--- name: "Bio::Tools::Run::Alignment::MSAProbs" section: "3pm" platform: "linux" package: "libbio-perl-run-perl" version: "1.7.3-13" release: "Debian 13 (Trixie)" platforms: ["linux"] url: "https://new.carta.tech/Bio::Tools::Run::Alignment::MSAProbs" --- # Bio::Tools::Run::Alignment::MSAProbs(3pm) Object for the calculation of a multiple sequence alignment (MSA) from a set of unaligned sequences using the MSAProbs program ## NAME Bio::Tools::Run::Alignment::MSAProbs - Object for the calculation of a multiple sequence alignment (MSA) from a set of unaligned sequences using the MSAProbs program ## SYNOPSIS ``` # Build a msaprobs alignment factory $factory = Bio::Tools::Run::Alignment::MSAProbs->new(@params); # Pass the factory a list of sequences to be aligned. $inputfilename = 't/cysprot.fa'; # $aln is a SimpleAlign object. $aln = $factory->align($inputfilename); # or where @seq_array is an array of Bio::Seq objects $seq_array_ref = \@seq_array; $aln = $factory->align($seq_array_ref); #There are various additional options and input formats available. #See the DESCRIPTION section that follows for additional details. ``` ## DESCRIPTION MSAProbs is Liu, Schmidt, and Maskell's (2010) alignment program using HMM and partition function posterior probabilities. For more a more in-depth description see the original publication: ``` Liu, Y., Schmidt, B., and Maskell, D. L. (2010) MSAProbs: multiple sequence alignment based on pair hidden Markov models and partition function posterior probabilities. I 26(16): 1958-1964 doi:10.1093/bioinformatics/btq338 -OR- http://bioinformatics.oxfordjournals.org/content/26/16/1958.abstract ``` You can download the source code from http://sourceforge.net/projects/msaprobs/ It is recommended you use at least version 0.9; behaviour with earlier versions is questionable. ### Helping the module find your executable You will need to help MSAProbs to find the 'msaprobs' executable. This can be done in (at least) three ways: ``` 1. Make sure the msaprobs executable is in your path (i.e. 'which msaprobs' returns a valid program) 2. define an environmental variable MSAPROBSDIR which points to a directory containing the 'msaprobs' app: In bash export MSAPROBSDIR=/home/progs/msaprobs or In csh/tcsh setenv MSAPROBSDIR /home/progs/msaprobs 3. include a definition of an environmental variable MSAPROBSDIR in every script that will BEGIN {$ENV{MSAPROBSDIR} = '/home/progs/msaprobs'; } use Bio::Tools::Run::Alignment::MSAProbs; ``` ## FEEDBACK ### Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. ``` bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists ``` ### Support Please direct usage questions or support issues to the mailing list: *bioperl-l@bioperl.org* rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. ### Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: ``` http://bugzilla.open-bio.org/ ``` ## AUTHOR - Jessen Bredeson Email jessenbredeson@berkeley.edu ## CONTRIBUTIONS This MSAProbs module was adapted from the Bio::Tools::Run::Alignment::Muscle module, written by Jason Stajich and almost all of the credit should be given to him. Email jason-at-bioperl-dot-org ## APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a \_ ### program\_name ``` Title : program_name Usage : $factory->program_name() Function: holds the program name Returns: string Args : None ``` ### program\_dir ``` Title : program_dir Usage : $factory->program_dir(@params) Function: returns the program directory, obtained from ENV variable. Returns: string Args : ``` ### version ``` Title : version Usage : exit if $prog->version() < 0.9.4 Function: Determine the version number of the program Example : Returns : float or undef Args : none ``` ### new ``` Title : new Usage : my $msaprobs = Bio::Tools::Run::Alignment::MSAProbs->new(); Function: Constructor Returns : Bio::Tools::Run::Alignment::MSAProbs Args : -outfile => $outname ``` ### run ``` Title : run Usage : my $output = $application->run(\@seqs); Function: Generic run of an application Returns : Bio::SimpleAlign object Args : Arrayref of Bio::PrimarySeqI objects or a filename to run on ``` ### align ``` Title : align Usage : $inputfilename = 't/data/cysprot.fa'; $aln = $factory->align($inputfilename); or $seq_array_ref = \@seq_array; # @seq_array is array of Seq objs $aln = $factory->align($seq_array_ref); Function: Perform a multiple sequence alignment Returns : Reference to a SimpleAlign object containing the sequence alignment. Args : Name of a file containing a set of unaligned fasta sequences or else an array of references to Bio::Seq objects. Throws an exception if argument is not either a string (eg a filename) or a reference to an array of Bio::Seq objects. If argument is string, throws exception if file corresponding to string name can not be found. If argument is Bio::Seq array, throws exception if less than two sequence objects are in array. ``` ### error\_string ``` Title : error_string Usage : $obj->error_string($newval) Function: Where the output from the last analysus run is stored. Returns : value of error_string Args : newvalue (optional) ``` ### infile ``` Title : infile Usage : $prog->infile($filename) Function: get/set the fasta (and only a fasta) file to run on or the array reference containing the Bio::SeqI objects Returns : name of input sequence file or object array ref Args : name of input sequence file or object array ref ``` ### outfile ``` Title : outfile Usage : $prog->outfile($filename) Function: get/set the file to save output to Returns : outfile name if set Args : newvalue (optional) ``` ### annot\_file ``` Title : annot_file Usage : $prog->annot_file($filename) Function: get/set the file name to write the MSA annotation to Returns : filename or undef Args : filename (optional) ``` ### num\_threads ``` Title : num_threads Usage : $prog->num_threads($cores) Function: get/set number of cores on your machine Returns : integer Args : integer (optional; executable auto-detects) ``` ### consistency ``` Title : consistency Usage : $prog->consistency($passes) Function: get/set the number of consistency transformation passes Returns : integer Args : integer 0..5, [default 2] (optional) ``` ### iterations ``` Title : iterations Usage : $prog->iterations($passes) Function: get/set the number of iterative-refinement passes Returns : integer Args : integer 0..1000, [default 10] (optional) ``` ### alignment\_order ``` Title : alignment_order Usage : $prog->alignment_order($bool) Function: specify whether or not to output aligned sequences in alignment order, not input order Returns : boolean Args : boolean [default: off] (optional) ``` ### clustalw ``` Title : clustalw Usage : $prog->clustalw($bool) Function: write output in clustalw format; makes no sense unless outfile() is also specified Returns : boolean Args : boolean [default: off] (optional) ``` ## Bio::Tools::Run::WrapperBase methods ### no\_param\_checks ``` Title : no_param_checks Usage : $obj->no_param_checks($newval) Function: Boolean flag as to whether or not we should trust the sanity checks for parameter values Returns : value of no_param_checks Args : newvalue (optional) ``` ### save\_tempfiles ``` Title : save_tempfiles Usage : $obj->save_tempfiles($newval) Function: Returns : value of save_tempfiles Args : newvalue (optional) ``` ### outfile\_name ``` Title : outfile_name Usage : my $outfile = $msaprobs->outfile_name(); Function: Get the name of the output file from a run (if you wanted to do something special) Returns : string Args : none ``` ### tempdir ``` Title : tempdir Usage : my $tmpdir = $self->tempdir(); Function: Retrieve a temporary directory name (which is created) Returns : string which is the name of the temporary directory Args : none ``` ### cleanup ``` Title : cleanup Usage : $msaprobs->cleanup(); Function: Will cleanup the tempdir directory Returns : none Args : none ``` ### io ``` Title : io Usage : $obj->io($newval) Function: Gets a L object Returns : L Args : none ``` ## Private Methods ### \_run ``` Title : _run Usage : Internal function, not to be called directly Function: makes actual system call to msaprobs program Example : Returns : nothing; msaprobs output is written to a temporary file OR specified output file Args : Name of a file containing a set of unaligned fasta sequences and hash of parameters to be passed to msaprobs ``` ### \_setinput ``` Title : _setinput Usage : Internal function, not to be called directly Function: Create input file for msaprobs program Example : Returns : name of file containing msaprobs data input AND Args : Arrayref of Seqs or input file name ``` ### \_setparams ``` Title : _setparams Usage : Internal function, not to be called directly Function: Create parameter inputs for msaprobs program Example : Returns : parameter string to be passed to msaprobs during align Args : name of calling object ``` ### aformat ``` Title : aformat Usage : my $alignmentformat = $self->aformat(); Function: Get/Set alignment format Returns : string Args : string ```