SHOWFEAT(1e)

🌸 showfeat — ok bestie, let's look at some FEATURES 🌸

So this is showfeat, a page from the EMBOSS Manual for Debian (yeah, the 1e manual). Sit down, grab a strawberry, we're rendering feature tables in pretty ASCII art and it's genuinely iconic. 💖

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✨ NAME ✨

showfeat — display features of a sequence in pretty format 💅

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🦋 SYNOPSIS 🦋

showfeat -sequence seqall [-sourcematch string] [-typematch string]
         [-tagmatch string] [-valuematch string] [-sort list]
         [-joinfeatures boolean] [-annotation range] -html boolean
         -id boolean -description boolean -scale boolean -width integer
         -collapse boolean -forward boolean -reverse boolean
         -unknown boolean -strand boolean -origin boolean
         -position boolean -type boolean -tags boolean -values boolean
         -stricttags boolean -outfile outfile

showfeat -help

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👑 DESCRIPTION 👑

showfeat is a command line program from EMBOSS — aka “the European Molecular Biology Open Software Suite” (they really said let's make the acronym work). It's part of the "Display,Feature tables" command group(s). No cap, that's literally its whole job description. 🌈

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💅 OPTIONS 💅

🌸 Input section 🌸

• -sequence seqall — the sequence you're showing off. Every icon needs a subject. 🫶

🎀 Additional section 🎀

• -sourcematch string — by default, any feature source in the feature table gets shown. But bestie, you can set this to match whatever source you actually wanna see. The source name is usually either the name of the program that detected the feature, or the feature table it came from (like EMBL). Wildcards work with '*', and if you want more than one source, separate the names with the character '|', e.g. gene* | embl. Default value: * ✨
• -typematch string — by default any feature type in the feature table is shown, but you can set this to match just the feature type you care about. Wanna know the EMBL feature types? Go peep http://www.ebi.ac.uk/embl/WebFeat/. Wanna know the Swissprot ones? That's Appendix A of the Swissprot user manual at http://www.expasy.org/sprot/userman.html. Wildcards via '*', multiple types separated with '|', e.g. *UTR | intron. Default value: * 💖
• -tagmatch string — tags are the types of extra values a feature can have. For example, in the EMBL feature table a 'CDS' type of feature may have the tags '/codon', '/codon_start', '/db_xref', '/EC_number', '/evidence', '/exception', '/function', '/gene', '/label', '/map', '/note', '/number', '/partial', '/product', '/protein_id', '/pseudo', '/standard_name', '/translation', '/transl_except', '/transl_table', or '/usedin'. Some of those tags also carry values — like '/gene' can hold the gene name. By default any feature tag in the feature table is shown; set this to match the ones you want. Wildcard with '*', multiple tags separated with '|', e.g. gene | label. Default value: * 🧚
• -valuematch string — tag values are the values attached to a feature tag, and tags are the types of extra values a feature may have. Same tea as above: in the EMBL feature table a 'CDS' type of feature may have the tags '/codon', '/codon_start', '/db_xref', '/EC_number', '/evidence', '/exception', '/function', '/gene', '/label', '/map', '/note', '/number', '/partial', '/product', '/protein_id', '/pseudo', '/standard_name', '/translation', '/transl_except', '/transl_table', or '/usedin'. Only some of these tags can have values — '/gene' can have the value of the gene name, for instance. By default any feature tag value in the feature table is shown; set this to match whichever value you want. Wildcards via '*', multiple values separated with '|', e.g. pax* | 10. Default value: * 🦋
• -sort list — Default value: start 🌸
• -joinfeatures boolean — Default value: N 🙈
• -annotation range — regions to annotate by marking them. If you leave this blank, then no annotation is added, simple as that. You specify a set of regions with a set of pairs of positions followed by optional text. The positions are integers. They're followed by any text (but not digits when you're on the command-line, ok?). Examples of region specifications are: 24-45 new domain, 56-78 match to Mouse, 1-100 First part, 120-156 oligo. And if you want a whole file of ranges to annotate — one range per line — you can specify it as '@filename'. 💜

🔥 Advanced section 🔥

• -html boolean — Default value: N ✨
• -id boolean — set this to be false if you don't wanna display the ID name of the sequence. Default value: Y 🎀
• -description boolean — set this to be false if you don't wanna display the description of the sequence. Default value: Y 💖
• -scale boolean — set this to be false if you don't wanna display the scale line. Default value: Y 📏
• -width integer — you can expand (or contract) the width of the ASCII-character graphics display of the positions of the features with this. For example, a width of 80 characters would cover a standard page width, and a width of 10 characters would be nearly unreadable (bestie, don't). If the width is set to less than 4, the graphics lines and the scale line will not be displayed. Default value: 60 🫶
• -collapse boolean — if this is set, then features from the same source and of the same type and sense are all printed on the same line. For instance, if there are several features from the EMBL feature table (same source) that are all of type 'exon' in the same sense, they all get displayed on the same line. Heads up though: this makes it hard to distinguish overlapping features. If it's set to false, then each feature gets its own separate line, making it way easier to see where features start and end. Default value: N 💀
• -forward boolean — set this to be false if you don't wanna display forward sense features. Default value: Y ➡️
• -reverse boolean — set this to be false if you don't wanna display reverse sense features. Default value: Y ⬅️
• -unknown boolean — set this to be false if you don't wanna display unknown sense features (i.e. features with no directionality — all protein features are this type, plus some nucleic features, for example CG-rich regions). Default value: Y ❓
• -strand boolean — set this if you wanna display the strand of the features. Protein features are always directionless (indicated by '0'), forward is indicated by '+' and reverse by '-'. Default value: N 🔀
• -origin boolean — set this if you wanna display the origin of the features. The source name is usually either the name of the program that detected the feature, or the name of the feature table (eg: EMBL) that the feature came from. Default value: N 🌍
• -position boolean — set this if you wanna display the start and end position of the features. If several features are being displayed on the same line, then the start and end positions get joined by a comma, for example: '189-189,225-225'. Default value: N 📍
• -type boolean — set this to be false if you don't wanna display the type of the features. Default value: Y 🏷️
• -tags boolean — set this to be false if you don't wanna display the tags and values of the features. Default value: N 🎫
• -values boolean — set this to be false if you don't wanna display the tag values of the features. If this is false, only the tag names get displayed. And if the tags aren't displayed, then the values won't be displayed either — they're a package deal, iykyk. Also, the value of the 'translation' tag is never displayed, because it's often extremely long. Default value: Y 💬
• -stricttags boolean — by default, if any tag/value pair in a feature matches the specified tag and value, then all the tag/value pairs of that feature get displayed. If this is set to true, then only those tag/value pairs in a feature that match the specified tag and value get displayed. Default value: N 🔒

🌈 Output section 🌈

• -outfile outfile — where the pretty output goes. 💾

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😭 BUGS 😭

Found a bug? Not the vibe. You can report it to the Debian Bug Tracking system at http://bugs.debian.org/emboss, or straight to the EMBOSS developers at http://sourceforge.net/tracker/?group_id=93650&atid=605031. They wanna know, fr fr. 🫶

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👀 SEE ALSO 👀

showfeat is fully documented via the tfm(1) system. Periodt. ✨

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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. Honestly? Slay. 👑

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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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Ok that's the whole page bestie, you're officially a feature-table girlie now 🎀

And a lil sign-off from me to you: this was EMBOSS 6.4.0, dated 05/11/2012, living in the SHOWFEAT(1e) era. Go render something gorgeous. 💅✨🦋