Bio::S...aryQual(3pm)

📦
version 1.7.8 · 3 versions
, in debian bookworm, debian trixie, ubuntu jammy, ubuntu noble

💖 NAME 💖

okay so bestie, meet Bio::Seq::PrimaryQual — it's the Bioperl lightweight Quality Object. that's the whole vibe. it holds quality values. that's it. slay. ✨

🦋 SYNOPSIS 🦋

use Bio::Seq::PrimaryQual;

# you can use either a space-delimited string for quality

my $string_quals = "10 20 30 40 50 40 30 20 10";
my $qualobj = Bio::Seq::PrimaryQual->new(
    -qual             => $string_quals,
    -id               => 'QualityFragment-12',
    -accession_number => 'X78121',
);

# _or_ you can use an array of quality values

my @q2 = split/ /,$string_quals;
$qualobj = Bio::Seq::PrimaryQual->new(
    -qual              => \@q2,
    -primary_id        => 'chads primary_id',
    -desc              => 'chads desc',
    -accession_number  => 'chads accession_number',
    -id                => 'chads id'
);

# to get the quality values out:

my @quals = @{$qualobj->qual()};

# to give _new_ quality values

my $newqualstring = "50 90 1000 20 12 0 0";
$qualobj->qual($newqualstring);

like, string OR array, pick your fighter. either way it eats. 💅

🌸 DESCRIPTION 🌸

so this module gives you a whole entire mechanism for storing quality values. but lowkey the real main character energy is when you use it as part of Bio::Seq::Quality, where those quality values get associated with the sequence information. that's the moment. 🫶

📬 FEEDBACK 📬

💌 Mailing Lists

bestie, user feedback is literally an integral part of the evolution of this and other Bioperl modules. 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, not just the teaser. 😭

🐛 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

👑 AUTHOR - Chad Matsalla 👑

Email bioinformatics@dieselwurks.com

✨ APPENDIX ✨

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

🌈 new()

Title   : new()
Usage   : $qual = Bio::Seq::PrimaryQual->new(
              -qual             => '10 20 30 40 50 50 20 10',
              -id               => 'human_id',
              -accession_number => 'AL000012',
          );

Function: Returns a new Bio::Seq::PrimaryQual object from basic
          constructors, being a string _or_ a reference to an array for the
          sequence and strings for id and accession_number. Note that you
          can provide an empty quality string.
Returns : a new Bio::Seq::PrimaryQual object

so new() is the birth of your lil quality object. you can hand it a string or an array ref for the sequence, plus strings for id and accession_number. and yes, an empty quality string is valid, no judgment. ✨

🎀 qual()

Title   : qual()
Usage   : @quality_values  = @{$obj->qual()};
Function: Get or set the quality as a reference to an array containing the
          quality values. An error is generated if the quality scores are
          invalid, see validate_qual().
Returns : A reference to an array.

get it or set it — either way you're getting back a reference to an array. and if the quality scores are invalid? error. see validate_qual(). it's giving consequences. 💅

🦋 seq()

Title    : seq()
Usager   : $sequence = $obj->seq();
Function : Returns the quality numbers as a space-separated string.
Returns  : Single string.
Args     : None.

(not me noticing it says Usager in the original — iconic typo, we respect it) anyway it hands you the quality numbers as a space-separated string. one string, no args. simple. clean. 🌸

🧚 validate_qual($qualstring)

Title   : validate_qual($qualstring)
Usage   : print("Valid.") if { &validate_qual($self, $quality_string); }
Function: Test that the given quality string is valid. It is expected to
          contain space-delimited numbers that can be parsed using split /\d+/.
          However, this validation takes shortcuts and only tests that the
          string contains characters valid in numbers: 0-9 . eE +-
          Note that empty quality strings are valid too.
Returns : 1 for a valid sequence, 0 otherwise
Args    : - Scalar containing the quality string to validate.
          - Boolean to optionally throw an error if validation failed

okay so real talk: this checks that your quality string is valid. it expects space-delimited numbers parseable with split /\d+/. BUT — and this is the tea — this validation takes shortcuts and only tests that the string contains characters valid in numbers: 0-9 . eE +-. that's it. also note: empty quality strings are valid too. returns 1 for valid, 0 otherwise. args are a scalar with the quality string to validate, and a boolean to optionally throw an error if validation failed. 🍓

💜 subqual($start,$end)

Title   : subqual($start,$end)
Usage   : @subset_of_quality_values = @{$obj->subqual(10,40)};
Function: returns the quality values from $start to $end, where the
          first value is 1 and the number is inclusive, ie 1-2 are the
          first two bases of the sequence. Start cannot be larger than
          end but can be equal.
Returns : A reference to an array.
Args    : a start position and an end position

grab a lil slice of quality values from $start to $end. the first value is 1 and the range is inclusive — so 1-2 are the first two bases of the sequence. start cannot be larger than end, but it can be equal. you get back a reference to an array. args are a start position and an end position. 🫶

🌟 display_id()

Title   : display_id()
Usage   : $id_string = $obj->display_id();
Function: returns the display id, aka the common name of the Quality
          object.
          The semantics of this is that it is the most likely string to be
          used as an identifier of the quality sequence, and likely to have
          "human" readability.  The id is equivalent to the ID field of the
          GenBank/EMBL databanks and the id field of the Swissprot/sptrembl
          database. In fasta format, the >(\S+) is presumed to be the id,
          though some people overload the id to embed other information.
          Bioperl does not use any embedded information in the ID field,
          and people are encouraged to use other mechanisms (accession
          field for example, or extending the sequence object) to solve
          this. Notice that $seq->id() maps to this function, mainly for
          legacy/convience issues
Returns : A string
Args    : None

the display id, aka the common name of the Quality object. the semantics here are that it's the most likely string to be used as an identifier of the quality sequence, and likely to have "human" readability. it's equivalent to the ID field of the GenBank/EMBL databanks and the id field of the Swissprot/sptrembl database. in fasta format, the >(\S+) is presumed to be the id, though some people overload the id to embed other information. Bioperl does not use any embedded information in the ID field, and people are encouraged to use other mechanisms (accession field for example, or extending the sequence object) to solve this. also notice that $seq->id() maps to this function, mainly for legacy/convience issues. returns a string, takes no args. 💖

Title   : header()
Usage   : $header = $obj->header();
Function: Get/set the header that the user wants printed for this
    quality object.
Returns : A string
Args    : None

get or set the header that the user wants printed for this quality object. returns a string, no args. ✨

🔥 accession_number()

Title   : accession_number()
Usage   : $unique_biological_key = $obj->accession_number();
Function: Returns the unique biological id for a sequence, commonly
       called the accession_number. For sequences from established
       databases, the implementors should try to use the correct
       accession number. Notice that primary_id() provides the unique id
       for the implementation, allowing multiple objects to have the same
       accession number in a particular implementation. For sequences
       with no accession number, this method should return "unknown".
Returns : A string
Args    : None

returns the unique biological id for a sequence, commonly called the accession_number. for sequences from established databases, the implementors should try to use the correct accession number. notice that primary_id() provides the unique id for the implementation, allowing multiple objects to have the same accession number in a particular implementation. for sequences with no accession number, this method should return "unknown". returns a string, no args. 👑

💅 primary_id()

Title   : primary_id()
Usage   : $unique_implementation_key = $obj->primary_id();
Function: Returns the unique id for this object in this implementation.
       This allows implementations to manage their own object ids in a
       way the implementation can control clients can expect one id to
       map to one object. For sequences with no accession number, this
       method should return a stringified memory location.
Returns : A string
Args    : None

returns the unique id for this object in this implementation. this lets implementations manage their own object ids in a way the implementation can control — clients can expect one id to map to one object. for sequences with no accession number, this method should return a stringified memory location. returns a string, no args. 🦋

🍓 desc()

Title   : desc()
Usage   : $qual->desc($newval);
          $description = $qual->desc();
Function: Get/set description text for a qual object
Example :
Returns : Value of desc
Args    : newvalue (optional)

get or set the description text for a qual object. returns the value of desc. args are newvalue (optional). (the Example line is empty in the original — we keep it empty, bestie, integrity) 🌸

🌈 id()

Title   : id()
Usage   : $id = $qual->id();
Function: Return the ID of the quality. This should normally be (and
          actually is in the implementation provided here) just a synonym
          for display_id().
Returns : A string.
Args    : None.

returns the ID of the quality. this should normally be (and actually is in the implementation provided here) just a synonym for display_id(). returns a string, no args. 💜

🧚 length()

Title   : length()
Usage   : $length = $qual->length();
Function: Return the length of the array holding the quality values.
          Under most circumstances, this should match the number of quality
          values but no validation is done when the PrimaryQual object is
          constructed and non-digits could be put into this array. Is this
          a bug? Just enough rope...
Returns : A scalar (the number of elements in the quality array).
Args    : None.

returns the length of the array holding the quality values. under most circumstances this should match the number of quality values — but no validation is done when the PrimaryQual object is constructed and non-digits could be put into this array. is this a bug? just enough rope... 😭 returns a scalar (the number of elements in the quality array). no args. 🎀

⭐ qualat()

Title   : qualat
Usage   : $quality = $obj->qualat(10);
Function: Return the quality value at the given location, where the
          first value is 1 and the number is inclusive, ie 1-2 are the first
          two bases of the sequence. Start cannot be larger than end but can
          be equal.
Returns : A scalar.
Args    : A position.

return the quality value at the given location, where the first value is 1 and the number is inclusive — ie 1-2 are the first two bases of the sequence. start cannot be larger than end but can be equal. returns a scalar. args are a position. 🔥

💖 to_string()

Title   : to_string()
Usage   : $quality = $obj->to_string();
Function: Return a textual representation of what the object contains.
          For this module, this function will return:
               qual
               display_id
               accession_number
               primary_id
               desc
               id
               length
Returns : A scalar.
Args    : None.

returns a textual representation of what the object contains. for this module, this function will return: qual, display_id, accession_number, primary_id, desc, id, length. a whole little mood board of your object. returns a scalar, no args. 🫶

and that's the whole page bestie 💖 no cap, you now know PrimaryQual better than it knows itself

this lil writeup came from perl v5.32.1, dated 2021-08-15, and it lives under Bio::S...aryQual(3pm) — go forth and validate some quals, you icon 👑💅

📦 where this page comes from