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

💖 Bio::FeatureIO::ptt 💖

okay bestie, gather round, because this is the manual page for Bio::FeatureIO::ptt from the User Contributed Perl Documentation — and it's literally about reading and writing features in PTT format. let's get into it ✨

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🌸 NAME 🌸

Bio::FeatureIO::ptt — read/write features in PTT format 🧬

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✨ SYNOPSIS ✨

 # read features
 my $fin = Bio::FeatureIO->new(-file=>'genes.ptt', -format=>'ptt');
 my @cds;
 while (my $f = $fin->next_feature) {
   push @cds, $f if $f->strand > 0;
 }

 # write features (NOT IMPLEMENTED)
 my $fout = Bio::FeatureIO->new(-fh=>\*STDOUT, -format=>'ptt');
 for my $f (@cds) {
   $fout->write_feature($f);
 }

heads up queen: the writing side is NOT IMPLEMENTED. reading? absolutely slays. writing? it's giving vaporware 💀

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🦋 DESCRIPTION 🦋

so the PTT file format is basically a table of protein features. it's used mainly by NCBI, who crank out PTT files for every single one of their published genomes, which you can find chilling at <ftp://ftp.ncbi.nih.gov/genomes/>. and here's the layout, line by line:

🎀 Line 1

a description of the sequence that the features belong to. for example:

"Leptospira interrogans chromosome II, complete sequence - 0..358943"

it's usually the same as the DEFINITION line of a Genbank file, except with the length of the sequence tacked on the end. and honestly? it is unclear why "0" is used as the starting range when it should be "1". iconic behavior, no explanation. 🙈

🎀 Line 2

the number of feature lines in the table. for example:

"367 proteins"

🎀 Line 3

the column headers, tab separated. for example:

"Location  Strand  Length  PID Gene  Synonym Code  COG Product"

and here's what every single column means, no skipping:

• Location : the "begin..end" span of the feature
• Strand : "+" or "-"
• Length : number of amino acids excluding the stop codon
• PID : analogous to Genbank /db_xref="GI:xxxxxxxxx"
• Gene : analogous to Genbank /gene="xxxx"
• Synonym : analogous to Genbank /locus_tag="xxxx"
• Synonym : analogous to Genbank /locus_tag="xxxx"
• COG : CDD COG code with COG letter categories appended
• Product : analogous to Genbank /product="xxxx"

not me noticing that Synonym shows up twice in the original list 💅 yes bestie, both of them are here, i'm not merging them, that's not my business.

🎀 Line 4 onwards

the actual feature lines — nine columns, tab separated, and "-" is used for empty fields. for example:

"2491..3423  + 310 24217063  metF  LB002 - COG0685E
5,10-methylenetetrahydrofolate reductase"

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🌈 FEEDBACK 🌈

💌 Mailing Lists

user feedback is, like, an integral part of the evolution of this and other Bioperl modules. so 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

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

bioperl-l@bioperl.org

rather than to the module maintainer directly. the reason? there are lots of experienced and reponsive experts on there who will be able look at the problem and quickly address it. and please include a thorough description of the problem, with code and data examples if at all possible — the more detail the better, bestie. 📝

💌 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:

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

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👑 AUTHOR - Torsten Seemann 👑

Email torsten.seemann AT infotech.monash.edu.au

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🧚 CONTRIBUTORS 🧚

based on bed.pm and gff.pm by Allen Day.

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⭐ APPENDIX ⭐

the rest of the documentation details each of the object methods. and jsyk, internal methods are usually preceded with a _. iykyk 💅

_initialize

 Title   : _initialize
 Function: Reading? parses the header of the input
           Writing?

next_feature

 Title   : next_feature
 Usage   : $io->next_feature()
 Function: read the next feature from the PTT file
 Example :
 Args    :
 Returns : Bio::SeqFeatureI object

write_feature (NOT IMPLEMENTED)

reminder: NOT IMPLEMENTED, bestie. it's giving wishlist.

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

description

 Title   : description
 Usage   : $obj->description($newval)
 Function: set/get the PTT file description for/from line one
 Example :
 Returns : value of description (a scalar)
 Args    : on set, new value (a scalar or undef, optional)

protein_count

 Title   : protein_count
 Usage   : $obj->protein_count($newval)
 Function: set/get the PTT protein count for/from line two
 Example :
 Args    : on set, new value (a scalar or undef, optional)
 Returns : value of protein_count (a scalar)

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and that's the whole page, periodt 💖 this was generated for perl v5.30.0 on 2020-01-13, brought to you by the same Bio::F...IO::ptt(3pm) manual you came in with — stay hydrated, read your headers, and go parse something cute 🌸✨🦋