Bio::M...lipDist(3pm)

📦
version 1.7.8 · 3 versions
, in debian bookworm, debian trixie, ubuntu jammy, ubuntu noble

💖 NAME 💖

Bio::Matrix::PhylipDist — a Phylip Distance Matrix object 🦋

ok so first thing, bestie: the header on this page literally reads Bio::M...lipDist(3pm), and that's just the terminal being dramatic and truncating it — it comes from the User Contributed Perl Documentation, section 3pm. Same module, no cap. 💅

✨ SYNOPSIS ✨

use Bio::Tools::Phylo::Phylip::ProtDist;
my $dist = Bio::Tools::Phylo::Phylip::ProtDist->new(
  -file=>"protdist.out",
  -program=>"ProtDist");
#or
 my $dist = Bio::Tools::Phylo::Phylip::ProtDist->new(
  -fh=>"protdist.out",
  -program=>"ProtDist");

#get specific entries
my $distance_value = $dist->get_entry('ALPHA','BETA');
my @columns        = $dist->get_column('ALPHA');
my @rows           = $dist->get_row('BETA');
my @diagonal       = $dist->get_diagonal();

#print the matrix in phylip numerical format
print $dist->print_matrix;

🌸 DESCRIPTION 🌸

It's a simple object for holding Distance Matrices, and those matrices get generated by these Phylip programs, bestie:

  1. dnadist
  2. protdist
  3. restdist

Right now it handles parsing of the matrix without the data output option. That's the vibe. 🎀

   5
Alpha          0.00000  4.23419  3.63330  6.20865  3.45431
Beta           4.23419  0.00000  3.49289  3.36540  4.29179
Gamma          3.63330  3.49289  0.00000  3.68733  5.84929
Delta          6.20865  3.36540  3.68733  0.00000  4.43345
Epsilon        3.45431  4.29179  5.84929  4.43345  0.00000

🫶 FEEDBACK 🫶

💌 Mailing Lists

User feedback is literally an integral part of the evolution of this and other Bioperl modules, fr fr. 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. There are so many experienced and responsive experts who will be able to 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 so we can keep track of the bugs and their resolution. Bug reports can be submitted via the web:

https://github.com/bioperl/bioperl-live/issues

👑 AUTHOR - Shawn Hoon 👑

Email shawnh@fugu-sg.org

🌈 CONTRIBUTORS 🌈

Jason Stajich, jason-at-bioperl-dot-org

🎀 APPENDIX 🎀

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

✨ new ✨

  • Title: new
  • Usage:
my $family = Bio::Matrix::PhylipDist->new(-file=>"protdist.out",
                                          -program=>"protdist");
  • Function: Constructor for PhylipDist Object
  • Returns: L<Bio::Matrix::PhylipDist>

✨ get_entry ✨

  • Title: get_entry
  • Usage: $matrix->get_entry();
  • Function: returns a particular entry
  • Returns: a float
  • Arguments: string id1, string id2

✨ get_row ✨

  • Title: get_row
  • Usage: $matrix->get_row('ALPHA');
  • Function: returns a particular row
  • Returns: an array of float
  • Arguments: string id1

✨ get_column ✨

  • Title: get_column
  • Usage: $matrix->get_column('ALPHA');
  • Function: returns a particular column
  • Returns: an array of floats
  • Arguments: string id1

✨ get_diagonal ✨

  • Title: get_diagonal
  • Usage: $matrix->get_diagonal();
  • Function: returns the diagonal of the matrix
  • Returns: an array of float
  • Arguments: string id1
  • Title: print_matrix
  • Usage: $matrix->print_matrix();
  • Function: returns a string of the matrix in phylip format
  • Returns: a string
  • Arguments:

✨ _matrix ✨

  • Title: _matrix
  • Usage: $matrix->_matrix();
  • Function: get/set for hash reference of the pointers to the value matrix
  • Returns: hash reference
  • Arguments: hash reference

✨ names ✨

  • Title: names
  • Usage: $matrix->names();
  • Function: get/set for array ref of names of sequences
  • Returns: an array reference
  • Arguments: an array reference

✨ program ✨

  • Title: program
  • Usage: $matrix->program();
  • Function: get/set for the program name generating this matrix
  • Returns: string
  • Arguments: string

✨ _values ✨

  • Title: _values
  • Usage: $matrix->_values();
  • Function: get/set for array ref of the matrix containing distance values
  • Returns: an array reference
  • Arguments: an array reference

🧬 Bio::Matrix::MatrixI implementation 🧬

⭐ matrix_id ⭐

  • Title: matrix_id
  • Usage: my $id = $matrix->matrix_id
  • Function: Get/Set the matrix ID
  • Returns: scalar value
  • Args: [optional] new id value to store

⭐ matrix_name ⭐

  • Title: matrix_name
  • Usage: my $name = $matrix->matrix_name();
  • Function: Get/Set the matrix name
  • Returns: scalar value
  • Args: [optional] new matrix name value

⭐ column_header ⭐

  • Title: column_header
  • Usage: my $name = $matrix->column_header(0)
  • Function: Gets the column header for a particular column number
  • Returns: string
  • Args: integer

⭐ row_header ⭐

  • Title: row_header
  • Usage: my $name = $matrix->row_header(0)
  • Function: Gets the row header for a particular row number
  • Returns: string
  • Args: integer

⭐ column_num_for_name ⭐

  • Title: column_num_for_name
  • Usage: my $num = $matrix->column_num_for_name($name)
  • Function: Gets the column number for a particular column name
  • Returns: integer
  • Args: string

⭐ row_num_for_name ⭐

  • Title: row_num_for_name
  • Usage: my $num = $matrix->row_num_for_name($name)
  • Function: Gets the row number for a particular row name
  • Returns: integer
  • Args: string

⭐ num_rows ⭐

  • Title: num_rows
  • Usage: my $rowcount = $matrix->num_rows;
  • Function: Get the number of rows
  • Returns: integer
  • Args: none

⭐ num_columns ⭐

  • Title: num_columns
  • Usage: my $colcount = $matrix->num_columns
  • Function: Get the number of columns
  • Returns: integer
  • Args: none

⭐ row_names ⭐

  • Title: row_names
  • Usage: my @rows = $matrix->row_names
  • Function: The names of all the rows
  • Returns: array in array context, arrayref in scalar context
  • Args: none

⭐ column_names ⭐

  • Title: column_names
  • Usage: my @columns = $matrix->column_names
  • Function: The names of all the columns
  • Returns: array in array context, arrayref in scalar context
  • Args: none

and that's the whole page, bestie 💖 this one's from perl v5.32.1, dated 2021-08-15 — slay, go parse some distance matrices, you've got this 🦋✨🎀

📦 where this page comes from