SHOWFEAT(1e) | EMBOSS Manual for Debian | SHOWFEAT(1e) |
NAME¶
showfeat - Display features of a sequence in pretty formatSYNOPSIS¶
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
DESCRIPTION¶
showfeat is a command line program from EMBOSS (“the European Molecular Biology Open Software Suite”). It is part of the "Display,Feature tables" command group(s).OPTIONS¶
Input section¶
-sequence seqallAdditional section¶
-sourcematch stringBy 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 '*'. 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: *
-tagmatch string
Tags are the types of extra values that a
feature may 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 these
tags also have values, for example '/gene' 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 '*'. 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. 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'. Only some of these tags can
have values, for example '/gene' 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 '*'. If you wish to show more than one tag value, separate
their names with the character '|', eg: pax* | 10 Default value: *
-sort list
Default value: start
-joinfeatures boolean
Default value: N
-annotation range
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 '@filename'.
Advanced section¶
-html booleanDefault value: N
-id 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
-scale boolean
Set this to be false if you do not wish to
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 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
-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 (ie. the
same source) which are all of type 'exon' 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
-forward boolean
Set this to be false if you do not wish to
display forward sense features. Default value: Y
-reverse boolean
Set this to be false if you do not wish to
display reverse sense features. Default value: Y
-unknown boolean
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
-strand boolean
Set this if you wish to display the strand of
the features. Protein features are always directionless (indicated by '0'),
forward is indicated by '+' and reverse is '-'. Default value: N
-origin boolean
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
-position boolean
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: '189-189,225-225'. Default value: N
-type boolean
Set this to be false if you do not wish to
display the type of the features. Default value: Y
-tags boolean
Set this to be false if you do not wish to
display the tags and values of the features. Default value: N
-values boolean
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 'translation' tag is never displayed
as it is 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 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
Output section¶
-outfile outfileBUGS¶
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).SEE ALSO¶
showfeat is fully documented via the tfm(1) system.AUTHOR¶
Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>Wrote the script used to autogenerate this
manual page.
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.05/11/2012 | EMBOSS 6.4.0 |