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

✨ NAME ✨

Bio::SearchIO::Writer::HSPTableWriter — tab-delimited data for Bio::Search::HSP::HSPI objects 💅

and yes bestie, she's a 3pm page, living her best life in the User Contributed Perl Documentation section. no cap.

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🌸 SYNOPSIS 🌸

okay so here's the vibe. Example 1: just roll with the default columns, she's already perfect ✨

use Bio::SearchIO;
use Bio::SearchIO::Writer::HSPTableWriter;

my $in = Bio::SearchIO->new();

my $writer = Bio::SearchIO::Writer::HSPTableWriter->new();

my $out = Bio::SearchIO->new( -writer => $writer );

while ( my $result = $in->next_result() ) {
    $out->write_result($result, ($in->report_count - 1 ? 0 : 1) );
}

Example 2: now we're picking and choosing which columns we want, main character energy 🎀

use Bio::SearchIO;
use Bio::SearchIO::Writer::HSPTableWriter;

my $in = Bio::SearchIO->new();

my $writer = Bio::SearchIO::Writer::HSPTableWriter->new(
                              -columns => [qw(
                                              query_name
                                              query_length
                                              hit_name
                                              hit_length
                                              rank
                                              frac_identical_query
                                              expect
                                              )]  );

my $out = Bio::SearchIO->new( -writer => $writer,
                              -file   => ">searchio.out" );

while ( my $result = $in->next_result() ) {
    $out->write_result($result, ($in->report_count - 1 ? 0 : 1) );
}

🦋 Custom Labels 🦋

and like, if the default column labels aren't giving what they need to give, you can rename them, periodt. Just pass a -labels hash reference when you build the HSPTableWriter object. the keys are the column number (and bestie, left-most column = 1, not zero, don't come for me) for whichever label(s) you're customizing. here's the moment:

my $writer = Bio::SearchIO::Writer::HSPTableWriter->new(
                           -columns => [qw( query_name
                                            query_length
                                            hit_name
                                            hit_length  )],
                           -labels  => { 1 => 'QUERY_GI',
                                         3 => 'HIT_IDENTIFIER' } );

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💖 DESCRIPTION 💖

Bio::SearchIO::Writer::HSPTableWriter generates output at the finest level of granularity for data within a search result. it's giving microscope 🔬. the data for each HSP inside each hit in a search result comes out in tab-delimited format, one row per HSP. slay.

⭐ Available Columns ⭐

here are all the columns you can name in the -columns parameter when you're creating an HSPTableWriter object. and lowkey important: if you don't pass a -columns parameter at all, this exact list, in this exact order, is the default. 👑

• query_name — sequence identifier of the query
• query_length — full length of the query sequence
• hit_name — sequence identifier of the hit
• hit_length — full length of the hit sequence
• round — round number for hit (PSI-BLAST)
• rank
• expect — expect value for the alignment
• score — score for the alignment (e.g., BLAST score)
• bits — bit score for the alignment
• frac_identical_query — fraction of identical substitutions in query
• frac_identical_hit — fraction of identical substitutions in hit
• frac_conserved_query — fraction of conserved substitutions in query
• frac_conserved_hit — fraction of conserved substitutions in hit
• length_aln_query — length of the aligned portion of the query sequence
• length_aln_hit — length of the aligned portion of the hit sequence
• gaps_query — number of gap characters in the aligned query sequence
• gaps_hit — number of gap characters in the aligned hit sequence
• gaps_total — number of gap characters in the aligned query and hit sequences
• start_query — starting coordinate of the aligned portion of the query sequence
• end_query — ending coordinate of the aligned portion of the query sequence
• start_hit — starting coordinate of the aligned portion of the hit sequence
• end_hit — ending coordinate of the aligned portion of the hit sequence
• strand_query — strand of the aligned query sequence
• strand_hit — strand of the aligned hit sequence
• frame — reading frame of the aligned query sequence
• hit_description — full description of the hit sequence
• query_description — full description of the query sequence
• frac_identical_total — fraction of total identical substitutions
• frac_conserved_total — fraction of total conserved substitutions

want the tea on any of these? 🍵 the docs for the corresponding method over in Bio::Search::HSP::HSPI have you covered.

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🙈 TODO 🙈

still gotta figure out the best way to work in algorithm-specific score columns. the best route is probably to have algorithm-specific subclasses (e.g., BlastHSPTableWriter, FastaHSPTableWriter). it's giving future era, not yet, bestie. 💀

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🫶 FEEDBACK 🫶

💌 Mailing Lists 💌

user feedback is, like, 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 so appreciated, genuinely 🥹

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 responsive experts will be able look at the problem and quickly address it. if at all possible, please include a thorough description of the problem with code and data examples. give them the full picture bestie, not just a vibe 🧚

🐛 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

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👑 AUTHOR 👑

Steve Chervitz <sac@bioperl.org>

see the FEEDBACK section for where to send bug reports and comments.

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📜 COPYRIGHT 📜

Copyright (c) 2001 Steve Chervitz. All Rights Reserved.

this library is free software; you can redistribute it and/or modify it under the same terms as Perl itself. iconic behavior honestly 💅

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💀 DISCLAIMER 💀

this software is provided "as is" without warranty of any kind. no promises, no cap, that's the deal.

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🔥 SEE ALSO 🔥

• Bio::SearchIO::Writer::HitTableWriter
• Bio::SearchIO::Writer::ResultTableWriter

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🧚 METHODS 🧚

🌟 to_string() 🌟

heads up bestie: this method is not intended for direct use. the SearchIO::write_result() method calls it automatically if the writer is hooked up to a SearchIO object, just like the SYNOPSIS section shows.

• Title — to_string()
• Usage — print $writer->to_string( $result_obj, [$include_labels] );
• Argument — $result_obj = a Bio::Search::Result::ResultI object; $include_labels = boolean, if true column labels are included (default: false)
• Returns — a string containing a tab-delimited set of data for each HSP in each Hit of the supplied ResultI object
• Throws — n/a

🌸 end_report 🌸

• Title — end_report
• Usage — $self->end_report()
• Function — the method to call when ending a report; this is mostly for cleanup for formats which require you to have something at the end of the document. nothing for a text message.
• Returns — string
• Args — none

💜 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

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and that's the whole page bestie 🎀 brought to you by perl v5.32.1, dated 2021-08-15, out of the User Contributed Perl Documentation for Bio::S...eWriter(3pm). go write some tab-delimited HSP rows, you're gonna eat 💅✨