Bio::T...TargetP(3pm)

💖 Bio::T...TargetP 💖

ok so bestie, you're looking at the manual page for Bio::T...TargetP, part of the User Contributed Perl Documentation set. it's giving "I parse your TargetP output so you don't have to" and honestly? iconic. 💅

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✨ NAME ✨

Bio::Tools::TargetP — the results of one TargetP run 🎀

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🌸 SYNOPSIS 🌸

ok so here's the vibe, literally just:

use Bio::Tools::TargetP;

#filename for  TargetP result :
$targetp = Bio::Tools::TargetP->new(-file => 'targetp.out');

# filehandle for TargetP :
$targetp = Bio::Tools::TargetP->new( -fh  => \*INPUT );

### targetp v1.1 prediction results ##################################
#Number of query sequences:  11
#Cleavage site predictions included.
#Using NON-PLANT networks.
#
#Name                  Len            mTP     SP  other  Loc  RC  TPlen
#----------------------------------------------------------------------
#swall|Q9LIP3|C72Y_AR  500          0.245  0.935  0.009   S    2     22
#swall|Q52813|AAPQ_RH  400          0.170  0.462  0.577   _    5      -
#swall|O86459|AAT_RHI  400          0.346  0.046  0.660   _    4      -

# parse the results
while($feature = $targetp->next_prediction()) {

    #$feature is a Bio::SeqFeature::Generic object
    my $method     = $targetp->analysis_method();
    my $vesion     = $targetp->analysis_method_version() || $feature->source();
    my $seqid      = $feature->seq_id();
    # ...
  }

# essential if you gave a filename at initialization (otherwise the file
# will stay open)
$targetp->close();

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🦋 DESCRIPTION 🦋

the TargetP modules serve up parsed info about protein localization, no cap. it reads in a targetp output file, parses those results, and hands you back a Bio::SeqFeature::Generic object for every sequence it finds that has a subcellular localization. one object per sequence, cute and orderly, we love to see it. ✨

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💌 FEEDBACK 💌

📬 Mailing Lists

fr fr, user feedback is a whole integral part of how this module (and every other Bioperl module) evolves. send your comments and suggestions 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 send usage questions and support issues 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 the list who'll be able to look at your problem and address it fast. if at all possible, include a thorough description of the problem along with code and data examples. periodt. 💅

🐛 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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👑 AUTHORS - Emmanuel Quevillon 👑

Email emmanuel.quevillon@versailles.inra.fr

Describe contact details here

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🎀 APPENDIX 🎀

the rest of the documentation goes into detail on each of the object methods. internal methods are usually preceded with a _. iykyk. 💜

analysis_method

• Usage — $self->analysis_method();
• Purpose — inherited method. overridden to ensure that the name matches
• Returns — String
• Argument — n/a

network

• Title — network
• Usage — $self->network($network)
• Function — this method Get/Set's the network used for the analysis (PLANT or NON-PLANT)
• Example —
• Returns — string
• Arguments — on set, the network used

cleavage

• Title — cleavage
• Usage — $self->cleavage($cleavage)
• Function — this method Get/Set's whether the SignalP program was used to run TargetP
• Example —
• Returns — 1 or 0
• Arguments — on set, the cleavage used or not

next_prediction

• Usage — $targetp->next_prediction()
• Purpose — returns the next TargetP prediction
• Returns — a Bio::SeqFeature::Generic object
• Arguments — n/a

create_feature

• Title — create_feature
• Usage — $self->create_feature(\%hash);
• Function — this method creates a new Bio::SeqFeature::Generic object
• Example —
• Returns — Bio::SeqFeature::Generic
• Arguments — hash reference

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🔒 PRIVATE METHODS 🔒

_initialize_state

• Title — _initialize_state
• Usage — n/a; usually called by _initialize() itself called by new()
• Function — this method is supposed to reset the state such that any 'history' is lost. State information that does not change during object lifetime is not considered as history, e.g. parent, name, etc shall not be reset. An inheriting object should only be concerned with state information it introduces itself, and for everything else call SUPER::_initialize_state(@args).

The argument syntax is the same as for new() and _initialize(), i.e., named parameters following the -name=>$value convention. The following parameters are dealt with by the implementation provided here:

• -INPUT, -FH, -FILE

(tags are case-insensitive).

• Example —
• Returns —
• Args —

_predictions

• Usage — $targetp->_prediction()
• Purpose — returns the number of TargetP predictions
• Returns — a scalar (number)
• Arguments — n/a

_parsed

• Title — _parsed
• Usage — $targetp->_parsed(1)
• Function — this method is used to know if the output result is parsed or not. For internal use only
• Example —
• Returns — 1/0
• Arguments — 1/0 for setting

_parse_results

• Title — _parse_results
• Usage — $self->_parse_results()
• Function — this method parses a TargetP output. For internal use only
• Example —
• Returns — n/a
• Arguments — none

_parse_line

• Title — _parse_line
• Usage — $self->_parse_line($line)
• Function — this method parses the line result. For internal use only
• Example —
• Returns — Hash reference
• Arguemnts — line to parse

_add_feature

• Title — _add_feature
• Usage — $self->_add_feature($feature)
• Function — this method stores a feature object. For internal use only
• Example —
• Returns — n/a
• Arguments — Bio::SeqFeature::Generic

_toString_location

• Title — _toString_location
• Usage — $self->_toString_location($key)
• Function — this method converts the 'one letter code' location to the corresponding definition. For internal use only
• Example —
• Returns — Location or undef
• Arguments — String

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ok that's the whole page bestie, you ate that 🍓✨ this gem was brought to you by perl v5.32.1, dated 2021-08-15, and filed under Bio::T...TargetP(3pm). go parse some proteins, mwah 💖🎀🦋