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

✨ NAME ✨

Bio::Tools::Run::Alignment::Gmap — it's a wrapper for running gmap, bestie. That's the whole job. 💅

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🦋 SYNOPSIS 🦋

okay so here's the vibe, literally copy-paste this energy:

use Bio::Tools::Run::Alignment::Gmap;
use Bio::SeqIO;

my $sio = Bio::SeqIO->new(-file=>$filename ,-format=>'fasta');
my @seq;
while(my $seq = $sio->next_seq()){
  push @seq,$seq;
}
my $mapper =Bio::Tools::Run::Gmap->new();
my $result = $mapper->run(\@seq);

like. look at that. she runs. 👑

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🌸 DESCRIPTION 🌸

So this is the Bioperl-run wrapper around gmap. If you wanna know about gmap itself, go peek at <http://www.gene.com/share/gmap/> — that's where the lore lives.

Here's what it wants from you: a reference to an array of bioperl SeqI objects. And here's what it gives back: a reference to a filehandle that you can read the gmap output from. Give seqs, get a filehandle. transactional. iconic. 🫶

Wanna set the genome database name yourself? The default is NHGD_R36, and you change it with the genome_db() method. No cap. You can also set the flags that get passed to gmap yourself using the flags() method — those default to '-f 9 -5 -e'.

And if you're feeling extra: the name of the gmap executable can be overridden with the program_name() method, and the directory where that executable lives can be overridden with the program_dir() method. customization queen. 💖

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💌 FEEDBACK 💌

📬 Mailing Lists

User feedback is an integral part of the evolution of this and other Bioperl modules. That's literally what they said, and honestly? true. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. fr fr.

bioperl-l@bioperl.org                  - General discussion
http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

🐛 Reporting Bugs

Report bugs to the Bioperl bug tracking system so we can keep track of the bugs and their resolution — like a little bug diary, but useful. Bug reports can be submitted via the web:

http://redmine.open-bio.org/projects/bioperl/

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👑 AUTHOR - George Hartzell 👑

Email hartzell@alerce.com

Describe contact details here

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🎀 CONTRIBUTORS 🎀

Additional contributors names and emails here

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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 an underscore, bestie, that's the backstage area, not the main stage. 🙈

⭐ new

Title   : new
Usage   : my $obj = new Bio::Tools::Run::Alignment::Gmap();
Function: Builds a new Bio::Tools::Run::Alignment::Gmap object
Returns : an instance of Bio::Tools::Run::Alignment::Gmap
Args    :

Builds you a brand new Bio::Tools::Run::Alignment::Gmap object, and hands you back an instance of one. The Args line is empty — she takes nothing. a mystery. a legend. ✨

⭐ version

Title   : version
Usage   : print "gmap version: " . $mapper->version() . "\n";
Function: retrieves and returns the version of the gmap package.
Example :
Returns : scalar string containing the version number.  Probably looks
          like YYYY-MM-DD.
Args    : none.

It goes and fetches the version of the gmap package for you and returns it. You get a scalar string with the version number — probably looks like YYYY-MM-DD, which is a little unhinged as a versioning scheme but we support her. No args. 💜

⭐ program_name

Title   : program_name
Usage   : $mapper->program_name('gmap-dev');
          my $pname = $mapper->program_name();
Function: sets/gets the name of the program to run.
Returns : string representing the name of the executable.
Args    : [optional] string representing the name of the executable
          to set.

Sets and gets the name of the program to run. You get back a string representing the name of the executable. Pass the optional string arg to set it, skip it to just read it. double duty icon. 💅

⭐ program_dir

Title   : program_dir
Usage   : $mapper->program_dir('/usr/local/sandbox/gmap/bin');
          my $pdir = $mapper->program_dir();
Function: sets/gets the directory path in which
          to find the gmap executable.
Returns : string representing the path to the directory.
Args    : [optional] string representing the directory path to set.

Sets/gets the directory path where the gmap executable can be found. Returns a string of the path. The arg is optional — give it a path to set, or leave it out and just vibe with the getter. 🦋

⭐ input_file

Title   : input_file
Usage   : $mapper->input_file('/tmp/moose.fasta');
          my $filename = $mapper->input_file();
Function: sets/gets the name of a file containing sequences
          to be mapped.
Returns : string containing the name of the query sequence.
Args    : [optional] string representing the directory path to set.

Sets/gets the name of a file that holds the sequences you wanna map. Returns a string with the name of the query sequence. Arg is optional — set it or get it, your call. yes the doc calls it a directory path, we're just repeating what it says, don't come for me. 😭

⭐ genome_db

Title   : genome_db
Usage   : $mapper->genome_db('NHGD_R36');
          my $genome_db = $mapper->genome_db();
Function: sets/gets the name of the genome database, this will be
          passed to gmap using its '-d' flag.
Returns : name of the genome database.
Args    : [optional] string representing the genome db to set.

Sets/gets the name of the genome database. Heads up: this gets passed to gmap using its -d flag. You get back the name of the genome database. Optional string arg to set it. simple, clean, effective. 🌈

⭐ flags

Title   : flags
Usage   : $mapper->flags('-A -e -5');
          my $flags = $mapper->flags();
Function: sets/gets the flags that will be passed to gmap.
Returns : the current value of the flags that will be passed to gmap.
Args    : [optional] the flags to set.

Sets/gets the flags that get passed to gmap. Returns the current value of those flags. Optional arg is the flags you wanna set. she's holding your flags. respect her. 🔥

⭐ run

Title   : run
Usage   : $mapper->run()
Function: runs gmap
Example :
Returns : a file handle, opened for reading, for gmap's output.
Args    : An array of references query sequences (as Bio::Seq objects)

It runs gmap. That's it, that's the function. You get back a file handle, opened for reading, holding gmap's output. The args are an array of references query sequences — as Bio::Seq objects. go girl give us everything. 👑

⭐ _build_fasta_input_file

Title   : _build_fasta_input_file
Usage   : my $seq_file = $self->_build_fasta_input_file(@_);
Function:
Example :
Returns : The name of the temporary file that contains the sequence.
Args    : A reference to an array of Bio::Seq objects.

Underscore alert 🚨 — internal method, backstage pass only. It returns the name of the temporary file that contains the sequence. Args: a reference to an array of Bio::Seq objects. The Function: and Example: lines are empty in the original, so we're leaving them empty, no inventing lore here bestie. 💖

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and that's the whole page!! this was Bio::T...::Gmap(3pm), served up in User Contributed Perl Documentation, and it's living on perl v5.36.0, dated 2023-01-22. periodt. 💅✨🫶