SHOWPEP(1e)

💖 showpep — bestie's guide to showing off your protein sequences 💖

okay so this is showpep, a manual page from the EMBOSS collection — the manual is called showpep and it lives in section 1e, iykyk. it's literally the glow-up station for your protein sequences, and we're gonna go through the whole thing together, no skips, no skimming, because every single flag here matters. 🫶

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✨ NAME ✨

showpep — displays protein sequences with features in pretty format 💅

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🌸 SYNOPSIS 🌸

showpep -sequence seqall -format list -things list [-uppercase range]
        [-highlight range] [-annotation range] [-sourcematch string]
        [-typematch string] [-minscore float] [-maxscore float]
        [-tagmatch string] [-valuematch string] [-stricttags boolean]
        -threeletter boolean -number boolean -width integer
        -length integer -margin integer -name boolean
        -description boolean -offset integer -html boolean
        -outfile outfile

showpep -help

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🦋 DESCRIPTION 🦋

so showpep is a command line program from EMBOSS (that's "the European Molecular Biology Open Software Suite", the full government name 💖). it belongs to the "Display" command group(s), so yeah — it's a display girlie, it makes things look cute.

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🎀 OPTIONS 🎀

🌈 Input section

• -sequence seqall — this is where you hand over your sequence, bestie.

👑 Required section

• -format list — Default value: 2
• -things list — okay so this one lets you specify a list of one or more code characters, in the order in which you wish things to be displayed, one above the other, going down the page. for example, if you wish to see things displayed in the order: sequence, ticks line, blank line — then you should enter 'S,T,B'. Default value: B,N,T,S,A,F

💜 Additional section

• -uppercase range — regions to put in uppercase. if you leave this blank, then the sequence case is left alone, untouched, unbothered. ✋ a set of regions is specified by a set of pairs of positions. the positions are integers. they are separated by any non-digit, non-alpha character. examples of region specifications are: 24-45, 56-78 1:45, 67=99;765..888 1,5,8,10,23,45,57,99
• -highlight range — regions to colour if formatting for HTML. if you leave this blank, then the sequence is left alone. a set of regions is specified by a set of pairs of positions. the positions are integers. they are followed by any valid HTML font colour. examples of region specifications are: 24-45 blue 56-78 orange 1-100 green 120-156 red — and a file of ranges to colour (one range per line) can be specified as '@filename'.
• -annotation range — regions to annotate by marking. if you leave this blank, then no annotation is added. a set of regions is specified by a set of pairs of positions followed by optional text. the positions are integers. they are followed by any text (but not digits when on the command-line). examples of region specifications are: 24-45 new domain 56-78 match to Mouse 1-100 First part 120-156 oligo — and a file of ranges to annotate (one range per line) can be specified as '@filename'.

🍓 Feature display options 🍓

• -sourcematch string — by default any feature source in the feature table is shown. you can set this to match any feature source you wish to show. the source name is usually either the name of the program that detected the feature, or it's the feature table (eg: EMBL) that the feature came from. the source may be wildcarded by using '*'. if you wish to show more than one source, separate their names with the character '|', eg: gene* | embl Default value: *
• -typematch string — by default any feature type in the feature table is shown. you can set this to match any feature type you wish to show. see http://www.ebi.ac.uk/embl/WebFeat/ for a list of the EMBL feature types, and see Appendix A of the Swissprot user manual in http://www.expasy.org/sprot/userman.html for a list of the Swissprot feature types. the type may be wildcarded by using '*'. if you wish to show more than one type, separate their names with the character '|', eg: *UTR | intron Default value: *
• -minscore float — minimum score of feature to display (see also maxscore). Default value: 0.0
• -maxscore float — maximum score of feature to display. if both minscore and maxscore are zero (the default), then any score is ignored. Default value: 0.0
• -tagmatch string — tags are the types of extra values that a feature may have. by default any feature tag in the feature table is shown. you can set this to match any feature tag you wish to show. the tag may be wildcarded by using '*'. if you wish to show more than one tag, separate their names with the character '|', eg: gene | label Default value: *
• -valuematch string — tag values are the values associated with a feature tag. tags are the types of extra values that a feature may have. by default any feature tag value in the feature table is shown. you can set this to match any feature tag value you wish to show. the tag value may be wildcarded by using '*'. if you wish to show more than one tag value, separate their names with the character '|', eg: pax* | 10 Default value: *
• -stricttags boolean — by default, if any tag/value pair in a feature matches the specified tag and value, then all the tags/value pairs of that feature will be displayed. if this is set to be true, then only those tag/value pairs in a feature that match the specified tag and value will be displayed. Default value: N

🧚 Advanced section 🧚

• -threeletter boolean — Default value: N
• -number boolean — Default value: N
• -width integer — Default value: 60
• -length integer — (no default listed, bestie, it just vibes)
• -margin integer — Default value: 10
• -name boolean — set this to be false if you do not wish to display the ID name of the sequence. Default value: Y
• -description boolean — set this to be false if you do not wish to display the description of the sequence. Default value: Y
• -offset integer — Default value: 1
• -html boolean — Default value: N

⭐ Output section ⭐

• -outfile outfile — where your finished masterpiece goes. 💾

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💀 BUGS 💀

found a bug? not cute, but okay — bugs can be reported to 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).

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🫶 SEE ALSO 🫶

showpep is fully documented via the tfm(1) system. go read it, bestie, it's giving thorough. 📚

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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.

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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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and that's the whole page, periodt. no cap, every single flag and caveat is in there. 💖

EMBOSS 6.4.0 · 05/11/2012 · SHOWPEP(1e) — mwah, slay, bye bestie 🦋✨