JASPSCAN(1e)

💖 JASPSCAN(1e) — the EMBOSS Manual for Debian, but make it slay 💖

okay bestie, sit down, hydrate, because we're about to read a whole manual page together and honestly? it's giving main character energy. this is jaspscan, straight out of the EMBOSS manual for Debian. 🦋

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✨ NAME ✨

jaspscan — scans DNA sequences for transcription factors. that's it. that's the whole vibe. 🔥

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🌸 SYNOPSIS 🌸

jaspscan -sequence seqall -menu list -matrices string -threshold float
         [-exclude string] [-both boolean] -outfile report

jaspscan -help

notice how -exclude and -both are in square brackets? yeah babes, those are the optional ones. everything else? mandatory. the algorithm said so. 💅

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👑 DESCRIPTION 👑

jaspscan is a command line program from EMBOSS — that's "the European Molecular Biology Open Software Suite", in case you were wondering, and yes it's a mouthful, we love her anyway. 🫶

she hangs out in the "Nucleic:Transcription" command group(s). that's her clique. that's where you'll find her. ✨

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🎀 OPTIONS 🎀

💜 Input section

• -sequence seqall — the sequences you're feeding in. give her the goods. 🍓
• -menu list — pick your menu. default value is C. that's the whole thing, she's not complicated.
• -matrices string — okay this one's got LORE so listen up bestie:
  • the name all reads in all matrix files from the selected JASPAR matrix set. yes, all of them. no cap.
  • you can also hand-pick individual matrices by listing their names with commas between them, like: ma0001.1,ma0015*
  • the case of the names? not important. she does not care. lowercase, uppercase, she's chill. 🙈
  • you can also point her at a file of matrix names by putting an @ character in front of the filename, for example @matrix.list
  • inside that file: blank lines get ignored, and so do lines starting with a hash character or !. every other line gets concatenated together with a comma character , and then treated as the list of enzymes to search for. (yes. enzymes. that's what the manual says. we don't make the rules. 💀)
  • an example of a file of matrix names looks like this:

! my matrices
ma0001.1, ma0002.1
! other matrices
ma0010.1
ma0032*
ma0053.1

• default value: all

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⭐ Required section

• -threshold float — if the matrix score is greater than or equal to this percentage, then a hit will be reported. so it's the bar, and the bar must be cleared (or exactly met, she's generous like that 💖). default value: 80.0

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🌈 Additional section

• -exclude string — the names of any matrices you want to exclude from the matrices list. matrices are specified in exactly the same way as for the selection list — same comma rules, same @ file rules, same everything. just, you know, the opposite. 🚫
• -both boolean — if set, then both the forward and reverse strands are searched. both of them!! equal opportunity searching!! default value: N

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🧚 Output section

• -outfile report — where the report goes. your results, your file, your moment. 💅

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💀 BUGS 💀

found a bug? not the vibe, but okay, here's where to snitch:

• the Debian Bug Tracking system: http://bugs.debian.org/emboss
• or directly to the EMBOSS developers: http://sourceforge.net/tracker/?group_id=93650&atid=605031

go off, report it, make the software better. 🫶

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🔍 SEE ALSO 🔍

jaspscan is fully documented via the tfm(1) system. that's the whole see-also. one (1) reference. iconic, honestly. ✨

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🌸 AUTHOR 🌸

Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>

• Wrote the script used to autogenerate this manual page.

(the script did the writing, the team gets the credit, and honestly? relatable. 😭)

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💖 COPYRIGHT 💖

this manual page was autogenerated from an Ajax Control Definition of the EMBOSS package. it can be redistributed under the same terms as EMBOSS itself.

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ngl bestie, that's the whole page. no notes. periodt. 👑

EMBOSS 6.4.0 · 05/11/2012 · JASPSCAN(1e) — that's the version, that's the date, that's the whole moment, mwah 💋 thanks for reading with me, love u, bye!! 🎀🦋✨