Bio::F...IO::bed(3pm)

💖 Bio::FeatureIO::bed — read/write features from UCSC BED format 💖

okay bestie, welcome to Bio::FeatureIO::bed(3pm), the little module that lets you vibe with the UCSC BED format 🦋 she reads, she writes, she's giving data-format icon energy. sit down, grab a boba, and let's get into it ✨

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🌸 SYNOPSIS 🌸

read mode, so you can pull features in like it's nothing:

my $in = Bio::FeatureIO(-format => 'bed', -file => 'file.bed');
for my $feat ($in->next_feature) {
  # do something with $feat (a Bio::SeqFeature::Annotated object)
}

and write mode, for when you're the one serving the features:

my $out = Bio::FeatureIO(-format=>'bed');
for my $feat ($seq->get_seqFeatures) {
  $out->write_feature($feat);
}

slay. that's the whole flow 💅

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✨ DESCRIPTION ✨

the full tea on BED lives here, go look:

<http://www.genome.ucsc.edu/goldenPath/help/customTrack.html#BED>

real talk though: right now, only the first 6 fields are supported, and that goes for both reading and writing. those six are chr, start, end, name, score, and strand. that's the roster. periodt 🎀

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🫶 FEEDBACK 🫶

💌 Mailing Lists

user feedback is literally an integral part of how this module and the other Bioperl modules evolve, no cap. 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

🌈 Support

okay so for usage questions and support issues, please direct them to the mailing list:

bioperl-l@bioperl.org

rather than sliding into the module maintainer's DMs directly. there are so many experienced and responsive experts on there who'll look at your problem and address it quickly. and please include a thorough description of the problem with code and data examples if at all possible — the more detail, the faster the fix, iykyk 💜

🐛 Reporting Bugs

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

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

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👑 AUTHOR - Allen Day 👑

Email allenday@ucla.edu

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🦋 CONTRIBUTORS 🦋

Sendu Bala, bix@sendu.me.uk

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💀 APPENDIX 💀

the rest of the docs are about the object methods, one by one. internal methods usually start with an underscore _, so if you see that, you know it's behind-the-scenes business 🙈

🧚 _initialize

Title   : _initialize
Function: initializes BED for reading/writing
Args    : all optional:
          name          description
          ----------------------------------------------------------
          -name         the name for the BED track, stored in header
                        name defaults to localtime()
          -description  the description for the BED track, stored in
                        header.  defaults to localtime().
          -use_score    whether or not the score attribute of
                        features should be used when rendering them.
                        the higher the score the darker the color.
                        defaults to 0 (false)

so like, all three args are optional, and both -name and -description default to localtime() if you don't pass them. and -use_score defaults to 0 (false) 💫

⭐ use_score

Title   : use_score
Usage   : $obj->use_score($newval)
Function: should score be used to adjust feature color when rendering?  set to true if so.
Example :
Returns : value of use_score (a scalar)
Args    : on set, new value (a scalar or undef, optional)

short version: should the score adjust the feature color when rendering? set it to true if so 🔥

🎀 name

Title   : name
Usage   : $obj->name($newval)
Function: name of BED track
Example :
Returns : value of name (a scalar)
Args    : on set, new value (a scalar or undef, optional)

it's the name of the BED track, bestie 💖

🌸 description

Title   : description
Usage   : $obj->description($newval)
Function: description of BED track
Example :
Returns : value of description (a scalar)
Args    : on set, new value (a scalar or undef, optional)

and this one's the description of the BED track. yes she has both, and yes she's obsessed with them 🌈

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and that's the whole page, bestie!! this little icon was brought to you by perl v5.30.0, dated 2020-01-13, as documented in Bio::F...IO::bed(3pm) under User Contributed Perl Documentation. mwah 💅💖✨