Bio::T...SeqBoot(3pm)

📦
version 1.7.3 · 3 versions
, in debian bookworm, ubuntu noble

🌸 NAME 🌸

Bio::Tools::Run::Phylo::Phylip::SeqBoot — Wrapper for the phylip program SeqBoot. aka the Bio::T...SeqBoot(3pm) page from User Contributed Perl Documentation, bestie 💖

✨ SYNOPSIS ✨

okay so bestie, first you make a SimpleAlign object, then you use seqboot to generate bootstrap alignments, and if you don't want PHYLIP truncating your sequence names, there's a whole three-step ritual. Here's the code, verbatim, no cap:

        #Create a SimpleAlign object
        @params = ('ktuple' => 2, 'matrix' => 'BLOSUM');
        $factory = Bio::Tools::Run::Alignment::Clustalw->new(@params);
        $inputfilename = 't/data/cysprot.fa';
        $aln = $factory->align($inputfilename); # $aln is a SimpleAlign object.

        # Use seqboot to generate bootstap alignments
        my @params = ('datatype'=>'SEQUENCE','replicates'=>100);
        my $seq = Bio::Tools::Run::Phylo::Phylip::SeqBoot->new(@params);

        my $aln_ref = $seq->run($aln);

        my $aio = Bio::AlignIO->new(-file=>">alignment.bootstrap",-format=>"phylip");
        foreach my $ai(@{$aln_ref}){
               $aio->write_aln($ai);
        }

        # To prevent PHYLIP from truncating sequence names:
        # Step 1. Shelf the original names:
        my ($aln_safe, $ref_name)=                  #  $aln_safe has serial names
                   $aln->set_displayname_safe();    #  $ref_name holds orginal names
        # Step 2. Run PHYLIP programs:
        $aln_ref = $seq->run($aln_safe);            #  Use $aln_safe instead of $aln
        # Step 3. Retrieve orgininal names
        $aio = Bio::AlignIO->new(
                   -file=>">alignment.bootstrap",
                   -format=>"fasta");               #  FASTA output to view full names
        foreach my $ai(@{$aln_ref}){
               my $new_aln=$ai->restore_displayname($ref_name); #  Restore names
               $aio->write_aln($new_aln);
        }

🦋 DESCRIPTION 🦋

So this is a wrapper for seqboot from the phylip package by Joseph Felsentein. It's giving "I just want to bootstrap my data sets" energy. 💅

Taken from the phylip doc, and I quote:

"SEQBOOT is a general boostrapping tool. It is intended to allow you to generate multiple data sets that are resampled versions of the input data set. SEQBOOT can handle molecular sequences, binary characters, restriction sites, or gene frequencies."

More documentation on using seqboot and setting parameters may be found in the phylip package. fr fr.

VERSION Support: This wrapper currently supports v3.5 of phylip. There is also support for v3.6 although this is still experimental as v3.6 is still under alpha release and not all functionalities maybe supported. so v3.6 is giving alpha, bestie — not everything might work 😭

🔥 PARAMETERS FOR SEQBOOT 🔥

okay so these are the knobs you can turn. turn them wisely. ✨

🎀 MODEL 🎀

  • Title: DATATYPE
  • Description: (optional)
    • This program supports 3 different datatypes
      • SEQUENCE: Molecular Sequences
      • MORPH: Discrete Morphological Characters
      • REST: Restriction Sites
      • GENEFREQ: Gene Frequencies
  • Defaults to SEQUENCE

🎀 PERMUTE 🎀

  • Title: PERMUTE
  • Description: (optional)
    • 3 different resampling methods are available:
      • BOOTSTRAP: creating a new data set by sampling N characters randomly with replacement. The resulting data set has the same size as the original, but some characters have been left out and others are duplicated.
      • JACKKNIFE: Delete-half-jackknifing. It involves sampling a random half of the characters, and including them in the data but dropping the others. The resulting data sets are half the size of the original, and no characters are duplicated.
      • PERMUTE: Permuting species within characters. It involves permuting the columns of the data matrix separately. This produces data matrices that have the same number and kinds of characters but no taxonomic structure.
  • Defaults to BOOTSTRAP

🎀 REPLICATES 🎀

  • Title: REPLICATES
  • Description: (optional)
    • This options allows the user to set the number of replicate data sets. Most statisticians would be happiest with 1000 to 10,000 replicates in a bootstrap, but 100 gives a good rough picture.
  • Defaults to 100

🎀 ALLELES 🎀

  • Title: ALLELES
  • Description: (optional)
    • This option is to be used with gene frequencies datatype option to specify that all alleles at each locus are in the input file.
  • Defaults to NULL

💌 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. 🫶

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. no cap, they want the tea ☕

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://redmine.open-bio.org/projects/bioperl/ — go off, bestie 🐛

👑 AUTHOR - Shawn Hoon 👑

Email: shawnh@fugu-sg.org — thank you Shawn, you ate 👑

📚 APPENDIX 📚

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _. iykyk.

🌟 program_name 🌟

  • Title: program_name
  • Usage: >program_name()
  • Function: holds the program name
  • Returns: string
  • Args: None

🌟 program_dir 🌟

  • Title: program_dir
  • Usage: ->program_dir()
  • Function: returns the program directory, obtained from ENV variable.
  • Returns: string
  • Args: (empty)

🌟 idlength 🌟

  • Title: idlength
  • Usage: $obj->idlength ($newval)
  • Function: (empty)
  • Returns: value of idlength
  • Args: newvalue (optional)

🌟 run 🌟

  • Title: run
  • Usage:
$inputfilename = 't/data/prot.phy';
$matrix= $seqboot_factory->run($inputfilename);

or

$seq_array_ref = \@seq_array; @seq_array is array of Seq objs
$aln = $clustalw_factory->align($seq_array_ref);
$aln_ref = $SeqBootfactory->run($aln);
  • Function: Create bootstrap sets of alignments
  • Example: (empty)
  • Returns: an array ref of Bio::SimpleAlign
  • Args: Name of a file containing a multiple alignment in Phylip format or an SimpleAlign object
  • Throws an exception if argument is not either a string (eg a filename) or a Bio::SimpleAlign object. If argument is string, throws exception if file corresponding to string name can not be found.

🌟 _run 🌟

  • Title: _run
  • Usage: Internal function, not to be called directly
  • Function: makes actual system call to SeqBoot program
  • Example: (empty)
  • Returns: an array ref of Bio::SimpleAlign
  • Args: Name of a file containing a set of multiple alignments in Phylip format and a parameter string to be passed to SeqBoot

🌟 _setinput() 🌟

  • Title: _setinput
  • Usage: Internal function, not to be called directly
  • Function: Create input file for SeqBoot program
  • Example: (empty)
  • Returns: name of file containing a multiple alignment in Phylip format
  • Args: SimpleAlign object reference or input file name

🌟 _setparams() 🌟

  • Title: _setparams
  • Usage: Internal function, not to be called directly
  • Function: Create parameter inputs for SeqBoot program
  • Example: (empty)
  • Returns: parameter string to be passed to SeqBoot
  • Args: name of calling object

Bio::Tools::Run::Wrapper 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: (empty)
  • Returns: value of save_tempfiles
  • Args: newvalue (optional)

outfile_name

  • Title: outfile_name
  • Usage: my $outfile = $SeqBoot->outfile_name();
  • Function: Get/Set the name of the output file for this run (if you wanted to do something special)
  • Returns: string
  • Args: [optional] string to set value to

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: $codeml->cleanup();
  • Function: Will cleanup the tempdir directory after a SeqBoot run
  • Returns: none
  • Args: none

io

  • Title: io
  • Usage: $obj->io($newval)
  • Function: Gets a Bio::Root::IO object
  • Returns: Bio::Root::IO
  • Args: none

made with 💖 by perl v5.36.0 on 2023-01-22, and this was Bio::T...SeqBoot(3pm) — bye bestie, slay! 💅✨

📦 where this page comes from