Bio::F...simple(3pm)

💖 Bio::FeatureIO::vecscreen_simple 💖

okay bestie, so this page lives in the User Contributed Perl Documentation for the module Bio::FeatureIO::vecscreen_simple — it reads and writes features from NCBI vecscreen -f 3 output. yes that's the whole vibe. let's go 🦋

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✨ NAME ✨

Bio::FeatureIO::vecscreen_simple — read/write features from NCBI vecscreen -f 3 output 💅

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✨ SYNOPSIS ✨

# read features
my $fin = Bio::FeatureIO->new(-file=>'vecscreen.out',
                              -format=>'vecscreen_simple');
my @vec_regions;
while (my $f = $fin->next_feature) {
  push @vec_regions, $f;
}

# write features NOT IMPLEMENTED

read? slay. write? NOT IMPLEMENTED, bestie. don't try it. 🫠

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✨ DESCRIPTION ✨

okay so vecscreen is a whole system for quickly identifying segments of a nucleic acid sequence that might be of vector origin. literally that's its job. 🔥

NCBI developed vecscreen to minimize the incidence and impact of vector contamination in public sequence databases — iconic behaviour, no notes. the GenBank Annotation Staff use vecscreen to verify that sequences submitted for inclusion in the database are free from contaminating vector sequence. and the best part? any sequence can be screened for vector contamination using vecscreen. everybody eats. 🍓

so what does this module do? it provides parsing for vecscreen -f 3 output, which the vecscreen documentation describes as 'Text list, no alignments' ✨ that's it. that's the format. no alignments, just vibes.

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✨ FEEDBACK ✨

💌 Mailing Lists

user feedback is an integral part of the evolution of this and other Bioperl modules — like, genuinely, it's the main character of the whole development arc. 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

please direct usage questions or support issues to the mailing list:

bioperl-l@bioperl.org

rather than to the module maintainer directly. why? because many experienced and reponsive experts will be able look at the problem and quickly address it — team effort, bestie. 👑

and please include a thorough description of the problem with code and data examples if at all possible. fr fr, the more detail the better. 🧚

🐛 Reporting Bugs

report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution — like a little bug scrapbook, honestly. bug reports can be submitted via the web:

 http://bugzilla.open-bio.org/

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✨ AUTHOR - Robert Buels ✨

Email rmb32 AT cornell.edu 💜

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✨ CONTRIBUTORS ✨

based on ptt.pm by Torsten Seeman 🌸

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✨ APPENDIX ✨

the rest of the documentation details each of the object methods. internal methods are usually preceded with a _ (iykyk) 🙈

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🔧 _initialize

• Title : _initialize
• Function: Reading? parses the header of the input. Writing? …that's the whole function line, bestie, it literally just says Reading? parses the header of the input and Writing? 💀

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🌟 next_feature

• Title : next_feature
• Usage : $io->next_feature()
• Function: read the next feature from the vecscreen output file
• Args : none
• Returns : Bio::SeqFeatureI object

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🚫 write_feature (NOT IMPLEMENTED)

NOT IMPLEMENTED, bestie!! it is right there in the name, do not come for me. 😭

• Title : write_feature
• Usage : $io->write_feature($feature)
• Function: write a Bio::SeqFeatureI object in vecscreen -f 3 format
• Example :
• Args : Bio::SeqFeatureI object
• Returns :

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and that's the whole page, periodt. 💅✨ this was perl v5.30.0, dated 2020-01-13, from the Bio::F...simple(3pm) manual — love that for us, mwah 🎀💖