VMATCHSELECT(1)

💖 VMATCHSELECT 💖

okay bestie, sit down, hydrate, because we're about to talk about vmatchselect — it's a page from the VMATCHSELECT(1) manual, and it's genuinely one of my faves. it sorts and selects matches. that's the whole vibe. slay.

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✨ NAME ✨

vmatchselect — sort and select matches 🎀

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🌸 SYNOPSIS 🌸

vmatchselect [options] matchfile

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🦋 DESCRIPTION 🦋

okay so. vmatchselect lets you pick out the interesting matches from the output of vmatch, based on criteria that you define. it hands off matches of your chosen length, degeneracy, or significance to whatever analysis routine you're running next. no cap. 💅

here's the tea: vmatchselect removes from the input all those matches that are contained in another match. and the way it does that efficiently? it sorts the matches by their position in the database sequence — so basically by the order the matches get output, unless you tell it otherwise. and that's not even all, bestie: the sequences of the virtual suffix tree that the match file was produced for can be clustered according to the matches. the input for vmatchselect is a file produced by vmatch, called a match file. 📄✨

the output of vmatchselect goes to standard output and it's sorted in ascending order of the positions of the left instance of a match. so:

• two matches where the left instance occurs at the same position → sorted in descending order of their length 🔥
• two matches of the same length where the left instance occurs in the same position → sorted in ascending order of the position of the right instance of the match ⭐

now, vmatchselect provides a subset of the options of vmatch. the main difference? vmatchselect gets its matches from a match file, while vmatch computes the matches from scratch. so that means the options specifying the index and/or the query sequences to be matched, plus the options specifying how to match — yeah, those are not available in vmatchselect. the options it does have mean the exact same thing as in vmatch, so for a description, see the corresponding documentation. iykyk 🫶

and — note — vmatchselect also supports the option -dbcluster. if you call vmatchselect with that option, it parses the given match file and performs single linkage clustering based on the matches in that file. so basically vmatch and vmatchselect can do hierarchical clustering together, like a little duo. 👑

how that flow goes:

1. first step: compute an initial set of matches with loose matching criteria, using vmatch.
2. then you cluster those matches by calling vmatchselect.
3. second round: you apply more strict choices for the matches by using the options -l, -leastscore, -evalue, or -identity, etc.

this facilitates stepwise refinement of clusters without much computational effort, and — iconic behaviour — with no new index construction for the sequence of a cluster. and the output of vmatchselect is the same as the output of vmatch. periodt. 💖

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💅 OPTIONS 💅

• -dbcluster <args> — cluster the database sequences.
  • first argument is percentage of shorter string to be included in match,
  • second argument is percentage of larger string to be included in match,
  • third optional argument is filenameprefix,
  • fourth optional argument is (minclustersize, maxclustersize)
• -nonredundant — generate file with non-redundant set of sequences; only works together with option -dbcluster.
• -selfun <file> — specify shared object file containing selection function.
• -l <length> — specify that match must have the given length, optionally specify minimum and maximum size of gaps between repeat instances.
• -leastscore <score> — specify the minimum score of a match.
• -evalue <value> — specify the maximum E-value of a match.
• -identity <value> — specify minimum identity of match in range [1..100%].
• -sort <mode> — sort the matches, additional argument is mode:
  • la: ascending order of length
  • ld: descending order of length
  • ia: ascending order of first position
  • id: descending order of first position
  • ja: ascending order of second position
  • jd: descending order of second position
  • ea: ascending order of Evalue
  • ed: descending order of Evalue
  • sa: ascending order of score
  • sd: descending order of score
  • ida: ascending order of identity
  • idd: descending order of identity
• -best <n> — show the best matches (those with smallest E-values), default is best 50.
• -s — show the alignment of matching sequences.
• -showdesc — show sequence description of match.
• -f — show filename where match occurs.
• -absolute — show absolute positions.
• -nodist — do not show distance of match.
• -noevalue — do not show E-value of match.
• -noscore — do not show score of match.
• -noidentity — do not show identity of match.
• -v — verbose mode.
• -version — show the version of the Vmatch package.
• -help — show help.

not me listing every single one of these because you deserve the full set, not a summary. we do NOT gatekeep options in this house. 🫶

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🌈 SEE ALSO 🌈

• vmatch(1)

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okay that's the whole page, bestie!! 🎀 this was the VMATCHSELECT(1) manual — the Vmatch package's own little corner of the docs, and yes it signs off with its own name right there at the bottom, VMATCHSELECT(1), like a queen leaving her signature. go forth and select some matches. you're gonna eat. 💖✨🌸🦋💅👑