblast

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::seqstat

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::showalign

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::showfeat

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::showorf

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::showseq

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::shuffleseq

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::sigcleave

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::siggen

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::sigscan

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::silent

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::splitter

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::sreformat

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::stretcher

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::stride

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::stssearch

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::supermatcher

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::syco

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::tacg

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::tfscan

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::tipdate

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::tmap

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::toppred

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::transeq

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::treealign

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::trimest

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::trimseq

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::trnascan

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::unroot

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::vectorstrip

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::water

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::weighbor

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::whichdb

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::wise2

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::wobble

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::wordcount

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::wordmatch

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::wublast2

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::xblast

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::xpound

Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseJob

Source code for Pise Factory and Application classes. Bio/Factory/Pise.pm: factory Bio/Tools/Run/PiseApplication.pm: base class for all programs Bio/Tools/Run/PiseJob.pm: class for a launched job Bio/Tools/Run/PiseJobParser.pm: XML parser for a job result page

Bio::Tools::Run::PiseJobParser

Source code for Pise Factory and Application classes. Bio/Factory/Pise.pm: factory Bio/Tools/Run/PiseApplication.pm: base class for all programs Bio/Tools/Run/PiseJob.pm: class for a launched job Bio/Tools/Run/PiseJobParser.pm: XML parser for a job result page

Bio::Tools::Run::Primate

Wrapper for Primate, Guy Slater's exact match finder

Modified how target and queries are fed

Fix tempdir bug

Bio::Tools::Run::Pseudowise

Added fixes and executable checking

Bio::Tools::Run::RemoteBlast

Pure perl (via HTTP) Remote blast submission and retrieval -- see test script for example usage

Quieter tests when verbose == 0, use tempfile for HTML -> text cleanup

Fixed tempfile filehandle handling in retrieve_blast().

Updated to use ncbi Blast.cgi script rather than blast.cgi Text formatting done by cgi rather than HTML tag stripping in module code

Status set to invalid on a failed retrieval

Documentation for retrieve_blast method

Sweeping change: Bio::Root::RootI is now a pure abstract interface and cannot be inherited from unless you implement several of its abstract methods. Most people will want to inherit from Bio::Root::Root. This change was necessary in order to support Bioperl objects that were not based on hashrefs.

Better synopsis and doc update

Merge main trunk changes which include using SearchIO by default and a better SYNOPSIS

SYNOPSIS needed -readmethod argument

Added example to set MATRIX_NAME and NCBI URL for CGI parameters

Bio::Tools::Run::RepeatMasker

Alpha Wrapper for RepeatMasker

Use the determined path to RP when attempting to find the version

Doc fix

POX fixes

Returns SeqFeature::Generic aot FeaturePair

Brought module in-line with new WrapperBase

Returns FeaturePairs now

Dump tempdir bug

Fixed nasty bug coming from Ensembl missing the first line of repeatmasker output file

Bio::Tools::Run::StandAloneBlast

Migrated code that runs tools to Bio::Tools::Run

Renaming packages for new dir structure

Fixed to PROPER usage of tempfile

Migrated to new Bio::Root::RootI chained new

Fixed several doc format bugs. (Why is an unprotected -p in the DESCRIPTION section disallowed and somewhere else it is not? Anyway, perldoc is quiet now.)

Fixed inclusion of 'use Bio::Root::RootI' instead of Bio::Root::Object. Fixed exists_blast() (didn't work due to missing braces).

Updated bptutorial and other documentation

BPlite changes to make BPlite a SeqAnalysisParserI object BPbl2seq now requires named input parameter (no longer can just pass in filehandle reference, must pass in -fh => $filehandle) Assundry changes made to related files to handle these changes

Changed to adopt Bio::Root::IO.

Io was not initialized, meaning tempfiles were not cleaned up - better argument matching

Intitialize io -- facilitate tempfile cleanup

Enabled BPbl2seq to read multiple HSPs. Also various documentation fixes.

Rewrote exists_blast(). Should now work properly on both Unix and MSWin.

Merged over exists_blast() rewrite and other fixes from the main trunk.

Fix to avoid bark in File::Spec.

Small fix to shut up File::Spec.

Sweeping change: Bio::Root::RootI is now a pure abstract interface and cannot be inherited from unless you implement several of its abstract methods. Most people will want to inherit from Bio::Root::Root. This change was necessary in order to support Bioperl objects that were not based on hashrefs.

Nice message printing when blast is not runnable

Find blast executeable in the PATH if possible -- bl2seq might still fail if one does not have .ncbirc set correctly

Use SearchIO not Tools::Blast

Call cleanup upon _setinput call

Io cleanup called at outset of an analyses -- from branch

Merge cleanup io from main trunk

StandAlone tests will detect that data dir is not set and exit test nicely

Remove debug code and tests for blastinstalled more efficiently

Merge changes from branch

Minor documentation fixes

Explicitly closing some filehandles appears to do a better job freeing resources

Bio::Tools::Run::TribeMCL

Wrapper for tribemcl program for protein family clustering using markov flow simulation based on blast scores

Modified the way input is fed.

Takes in HSP as well

More robust program finding

Print data to file right away rather than holding array in memory - there appeared to be a memory leak otherwise anyways with the simple blast file parsing returning an array ref.

Inherit from WrapperBase, inline with ProtML

Makefile.PL

Makefile

Prompt user when Makefile.PL is run

Makefile.PL with sub_test option

examples/pise/blast2.pl

Added t and examples directories together with Pise files

examples/pise/clustalw.pl

Added t and examples directories together with Pise files

examples/pise/dnadist.pl

Added t and examples directories together with Pise files

examples/pise/genscan.pl

Added t and examples directories together with Pise files

examples/pise/needle.pl

Added t and examples directories together with Pise files

examples/pise/toppred.pl

Added t and examples directories together with Pise files