Bio::S...map_f9(3pm)

💖 Bio::S...map_f9(3pm) 💖

okay bestie, so this is a page from the User Contributed Perl Documentation and honestly? it's giving parser-core. buckle up, we're getting into it 🦋

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✨ NAME ✨

Bio::SearchIO::gmap_f9 — event generator for parsing gmap reports (Z format) 👑

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🌸 SYNOPSIS 🌸

not me about to say the most important thing first: do NOT use this object directly. it's not that kind of girl. it's a behind-the-scenes worker bee inside the Bio::SearchIO system 🐝

# Do not use this object directly - it is used as part of the
# Bio::SearchIO system.

use Bio::SearchIO;
my $searchio = Bio::SearchIO->new(-format => 'gmap',
                                  -file   => 't/data/her2.gmapz');
while( my $result = $searchio->next_result ) {
    while( my $hit = $result->next_hit ) {
        while( my $hsp = $hit->next_hsp ) {
            # ...
        }
    }
}

like, nested loops three deep? the way that just works? we love a triple-nested slay 💅

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🎀 DESCRIPTION 🎀

this object encapsulates all the necessary methods for generating events suitable for building Bio::Search objects out of a GMAP "compressed" report — and when we say compressed we mean a gmap run that was done with the -Z flag, iykyk. 🔥

if you wanna know how to actually use this, go read the Bio::SearchIO docs, bestie, that's where the lore lives. 📖✨

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🧬 REVERSE STRAND AND BIOPERL COORDINATES 🧬

okay so the author (we'll get to them, they're iconic) says they believe they're doing the correct thing when reporting hits on the negative strand of the genome. and how do they know? they literally compared the "exons" this code generates against the set returned by ncbi's megablast web service. 🌈

the tea: NCBI's hsp's are ordered differently and have a different genomic location (off by ~18,000,000 bases — padding?? 🙈) but the starts, ends, and lengths were similar, and the strand handling matches theirs. fr fr.

E.g.

CDNA                            GENOME
start  end    strand   start           end             strand

blast
  1913 2989 1    86236731  86237808  -1
  1    475  1    86260509  86260983  -1
  1510 1727 1    86240259  86240476  -1
  841  989  1    86243034  86243182  -1
  1381 1514 1    86240630  86240763  -1
  989  1122 1    86242457  86242590  -1
  599  729  1    86247470  86247600  -1
  473  608  1    86259972  86260107  -1
  1255 1382 1    86240837  86240964  -1
  730  842  1    86244040  86244152  -1
  1813 1921 1    86238123  86238231  -1
  1725 1814 1    86239747  86239836  -1
  1167 1256 1    86241294  86241383  -1
  1120 1188 1    86242319  86242387  -1

gmap
  1    475  1    104330509 104330983 -1
  476  600  1    104329980 104330104 -1
  601  729  1    104317470 104317598 -1
  730  841  1    104314041 104314152 -1
  842  989  1    104313034 104313181 -1
  990  1121 1    104312458 104312589 -1
  1122 1187 1    104312320 104312385 -1
  1188 1256 1    104311294 104311362 -1
  1257 1382 1    104310837 104310962 -1
  1383 1511 1    104310633 104310761 -1
  1512 1726 1    104310260 104310474 -1
  1727 1814 1    104309747 104309834 -1
  1815 1917 1    104308127 104308229 -1
  1918 2989 1    104306731 104307802 -1

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💌 FEEDBACK 💌

📬 Mailing Lists 📬

user feedback is an integral part of the evolution of this and other Bioperl modules — like, the whole ecosystem thrives on your input, bestie. 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

🐛 Reporting Bugs 🐛

found a bug? report it to the Bioperl bug tracking system so everyone can keep track of the bugs and their resolution. bug reports can be submitted via the web:

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

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👑 AUTHOR - George Hartzell 👑

Email hartzell@alerce.com

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🌟 CONTRIBUTORS 🌟

Additional contributors names and emails here

(yes, that's literally what it says, we're keeping it 100 💀)

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📎 APPENDIX 📎

the rest of the documentation details each of the object methods. internal methods are usually preceded with an underscore (_) — that's the secret handshake, iykyk 🤫

⭐ next_result ⭐

• Title: next_result
• Usage: $result = stream->next_result
• Function: Reads the next ResultI object from the stream and returns it.
• Returns: A Bio::Search::Result::ResultI object
• Args: n/a

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and that's the whole page, bestie!! 🦋🌸 this little number ships with perl v5.32.1, dated 2021-08-15, and it's part of the User Contributed Perl Documentation. no cap, go forth and parse some gmap reports 💖✨🎀