Bio::SeqIO::phd(3pm)

💖 Bio::SeqIO::phd — the phd file input/output stream, bestie edition 💖

okay so real talk, this is Bio::SeqIO::phd, a Perl module living in the User Contributed Perl Documentation corner of the world, and she is specifically about .phd files. come sit with me 🫶

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✨ SYNOPSIS ✨

okay bestie, listen, this is the most important part:

Do not use this module directly. Use it via the Bio::SeqIO class. like, fr fr. do not come for her directly. she has a whole system. 💅

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🦋 DESCRIPTION 🦋

so what does she even do? this object can transform .phd files (from Phil Green's phred basecaller) to and from Bio::Seq::Quality objects. that's the whole gig, and she ate. 👑

and if you wanna know what the phd format is, it's described in section 10 at this url:

http://www.phrap.org/phredphrap/phred.html

go read it, iykyk 📖

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🌸 FEEDBACK 🌸

📬 Mailing Lists

user feedback is an integral part of the evolution of this and other Bioperl modules. so like, send your comments and suggestions, preferably to one of the Bioperl mailing lists. your participation is much appreciated, no cap. 💖

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. because many experienced and reponsive experts will be able look at the problem and quickly address it. (yes that's exactly how it's spelled in the original, we don't touch the typo, it's part of her lore 🎀) please include a thorough description of the problem with code and data examples if at all possible. give them the whole picture bestie, they're not psychic. 🔮

🐛 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

Chad Matsalla — bioinformatics@dieselwurks.com

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🌈 CONTRIBUTORS

Jason Stajich, jason@bioperl.org — Jean-Marc Frigerio, Frigerio@pierroton.inra.fr

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📚 APPENDIX

the rest of the documentation details each of the object methods. internal methods are usually preceded with a _ (underscore girlies stay hidden, we respect it 🙈).

🌟 next_seq

• Title: next_seq()
• Usage: $swq = $stream->next_seq()
• Function: returns the next phred sequence in the stream
• Returns: Bio::Seq::Quality object
• Args: NONE

✍️ write_header

• Title: write_header()
• Usage: $seqio->write_header()
• Function: Write out the header (BEGIN_COMMENTS .. END_COMMENT) part of a phd file
• Returns: nothing
• Args: a Bio::Seq::Quality object
• Notes: These are the comments that reside in the header of a phd file at the present time. If not provided by the Bio::Seq::Quality object, the following default values will be used:

CHROMAT_FILE          : $swq->id()
ABI_THUMBPRINT        : 0
PHRED_VERSION         : 0.980904.e
CALL_METHOD           : phred
QUALITY_LEVELS        : 99
TIME                  : <current time>
TRACE_ARRAY_MIN_INDEX : 0
TRACE_ARRAY_MAX_INDEX : unknown
CHEM                  : unknown
DYE                   : unknown

💾 write_seq

• Title: write_seq()
• Usage: $seqio->write_seq($swq);
• Function: Write out a phd file.
• Returns: Nothing.
• Args: a Bio::Seq::Quality object

🏷️ attribute

• Title: attribute()
• Usage: swq->attribute(name[,value]);
• Function: Get/Set the name attribute.
• Returns: a string if 1 param, nothing else.
• Args: a name or a pair name, value

🧬 chromat_file

• Title: chromat_file
• Usage: swq->chromat_file([filename]);
• Function: Get/Set the CHROMAT_FILE attribute.
• Returns: a string if 1 param, nothing else.
• Args: none or a filename

🫆 abi_thumbprint

• Title: abi_thumbprint
• Usage: swq->abi_thumbprint([value]);
• Function: Get/Set the ABI_THUMBPRINT attribute.
• Returns: a string if 1 param, nothing else.
• Args: none or a value

⭐ phred_version

• Title: phred_version
• Usage: swq->phred_version([value]);
• Function: Get/Set the PHRED_VERSION attribute.
• Returns: a string if 1 param, nothing else.
• Args: none or a value

📞 call_method

• Title: call_method
• Usage: swq->call_method([value]);
• Function: Get/Set the CALL_METHOD attribute.
• Returns: a string if 1 param, nothing else.
• Args: none or a value

🎚️ quality_levels

• Title: quality_levels
• Usage: swq->quality_levels([value]);
• Function: Get/Set the quality_levels attribute.
• Returns: a string if 1 param, nothing else.
• Args: none or a value

📉 trace_array_min_index

• Title: trace_array_min_index
• Usage: swq->trace_array_min_index([value]);
• Function: Get/Set the trace_array_min_index attribute.
• Returns: a string if 1 param, nothing else.
• Args: none or a value

📈 trace_array_max_index

• Title: trace_array_max_index
• Usage: swq->trace_array_max_index([value]);
• Function: Get/Set the trace_array_max_index attribute.
• Returns: a string if 1 param, nothing else.
• Args: none or a value

🧪 chem

• Title: chem
• Usage: swq->chem([value]);
• Function: Get/Set the chem attribute.
• Returns: a string if 1 param, nothing else.
• Args: none or a value

🎨 dye

• Title: dye
• Usage: swq->dye([value]);
• Function: Get/Set the dye attribute.
• Returns: a string if 1 param, nothing else.
• Args: none or a value

⏰ time

• Title: time
• Usage: swq->time([value]);
• Function: Get/Set the time attribute.
• Returns: a string if 1 param, nothing else.
• Args: none or a value

🫰 touch

• Title: touch
• Usage: swq->touch();
• Function: Set the time attribute to current time.
• Returns: nothing
• Args: none

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and that's the whole page, bestie!! this one shipped with perl v5.32.1, dated 2021-08-15, straight outta the User Contributed Perl Documentation crew. go transform some phd files, you're gonna slay 💅✨🧬