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

💖 NAME 💖

Bio::SeqFeature::PositionProxy — the iconique little handler for when your truncation/revcom sequences go and span a feature. 🧚✨

Oh also, hi bestie, you're reading the User Contributed Perl Documentation version of Bio::S...nProxy(3pm). Yes, that's the whole title, we're keeping it real. 💅

---

✨ SYNOPSIS ✨

$proxy = Bio::SeqFeature::PositionProxy->new( -loc => $loc,
                                              -parent => $basefeature);

$seq->add_SeqFeature($feat);

that's literally it, she's so simple, I'm obsessed 😭🫶

---

🌸 DESCRIPTION 🌸

Okay so. PositionProxy is a Proxy Sequence Feature — main character energy — and her whole job is to handle truncation and revcomp without duplicating all the data living inside your sequence features. Not her being efficient. 💀

She holds:

• a new location for a sequence feature, and
• the original feature it came from,

so you still get all the extra annotation info without copy-pasting your whole life. Iconic behaviour, no cap. 👑

---

🎀 FEEDBACK 🎀

💌 Mailing Lists

User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated — like genuinely, we love to see it. 🌈

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 so many experienced and responsive experts will be able to look at the problem and quickly address it. Teamwork makes the dream work, fr fr. ✨

If at all possible, please include a thorough description of the problem with code and data examples. The more context you give, the faster someone can help. 🙈

🐛 Reporting Bugs

Report bugs to the Bioperl bug tracking system so we can keep track of the bugs and their resolutions. Bug reports can be submitted via the web:

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

do it do it do it, we're tracking everything 👀

---

👑 AUTHOR - Ewan Birney

Ewan Birney <birney@sanger.ac.uk>

---

🌟 DEVELOPERS 🌟

This class has been written with an eye out of inheritance. The fields the actual object hash are:

_gsf_tag_hash  = reference to a hash for the tags
_gsf_sub_array = reference to an array for sub arrays
_gsf_start     = scalar of the start point
_gsf_end       = scalar of the end point
_gsf_strand    = scalar of the strand

look at her internals. stunning. 💅

---

🦋 APPENDIX 🦋

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

🔍 location

• Title: location
• Usage: my $location = $seqfeature->location()
• Function: returns a location object suitable for identifying location of feature on sequence or parent feature
• Returns: Bio::LocationI object
• Args: none

🔍 parent

• Title: parent
• Usage: my $sf = $proxy->parent()
• Function: returns the seqfeature parent of this proxy
• Returns: Bio::SeqFeatureI object
• Args: none

🔍 start

• Title: start
• Usage:

$start = $feat->start
$feat->start(20)

• Function: Get
• Returns: integer
• Args: none

🔍 end

• Title: end
• Usage:

$end = $feat->end
$feat->end($end)

• Function: get
• Returns: integer
• Args: none

🔍 length

• Title: length
• Usage:
• Function:
• Example:
• Returns:
• Args:

yes bestie she's a mystery, all the fields are empty, that's literally what the page says, I'm not making it up 😭

🔍 strand

• Title: strand
• Usage:

$strand = $feat->strand()
$feat->strand($strand)

• Function: get/set on strand information, being 1, -1 or 0
• Returns: -1, 1 or 0
• Args: none

🔍 attach_seq

• Title: attach_seq
• Usage: $sf->attach_seq($seq)
• Function: Attaches a Bio::Seq object to this feature. This Bio::Seq object is for the entire sequence: ie from 1 to 10000
• Example:
• Returns: TRUE on success
• Args:

🔍 seq

• Title: seq
• Usage: $tseq = $sf->seq()
• Function: returns the truncated sequence (if there) for this
• Example:
• Returns: sub seq on attached sequence bounded by start & end
• Args: none

🔍 entire_seq

• Title: entire_seq
• Usage: $whole_seq = $sf->entire_seq()
• Function: gives the entire sequence that this seqfeature is attached to
• Example:
• Returns:
• Args:

🔍 seqname

• Title: seqname
• Usage: $obj->seq_id($newval)
• Function: There are many cases when you make a feature that you do know the sequence name, but do not know its actual sequence. This is an attribute such that you can store the seqname.

This attribute should not be used in GFF dumping, as that should come from the collection in which the seq feature was found.

• Returns: value of seqname
• Args: newvalue (optional)

🔗 Proxies

These functions chain back to the parent for all non sequence related stuff. 🫶

🔍 primary_tag

• Title: primary_tag
• Usage: $tag = $feat->primary_tag()
• Function: Returns the primary tag for a feature, eg 'exon'
• Returns: a string
• Args: none

🔍 source_tag

• Title: source_tag
• Usage: $tag = $feat->source_tag()
• Function: Returns the source tag for a feature, eg, 'genscan'
• Returns: a string
• Args: none

🔍 has_tag

• Title: has_tag
• Usage: $tag_exists = $self->has_tag('some_tag')
• Function:
• Returns: TRUE if the specified tag exists, and FALSE otherwise
• Args:

🔍 get_tag_values

• Title: get_tag_values
• Usage: @values = $self->get_tag_values('some_tag')
• Function:
• Returns: An array comprising the values of the specified tag.
• Args:

🔍 get_all_tags

• Title: get_all_tags
• Usage: @tags = $feat->get_all_tags()
• Function: gives all tags for this feature
• Returns: an array of strings
• Args: none

---

okay that's the whole page, you ate that, congrats 🎉

This lil masterpiece is running on perl v5.32.1, dated 2021-08-15 — and it's filed under Bio::S...nProxy(3pm). mwah, take care bestie 💖💅✨