Bio::M...::meme(3pm)

💖 Bio::M...::meme 💖

okay bestie, you found the manual page for Bio::M...::meme(3pm) — it's part of the User Contributed Perl Documentation, and it's literally the whole vibe for this module. sit down, grab a boba, let's go 🧋✨

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✨ NAME ✨

Bio::Matrix::PSM::IO::meme — the PSM meme parser implementation. that's it, that's the whole name, and yes it ate 💅

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🌸 SYNOPSIS 🌸

see Bio::Matrix::PSM::IO for the detailed documentation on how to actually use PSM parsers, because that's where the real tea is 🫖

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🦋 DESCRIPTION 🦋

it's a parser for meme. periodt.

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💌 FEEDBACK 💌

📬 Mailing Lists

user feedback is an integral part of the evolution of this and other Bioperl modules, no cap. send your comments and suggestions preferably to one of the Bioperl mailing lists. 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. many experienced and reponsive experts will be able look at the problem and quickly address it. please include a thorough description of the problem with code and data examples if at all possible. give them the full lore, bestie 📝

🐛 Reporting Bugs

report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. bug reports can be submitted via the web:

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

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👑 AUTHOR - Stefan Kirov 👑

Email skirov@utk.edu

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🎀 APPENDIX 🎀

🌟 new

• Title: new
• Usage:

my $psmIO =  Bio::Matrix::PSM::IO->new(-format=>'meme',
                                        -file=>$file);

• Function: associates a file with the appropriate parser
• Throws: throws if the file passed is in HTML format or if the MEME header cannot be found. so if you hand it HTML it WILL be dramatic about it 😭
• Example:
• Args: hash
• Returns: "Bio::Matrix::PSM::$format"->new(@args);

🌈 _parse_coordinates

• Title: _parse_coordinates
• Usage:
• Function:
• Throws:
• Example: Internal stuff
• Returns:
• Args:

🍓 header

• Title: header
• Usage: my %header=$psmIO->header;
• Function: returns the header for the MEME file
• Throws:
• Example: fetching all the sequences included in the MEME analysis, being parsed

my %header=$psmIO->header;
 foreach my $seqid (@{$header{instances}}) {
    my $seq=$db->get_Seq_by_acc($id);
    #Do something with the sequence
 }
 where $db might be Bio::DB:GenBank object, see

• Returns: hash with three keys: instances, weights and lengths, which should be self-explenatory. each value is an array reference. each array element corresponds to the same element in the other two arrays. so $header{instances}->[$i] will refer to the same sequence in the motif file as $header{weights}->[$i] and $header{lengths}->[$i] 🔥
• Args: none
• Notes: OBSOLETE! 💀 yeah girl, it said what it said

💜 next_psm

• Title: next_psm
• Usage: my $psm=$psmIO->next_psm();
• Function: reads the next PSM from the input file, associated with this object
• Throws: throws if the format is inconsistent with the rules for MEME 3.0.4: no SUMMARY Section present or some keywords are missing/altered. so keep your file formatted correctly or catch these hands 🙈
• Example:
• Returns: Bio::Matrix::PSM::Psm object
• Args: none

🧚 _parseMatrix

• Title: _parseMatrix
• Usage:
• Function: parses the next site matrix information in the meme file
• Throws:
• Example: Internal stuff
• Returns: hash as for constructing a SiteMatrix object (see SiteMatrixI)
• Args: string

⭐ _parse_logs

• Title: _parse_logs
• Usage:
• Function: parses the next site matrix log values in the meme file
• Throws:
• Example: Internal stuff
• Returns: array of array refs
• Args: string

🌸 _parseInstance

• Title: _parseInstance
• Usage:
• Function: parses the next sites instances from the meme file
• Throws:
• Example: Internal stuff
• Returns: Bio::Matrix::PSM::InstanceSite object
• Args: none

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and that's the whole page, bestie!! 💖 this was perl v5.32.1, dated 2021-08-15, and it's the manual page for Bio::M...::meme(3pm) — go forth and parse those matrices, you absolute main character 👑✨🦋