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

🦋 NAME 🦋

okay bestie, so this page — from the User Contributed Perl Documentation — is all about Bio::Tools::Run::Phylo::Phylip::ProtPars, which is an object for creating a Bio::Tree object from a multiple alignment file or a SimpleAlign object. 💖

and literally right there in the name section, the vibe check says:

14 Nov 2002 Shawn Works with Phylip version 3.6

so yeah, vintage era, works with Phylip version 3.6. periodt.

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✨ SYNOPSIS ✨

like, here's the whole flow, 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 = $factory->run($inputfilename); # $aln is a SimpleAlign object.

#Create the Tree
#using a threshold value of 30 and id name lengths limit of 30
#note to use id name length greater than the standard 10 in protpars,
# you will need to modify the protpars source code
$tree_factory = Bio::Tools::Run::Phylo::Phylip::ProtPars->
   new(idlength=>30,threshold=>10,jumble=>"17,10",outgroup=>2);
$tree = $tree_factory->run($aln);

#Or one can pass in a file name containing a multiple alignment
#in phylip format:

$tree_factory =
  Bio::Tools::Run::Phylo::Phylip::ProtPars->new(idlength=>30,threshold=>10);
$tree = $tree_factory->run("/usr/users/shawnh/COMPARA/prot.phy");

# 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 original names
# Step 2. Run ProtPars:
   $tree = $protpars_factory->run($aln_safe);    #  Use $aln_safe instead of $aln
# Step 3. Retrieve orgininal OTU names:
   use Bio::Tree::Tree;
   my @nodes=$tree->get_nodes();
       foreach my $nd (@nodes){
          $nd->id($ref_name->{$nd->id_output}) if $nd->is_Leaf;
       }

lowkey important, bestie: that comment up there about idlength is fr fr — if you wanna use id name length greater than the standard 10 in protpars, you will need to modify the protpars source code. not me telling you to go edit source, but. 😭

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🌸 PARAMTERS FOR PROTPARS COMPUTATION 🌸

(yes, "PARAMTERS" — the typo is iconic, we keep it, we don't fix it, we honor it 💅)

🌈 THRESHOLD

• Title: THRESHOLD
• Description: (optional)

so this one sets a threshold such that if the number of steps counted in a character is higher than the threshold, it will be taken to be the threshold value rather than the actual number of steps. you should use a positive real number greater than 1. and pls pls pls, please see the documetation from the phylip package for more information. 🫶

🎀 OUTGROUP

• Title: OUTGROUP
• Description: (optional)

this specifies which species is to be used to root the tree by having it become the outgroup. input values are integers specifying which species to use. Defaults to 1. 👑

⭐ JUMBLE

• Title: JUMBLE
• Description: (optional)

this enables you to tell the program to use a random number generator to choose the input order of species. input values is of the format: seed,iterations eg 17,10.

• seed: an integer between 1 and 32767 and of the form 4n+1 which means that it must give a remainder of 1 when divided by 4. each different seed leads to a different sequence of addition of species. by simply changing the random number seed and re-running programs one can look for other, and better trees. 🌱
• iterations: for a value of 10, this will tell the program to try ten different orders of species in constructing the trees, and the results printed out will reflect this entire search process (that is, the best trees found among all 10 runs will be printed out, not the best trees from each individual run). the way that it aggregates across runs instead of per-run is genuinely such a slay detail, iykyk.

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💜 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. fr fr, they mean it.

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. 🥺 like give them the full context, they'll eat.

🎀 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/

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👑 AUTHOR - Shawn Hoon 👑

Email shawnh@fugu-sg.org

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🌈 CONTRIBUTORS 🌈

Email jason-AT-bioperl_DOT_org

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✨ APPENDIX ✨

the rest of the documentation details each of the object methods. internal methods are usually preceded with a _ — so if you see a leading underscore, that's your sign it's backstage, not main character energy. 💅

🧚 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:

💖 idlength

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

ngl the Function line is literally empty in the original. we don't invent facts here. it's giving mystery. 🫶

⭐ run

• Title: run
• Usage:

$inputfilename = 't/data/prot.phy';
$tree = $factory->run($inputfilename);

or

$seq_array_ref = \@seq_array; @seq_array is array of Seq objs
$aln = $factory->run($seq_array_ref);
$tree = $treefactory->run($aln);

• Function: Create a protpars tree from a SimpleAlign object
• Example:
• Returns: Bio::Tree object
• 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. so like, feed it the right thing or it WILL be dramatic about it. 💀

🎀 create_tree

• Title: create_tree
• Usage:

$inputfilename = 't/data/prot.phy';
$tree = $factory->create_tree($inputfilename);

or

$seq_array_ref = \@seq_array; @seq_array is array of Seq objs
$aln = $factory->align($seq_array_ref);
$tree = $treefactory->create_tree($aln);

• Function: Create a protpars tree from a SimpleAlign object
• Example:
• Returns: Bio::Tree object
• 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. same energy as run, bestie, don't be shocked. ✨

🦋 _run

• Title: _run
• Usage: Internal function, not to be called directly
• Function: makes actual system call to protpars program
• Example:
• Returns: Bio::Tree object
• Args: Name of a file containing a set of multiple alignments in Phylip format and a parameter string to be passed to protpars

do NOT call this directly, it says it right there. it's an internal function. respect the boundary. 🙈

💜 _setinput()

• Title: _setinput
• Usage: Internal function, not to be called directly
• Function: Create input file for protpars program
• Example:
• 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 protpars program
• Example:
• Returns: parameter string to be passed to protpars
• Args: name of calling object

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and that's the whole page, bestie! 🎀 this documentation shipped with perl v5.36.0, dated 2023-01-22, and the manual page itself is Bio::T...otPars(3pm) from the User Contributed Perl Documentation. go build a tree, you've got this. 💖🌱🦋