Bio::S...owseGFF(3pm)

💅 NAME 💅

Bio::SearchIO::Writer::GbrowseGFF — bestie, it's the interface for spitting out your parsed search results in Gbrowse GFF format. That's it. That's the whole job. And it does it gorgeously. ✨

Oh also, hi, you're reading the page for Bio::S...owseGFF(3pm) — yeah the name got truncated in the header, it's giving ✨mysterious✨, but it's us. 🫶

---

🎀 SYNOPSIS 🎀

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

use Bio::SearchIO;
my $in = Bio::SearchIO->new(-file   => 'result.blast',
                           -format => 'blast');
my $out = Bio::SearchIO->new(-output_format  => 'GbrowseGFF',
                            -output_cigar   => 1,
                            -output_signif  => 1,
                            -file           => ">result.gff");
while( my $r = $in->next_result ) {
  $out->write_result($r);
}

like. read the blast, write the gff, loop. main character pipeline behavior fr fr. 🔥

---

🌸 DESCRIPTION 🌸

This writer takes a Search::Result object and turns it into Gbrowse flavour GFF. That's the whole personality. Lowkey iconic. 💖

---

👑 AUTHOR 👑

Mark Wilkinson

Email: markw-at-illuminae-dot-com

(yeah, the -at- and -dot- are intentional, we're being cute about spam bots, respect it 🎀)

---

🦋 CONTRIBUTORS 🦋

• Susan Miller — sjmiller at email-DOT-arizon-DOT-edu
• Jason Stajich — jason at bioperl-dot-org

shoutout to the girlies who made this happen 💜

---

💌 FEEDBACK 💌

📬 Mailing Lists

ngl, user feedback is a whole integral part of how this module and the other Bioperl modules evolve. So send your comments and suggestions, preferably to the Bioperl mailing list. Your participation is much appreciated. 🥹

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

🫶 Support

okay so listen — please direct usage questions and support issues to the mailing list:

bioperl-l@bioperl.org

...rather than sliding into the module maintainer's DMs directly. The way that so many experienced and responsive experts will be able to look at the problem and quickly address it — that's the whole point. And please include a thorough description of the problem with code and data examples if at all possible. give us the ✨lore✨, not just "it broke". 🙈

🐛 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

---

📖 APPENDIX 📖

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

✨ new

Title   : new
Usage   : my $obj = Bio::SearchIO::Writer::GbrowseGFF->new(@args);
Function: Builds a new Bio::SearchIO::Writer::GbrowseGFF object
Returns : an instance of Bio::SearchIO::Writer::GbrowseGFF
Args    :  -e_value => 10   : set e_value parsing cutoff (default undef)
           (note the -e_value flag is deprecated.)

builds you a whole new writer object, slay. the args are:

• -e_value => 10 — sets the e_value parsing cutoff, default is undef.

🚨 heads up bestie: the -e_value flag is deprecated. still there, still works, but it's giving legacy. 💀

💫 to_string

Purpose   : Produce the Gbrowse format GFF lines for a Result
Usage     : print $writer->to_string( $result_obj, @args);
Argument  : $result_obj = A Bio::Search::Result::ResultI object
            -version => 1|2|2.5|3  ; the GFF format you want to output (default 3)
            -match_tag => match|cDNA_match|EST_match|translated_nucleotide_match
                          nucleotide_to_protein_match|nucleotide_motif
                          This is the SO term to be placed in GFF column 3.
            -prefix => String to prefix the group by, default is EST
                       (see %Defaults class variable) A default can also
                       be set on object init
Returns   : String containing data for each search Result or any of its
          : sub-objects (Hits and HSPs).
Throws    : n/a

breaking that down for you bestie:

• $result_obj — a Bio::Search::Result::ResultI object. that's the input, that's the main character.
• -version => 1|2|2.5|3 — the GFF format you want to output. default is 3.
• -match_tag — one of match, cDNA_match, EST_match, translated_nucleotide_match, nucleotide_to_protein_match, or nucleotide_motif. This is the SO term that gets placed in GFF column 3. yes, column three specifically. very precise of her. 💅
• -prefix — a String to prefix the group by, default is EST (peep the %Defaults class variable). A default can also be set on object init, if you're fancy like that. ✨

Returns: a String containing data for each search Result or any of its sub-objects (Hits and HSPs).

Throws: n/a. nothing. she's chill. 😌

🎀 start_report

Title   : start_report
Usage   : $self->start_report()
Function: has no function, returns nothing
Returns : empty string
Args    : none

no cap, this one has no function. it returns nothing. it returns an empty string. there are no args. it's literally just there. and honestly? we respect the commitment. 🌈

🌸 end_report

Title   : end_report
Usage   : $self->end_report()
Function: has no function, returns nothing
Returns : empty string
Args    : none

same situation bestie — no function, returns nothing, returns an empty string, no args. a matching set. 🎀✨

🧚 filter

Title   : filter
Usage   : $writer->filter('hsp', \&hsp_filter);
Function: Filter out either at HSP,Hit,or Result level
Returns : none
Args    : string => data type,
          CODE reference
Note    : GbrowseGFF.pm makes no changes to the default filter code

filters stuff out at the HSP, Hit, or Result level. you pass it a string for the data type and a CODE reference. returns none.

📌 note: GbrowseGFF.pm makes no changes to the default filter code. so whatever the default filter does, that's what you're getting. no surprises. 💜

---

and that's the page bestie!!! 🦋💖 this was documented with perl v5.32.1, dated 2021-08-15, and it's the Bio::S...owseGFF(3pm) page from the User Contributed Perl Documentation. go forth and write some GFF, you absolute icon. periodt. 👑💅