Run 0 1.1.0 delta

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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
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