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

🦋 NAME 🦋

Bio::Tools::Run::Alignment::StandAloneFasta — the object that runs the Fasta3 programs locally on your own machine. That's (t)fasta3, (t)fastx3, (t)fasty3, and ssearch3. (The page header is truncated to Bio::T...neFasta(3pm) because Unix manual titles are cowards, but bestie, this is the full name 💅)

---

✨ SYNOPSIS ✨

#!/usr/bin/perl
use Bio::Tools::Run::Alignment::StandAloneFasta;
use Bio::SeqIO;
use strict;
my @arg=(
'b' =>'15',
'O' =>'resultfile',
'H'=>'',
'program'=>'fasta34'
);

my $factory=Bio::Tools::Run::Alignment::StandAloneFasta->new(@arg);
$factory->ktup(1);

$factory->library('p');

#print result file name
print $factory->O;

my @fastreport=$factory->run($ARGV[0]);

foreach  (@fastreport) {
      print "Parsed fasta report:\n";
  my $result = $_->next_result;
  while( my $hit = $result->next_hit()) {
     print "\thit name: ", $hit->name(), "\n";
       while( my $hsp = $hit->next_hsp()) {
       print "E: ", $hsp->evalue(), "frac_identical: ",
      $hsp->frac_identical(), "\n";
       }
    }
  }

 #pass in seq objects
 my $sio = Bio::SeqIO->new(-file=>$ARGV[0],-format=>"fasta");
 my $seq = $sio->next_seq;
 my @fastreport=$factory->run($ARGV[0]);

---

💖 DESCRIPTION 💖

This wrapper works with version 3 of the FASTA program package. The citations, no cap, straight from the source:

• W. R. Pearson and D. J. Lipman (1988), "Improved Tools for Biological Sequence Analysis", PNAS 85:2444-2448 (Pearson and Lipman, 1988)
• W. R. Pearson (1996) "Effective protein sequence comparison" Meth. Enzymol. 266:227-258 (Pearson, 1996)
• Pearson et. al. (1997) Genomics 46:24-36 (Zhang et al., 1997)
• Pearson, (1999) Meth. in Molecular Biology 132:185-219 (Pearson, 1999)

Version 3 of the FASTA packages contains many programs for searching DNA and protein databases and one program (prss3) for evaluating statistical significance from randomly shuffled sequences. Iconic behaviour honestly.

Fasta is available at ftp://ftp.virginia.edu/pub/fasta 🫶

---

🌈 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.

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. (The way that "reponsive" is spelled in here? Not me noticing. Anyway 💀)

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/

---

👑 AUTHOR - Tiequan Zhang 👑

• Adapted for bioperl by Shawn Hoon
• Enhanced by Jason Stajich

Email:

tqzhang1973@yahoo.com
shawnh@fugu-sg.org
jason-at-bioperl.org

---

🧚 Appendix 🧚

The rest of the documendation details each of the object methods. Internal methods are preceded with a underscore.

---

program_name

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

executable

• Title: executable
• Usage: my $exe = $blastfactory->executable('blastall');
• Function: Finds the full path to the 'codeml' executable
• Returns: string representing the full path to the exe
• Args:
  • [optional] name of executable to set path to
  • [optional] boolean flag whether or not warn when exe is not found

program_dir

• Title: program_dir
• Usage: $factory->program_dir(@params)
• Function: returns the program directory, obtained from ENV variable.
• Returns: string
• Args: (none)

run

• Title: run
• Usage:

my @fasta_object = $factory->($input,$onefile);

where $factory is the name of executable FASTA program; $input is file name containing the sequences in the format of fasta or Bio::Seq object or array of Bio::Seq object; $onefile is 0 if you want to save the outputs to different files. Default: outputs are saved in one file.

• Function: Attempts to run an executable FASTA program and return array of fasta objects containing the fasta report
• Returns: aray of fasta report object. If the user specify the output file(s), the raw fasta report will be saved
• Args:
  • sequence object OR array reference of sequence objects
  • filename of file containing fasta formatted sequences

library

• Title: library
• Usage: my $lb = $self->library
• Function: Fetch or set the name of the library to search against
• Returns: The name of the library
• Args: No argument if user wants to fetch the name of library file; A letter or a string of letter preceded by %; (e.g. P or %pn, the letter is the character in the third field of any line of fastlibs file) or the name of library file (if environmental variable FASTLIBS is not set); if user wants to set the name of library file to search against

output

• Title: output
• Usage: $obj->output($newval)
• Function: The output directory if we want to use this
• Example: (none)
• Returns: value of output (a scalar)
• Args: on set, new value (a scalar or undef, optional)

ktup

• Title: ktup
• Usage: my $ktup = $self->ktup
• Function: Fetch or set the ktup value for executable FASTA programs
• Example: (none)
• Returns: The value of ktup if defined, else undef is returned
• Args: No argument if user want to fetch ktup value; A integer value between 1-6 if user want to set the ktup value

_setinput

• Title: _setinput
• Usage: Internal function, not to be called directly
• Function: Create input file(s) for Blast executable
• Example: (none)
• Returns: array of Bio::Seq object reference
• Args: Seq object reference or input file name

_exist

• Title: _exist
• Usage: Internal function, not to be called directly
• Function: Determine whether a executable FASTA program can be found. Cf. the DESCRIPTION section of this POD for how to make sure for your FASTA installation to be found. This method checks for existence of the blastall executable in the path.
• Returns: 1 if FASTA program found at expected location, 0 otherwise.
• Args: none

_setparams

• Title: _setparams
• Usage: Internal function, not to be called directly
• Function: Create parameter inputs for FASTA executable
• Returns: part of parameter string to be passed to FASTA program
• Args: none

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And that's the whole page bestie!! This one shipped as part of perl v5.36.0, dated 2023-01-22, filed under User Contributed Perl Documentation with the ever-mysterious title Bio::T...neFasta(3pm). Go run some FASTA searches, you've got this 💖✨🎀🦋🌸💅🫶