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

✨ NAME ✨

okay so welcome to Bio::S...stUtils(3pm), straight out of the User Contributed Perl Documentation 💖

Bio::Search::BlastUtils — utility functions for Bio::Search:: BLAST objects. that's it, that's the whole vibe 🧬✨

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🌈 SYNOPSIS 🌈

# This module is just a collection of subroutines, not an object.

See Bio::Search::Hit::BlastHit.

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💅 DESCRIPTION 💅

so BlastUtils.pm is literally just a lil collection of subroutines, no cap. they're used primarily by Bio::Search::Hit::BlastHit objects to handle some of the extra functionality, like HSP tiling 🧚

right now BlastUtils is just a bunch of methods — not an object — and it's tightly coupled to Bio::Search::Hit::BlastHit. like, glued. inseparable. main character energy, but codependent 😭

a goal for the future (manifesting ✨) is to generalize it so it works based on the Bio::Search interfaces, and then it could work with any objects that implement them. iconic if true 🫶

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👑 AUTHOR 👑

Steve Chervitz <sac@bioperl.org>

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🎀 tile_hsps 🎀

• Usage — tile_hsps( $sbjct );
• Usage — This is called automatically by Bio::Search::Hit::BlastHit during object construction or as needed by methods that rely on having tiled data.
• Purpose — Collect statistics about the aligned sequences in a set of HSPs. Calculates the following data across all HSPs:
  • total alignment length
  • total identical residues
  • total conserved residues
• Returns — n/a
• Argument — A Bio::Search::Hit::BlastHit object
• Throws — n/a
• Comments — This method is strongly coupled to Bio::Search::Hit::BlastHit (it accesses BlastHit data members directly).
• Comments — TODO: Re-write this to the Bio::Search::Hit::HitI interface.
• Comments — This method performs more careful summing of data across all HSPs in the Sbjct object. Only HSPs that are in the same strand and frame are tiled. Simply summing the data from all HSPs in the same strand and frame will overestimate the actual length of the alignment if there is overlap between different HSPs (often the case).
• Comments — The strategy is to tile the HSPs and sum over the contigs, collecting data separately from overlapping and non-overlapping regions of each HSP. To facilitate this, the HSP.pm object now permits extraction of data from sub-sections of an HSP.
• Comments — Additional useful information is collected from the results of the tiling. It is possible that sub-sequences in different HSPs will overlap significantly. In this case, it is impossible to create a single unambiguous alignment by concatenating the HSPs. The ambiguity may indicate the presence of multiple, similar domains in one or both of the aligned sequences. This ambiguity is recorded using the ambiguous_aln() method.
• Comments — This method does not attempt to discern biologically significant vs. insignificant overlaps. The allowable amount of overlap can be set with the overlap() method or with the -OVERLAP parameter used when constructing the Blast & Sbjct objects.
• Comments — For a given hit, both the query and the sbjct sequences are tiled independently.
  • If only query sequence HSPs overlap, this may suggest multiple domains in the sbjct.
  • If only sbjct sequence HSPs overlap, this may suggest multiple domains in the query.
  • If both query & sbjct sequence HSPs overlap, this suggests multiple domains in both.
  • If neither query & sbjct sequence HSPs overlap, this suggests either no multiple domains in either sequence OR that both sequences have the same distribution of multiple similar domains.
• Comments — This method can deal with the special case of when multiple HSPs exactly overlap.
• Comments — Efficiency concerns: Speed will be an issue for sequences with numerous HSPs.
• Bugs — Currently, tile_hsps() does not properly account for the number of non-tiled but overlapping HSPs, which becomes a problem as overlap() grows. Large values overlap() may thus lead to incorrect statistics for some hits. For best results, keep overlap() below 5 (DEFAULT IS 2). For more about this, see the "HSP Tiling and Ambiguous Alignments" section in L<Bio::Search::Hit::BlastHit>.
• See Also — _adjust_contigs(), Bio::Search::Hit::BlastHit

bestie the bug note is REAL. keep overlap() below 5. the default is 2. don't be a hero 💀

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🦋 _adjust_contigs 🦋

• Usage — n/a; called automatically during object construction.
• Purpose — Builds HSP contigs for a given BLAST hit. Utility method called by _tile_hsps()
• Returns — (nothing, it's just blank here, no thoughts head empty 🙈)
• Argument — (also blank 💀)
• Throws — Exceptions propagated from Bio::Search::Hit::BlastHSP::matches() for invalid sub-sequence ranges.
• Status — Experimental
• Comments — This method does not currently support gapped alignments. Also, it does not keep track of the number of HSPs that overlap within the amount specified by overlap(). This will lead to significant tracking errors for large overlap values.
• See Also — tile_hsps(), Bio::Search::Hit::BlastHSP::matches

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🌸 get_exponent 🌸

• Usage — &get_exponent( number );
• Purpose — Determines the power of 10 exponent of an integer, float, or scientific notation number.
• Example —

&get_exponent("4.0e-206");
&get_exponent("0.00032");
&get_exponent("10.");
&get_exponent("1000.0");
&get_exponent("e+83");

• Argument — Float, Integer, or scientific notation number
• Returns — Integer representing the exponent part of the number (+ or -). If argument == 0 (zero), return value is "-999".
• Comments — Exponents are rounded up (less negative) if the mantissa is >= 5. Exponents are rounded down (more negative) if the mantissa is <= -5.

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🍓 collapse_nums 🍓

• Usage — @cnums = collapse_nums( @numbers );
• Purpose — Collapses a list of numbers into a set of ranges of consecutive terms: Useful for condensing long lists of consecutive numbers.

EXPANDED:

1 2 3 4 5 6 10 12 13 14 15 17 18 20 21 22 24 26 30 31 32

COLLAPSED:

1-6 10 12-15 17 18 20-22 24 26 30-32

• Argument — List of numbers sorted numerically.
• Returns — List of numbers mixed with ranges of numbers (see above).
• Throws — n/a
• See Also — Bio::Search::Hit::BlastHit::seq_inds()

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💜 strip_blast_html 💜

• Usage — $boolean = &strip_blast_html( string_ref );
• Usage — This method is exported.
• Purpose — Removes HTML formatting from a supplied string. Attempts to restore the Blast report to enable parsing by Bio::SearchIO::blast.pm
• Returns — Boolean: true if string was stripped, false if not.
• Argument — string_ref = reference to a string containing the whole Blast report containing HTML formatting.
• Throws — Croaks if the argument is not a scalar reference.
• Comments — Based on code originally written by Alex Dong Li (ali@genet.sickkids.on.ca).
• Comments — This method does some Blast-specific stripping (adds back a '>' character in front of each HSP alignment listing).
• Comments — THIS METHOD IS VERY SENSITIVE TO BLAST FORMATTING CHANGES!
• Comments — Removal of the HTML tags and accurate reconstitution of the non-HTML-formatted report is highly dependent on structure of the HTML-formatted version. For example, it assumes that first line of each alignment section (HSP listing) starts with a <a name=..> anchor tag. This permits the reconstruction of the original report in which these lines begin with a ">". This is required for parsing.
• Comments — If the structure of the Blast report itself is not intended to be a standard, the structure of the HTML-formatted version is even less so. Therefore, the use of this method to reconstitute parsable Blast reports from HTML-format versions should be considered a temporary solution.

ok the all-caps warning is not a drill bestie, it's giving "one formatting tweak and everything crumbles" 😭 temporary solution fr fr

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and that's the whole page 🫶 this one's from perl v5.32.1, dated 2021-08-15, and it's the Bio::S...stUtils(3pm) page. go forth and tile those HSPs, you absolute icon 👑💖