'\" t .\" Title: SHOWFEAT .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "SHOWFEAT" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" showfeat \- Display features of a sequence in pretty format .SH "SYNOPSIS" .HP \w'\fBshowfeat\fR\ 'u \fBshowfeat\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR [\fB\-sourcematch\ \fR\fB\fIstring\fR\fR] [\fB\-typematch\ \fR\fB\fIstring\fR\fR] [\fB\-tagmatch\ \fR\fB\fIstring\fR\fR] [\fB\-valuematch\ \fR\fB\fIstring\fR\fR] [\fB\-sort\ \fR\fB\fIlist\fR\fR] [\fB\-joinfeatures\ \fR\fB\fIboolean\fR\fR] [\fB\-annotation\ \fR\fB\fIrange\fR\fR] \fB\-html\ \fR\fB\fIboolean\fR\fR \fB\-id\ \fR\fB\fIboolean\fR\fR \fB\-description\ \fR\fB\fIboolean\fR\fR \fB\-scale\ \fR\fB\fIboolean\fR\fR \fB\-width\ \fR\fB\fIinteger\fR\fR \fB\-collapse\ \fR\fB\fIboolean\fR\fR \fB\-forward\ \fR\fB\fIboolean\fR\fR \fB\-reverse\ \fR\fB\fIboolean\fR\fR \fB\-unknown\ \fR\fB\fIboolean\fR\fR \fB\-strand\ \fR\fB\fIboolean\fR\fR \fB\-origin\ \fR\fB\fIboolean\fR\fR \fB\-position\ \fR\fB\fIboolean\fR\fR \fB\-type\ \fR\fB\fIboolean\fR\fR \fB\-tags\ \fR\fB\fIboolean\fR\fR \fB\-values\ \fR\fB\fIboolean\fR\fR \fB\-stricttags\ \fR\fB\fIboolean\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR .HP \w'\fBshowfeat\fR\ 'u \fBshowfeat\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBshowfeat\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Display,Feature tables" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-sequence\fR \fIseqall\fR .RS 4 .RE .SS "Additional section" .PP \fB\-sourcematch\fR \fIstring\fR .RS 4 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 is the feature table (eg: EMBL) that the feature came from\&. The source may be wildcarded by using \*(Aq*\*(Aq\&. If you wish to show more than one source, separate their names with the character \*(Aq|\*(Aq, eg: gene* | embl Default value: * .RE .PP \fB\-typematch\fR \fIstring\fR .RS 4 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 \*(Aq*\*(Aq\&. If you wish to show more than one type, separate their names with the character \*(Aq|\*(Aq, eg: *UTR | intron Default value: * .RE .PP \fB\-tagmatch\fR \fIstring\fR .RS 4 Tags are the types of extra values that a feature may have\&. For example in the EMBL feature table, a \*(AqCDS\*(Aq type of feature may have the tags \*(Aq/codon\*(Aq, \*(Aq/codon_start\*(Aq, \*(Aq/db_xref\*(Aq, \*(Aq/EC_number\*(Aq, \*(Aq/evidence\*(Aq, \*(Aq/exception\*(Aq, \*(Aq/function\*(Aq, \*(Aq/gene\*(Aq, \*(Aq/label\*(Aq, \*(Aq/map\*(Aq, \*(Aq/note\*(Aq, \*(Aq/number\*(Aq, \*(Aq/partial\*(Aq, \*(Aq/product\*(Aq, \*(Aq/protein_id\*(Aq, \*(Aq/pseudo\*(Aq, \*(Aq/standard_name\*(Aq, \*(Aq/translation\*(Aq, \*(Aq/transl_except\*(Aq, \*(Aq/transl_table\*(Aq, or \*(Aq/usedin\*(Aq\&. Some of these tags also have values, for example \*(Aq/gene\*(Aq can have the value of the gene name\&. 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 \*(Aq*\*(Aq\&. If you wish to show more than one tag, separate their names with the character \*(Aq|\*(Aq, eg: gene | label Default value: * .RE .PP \fB\-valuematch\fR \fIstring\fR .RS 4 Tag values are the values associated with a feature tag\&. Tags are the types of extra values that a feature may have\&. For example in the EMBL feature table, a \*(AqCDS\*(Aq type of feature may have the tags \*(Aq/codon\*(Aq, \*(Aq/codon_start\*(Aq, \*(Aq/db_xref\*(Aq, \*(Aq/EC_number\*(Aq, \*(Aq/evidence\*(Aq, \*(Aq/exception\*(Aq, \*(Aq/function\*(Aq, \*(Aq/gene\*(Aq, \*(Aq/label\*(Aq, \*(Aq/map\*(Aq, \*(Aq/note\*(Aq, \*(Aq/number\*(Aq, \*(Aq/partial\*(Aq, \*(Aq/product\*(Aq, \*(Aq/protein_id\*(Aq, \*(Aq/pseudo\*(Aq, \*(Aq/standard_name\*(Aq, \*(Aq/translation\*(Aq, \*(Aq/transl_except\*(Aq, \*(Aq/transl_table\*(Aq, or \*(Aq/usedin\*(Aq\&. Only some of these tags can have values, for example \*(Aq/gene\*(Aq can have the value of the gene name\&. 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 \*(Aq*\*(Aq\&. If you wish to show more than one tag value, separate their names with the character \*(Aq|\*(Aq, eg: pax* | 10 Default value: * .RE .PP \fB\-sort\fR \fIlist\fR .RS 4 Default value: start .RE .PP \fB\-joinfeatures\fR \fIboolean\fR .RS 4 Default value: N .RE .PP \fB\-annotation\fR \fIrange\fR .RS 4 Regions to annotate by marking\&. If this is left 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 A file of ranges to annotate (one range per line) can be specified as \*(Aq@filename\*(Aq\&. .RE .SS "Advanced section" .PP \fB\-html\fR \fIboolean\fR .RS 4 Default value: N .RE .PP \fB\-id\fR \fIboolean\fR .RS 4 Set this to be false if you do not wish to display the ID name of the sequence\&. Default value: Y .RE .PP \fB\-description\fR \fIboolean\fR .RS 4 Set this to be false if you do not wish to display the description of the sequence\&. Default value: Y .RE .PP \fB\-scale\fR \fIboolean\fR .RS 4 Set this to be false if you do not wish to display the scale line\&. Default value: Y .RE .PP \fB\-width\fR \fIinteger\fR .RS 4 You can expand (or contract) the width of the ASCII\-character graphics display of the positions of the features using this value\&. For example, a width of 80 characters would cover a standard page width and a width a 10 characters would be nearly unreadable\&. If the width is set to less than 4, the graphics lines and the scale line will not be displayed\&. Default value: 60 .RE .PP \fB\-collapse\fR \fIboolean\fR .RS 4 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 (ie\&. the same source) which are all of type \*(Aqexon\*(Aq in the same sense, then they will all be displayed on the same line\&. This makes it hard to distinguish overlapping features\&. If this is set to false then each feature is displayed on a separate line making it easier to distinguish where features start and end\&. Default value: N .RE .PP \fB\-forward\fR \fIboolean\fR .RS 4 Set this to be false if you do not wish to display forward sense features\&. Default value: Y .RE .PP \fB\-reverse\fR \fIboolean\fR .RS 4 Set this to be false if you do not wish to display reverse sense features\&. Default value: Y .RE .PP \fB\-unknown\fR \fIboolean\fR .RS 4 Set this to be false if you do not wish to display unknown sense features\&. (ie\&. features with no directionality \- all protein features are of this type and some nucleic features (for example, CG\-rich regions))\&. Default value: Y .RE .PP \fB\-strand\fR \fIboolean\fR .RS 4 Set this if you wish to display the strand of the features\&. Protein features are always directionless (indicated by \*(Aq0\*(Aq), forward is indicated by \*(Aq+\*(Aq and reverse is \*(Aq\-\*(Aq\&. Default value: N .RE .PP \fB\-origin\fR \fIboolean\fR .RS 4 Set this if you wish to display the origin of the features\&. The source name is usually either the name of the program that detected the feature or it is the name of the feature table (eg: EMBL) that the feature came from\&. Default value: N .RE .PP \fB\-position\fR \fIboolean\fR .RS 4 Set this if you wish to 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 will be joined by a comma, for example: \*(Aq189\-189,225\-225\*(Aq\&. Default value: N .RE .PP \fB\-type\fR \fIboolean\fR .RS 4 Set this to be false if you do not wish to display the type of the features\&. Default value: Y .RE .PP \fB\-tags\fR \fIboolean\fR .RS 4 Set this to be false if you do not wish to display the tags and values of the features\&. Default value: N .RE .PP \fB\-values\fR \fIboolean\fR .RS 4 Set this to be false if you do not wish to display the tag values of the features\&. If this is set to be false, only the tag names will be displayed\&. If the tags are not displayed, then the values will not be displayed\&. The value of the \*(Aqtranslation\*(Aq tag is never displayed as it is often extremely long\&. Default value: Y .RE .PP \fB\-stricttags\fR \fIboolean\fR .RS 4 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 .RE .SS "Output section" .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 .RE .SH "BUGS" .PP 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)\&. .SH "SEE ALSO" .PP showfeat is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP 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\&. .sp