Bio::C...::dbsnp(3pm)

✨ Bio::ClusterIO::dbsnp ✨

okay bestie, welcome to the Bio::ClusterIO::dbsnp page 💖 this is part of the User Contributed Perl Documentation and it's literally the dbSNP input stream module, no cap.

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🌸 NAME 🌸

Bio::ClusterIO::dbsnp — dbSNP input stream 🧬✨

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🎀 SYNOPSIS 🎀

bestie do NOT use this module directly, I'm so serious 😭

Do not use this module directly.  Use it via the Bio::ClusterIO class.

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🦋 DESCRIPTION 🦋

so basically it parses dbSNP XML files, one refSNP entry at a time 💅

but listen — this handles dbSNPp output generated by NBCI's eutils, and it does NOT parse output derived from SNP's XML format (which lives over at ftp://ftp.ncbi.nih.gov/snp/). read that again, bestie, because that's a whole different vibe 🫶

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💌 FEEDBACK 💌

🌈 Mailing Lists

user feedback is an integral part of the evolution of this and other Bioperl modules, fr fr — your comments and suggestions are so wanted. send them preferably to one of the Bioperl mailing lists, your participation is much appreciated 🥹✨

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 👑 there are so many experienced and reponsive experts who will be able to 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, that's the good stuff 💖

🐛 Reporting Bugs

report bugs to the Bioperl bug tracking system to help us 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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🌟 AUTHOR 🌟

Allen Day <allenday@ucla.edu> 💜

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📖 APPENDIX 📖

the rest of the documentation details each of the object methods. internal methods are usually preceded with a _ (iykyk) 🙈

🍓 next_cluster

• Title: next_cluster
• Usage: $dbsnp = $stream->next_cluster()
• Function: returns the next refSNP in the stream 🔥
• Returns: Bio::Variation::SNP object representing composite refSNP and its component subSNP(s)
• Args: NONE

🧚 SAX methods

💫 start_document

• Title: start_document
• Usage: $parser->start_document;
• Function: SAX method to indicate starting to parse a new document. Creates a Bio::Variation::SNP ✨
• Returns: none
• Args: none

💫 end_document

• Title: end_document
• Usage: $parser->end_document;
• Function: SAX method to indicate finishing parsing a new document
• Returns: none
• Args: none

💫 start_element

• Title: start_element
• Usage: $parser->start_element($data)
• Function: SAX method to indicate starting a new element
• Returns: none
• Args: hash ref for data

💫 end_element

• Title: end_element
• Usage: $parser->end_element($data)
• Function: signals finishing an element
• Returns: none
• Args: hash ref for data

💫 characters

• Title: characters
• Usage: $parser->characters($data)
• Function: signals new characters to be processed
• Returns: characters read
• Args: hash ref with the key 'Data'

💫 use_tempfile

• Title: use_tempfile
• Usage: $obj->use_tempfile($newval)
• Function: get/set boolean flag on whether or not use a tempfile 🎀
• Example:
• Returns: value of use_tempfile
• Args: newvalue (optional)

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and that's the whole page bestie, you ate that 💅🌈 this lil doc is from perl v5.34.0, dated 2022-03-27 — catch you on the flip side, mwah 💖🎀🦋