NAME¶
showpep - Displays protein sequences with features in pretty
format
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
DESCRIPTION¶
showpep is a command line program from EMBOSS (“the
European Molecular Biology Open Software Suite”). It is part of the
"Display" command group(s).
OPTIONS¶
Required section¶
-format list
Default value: 2
-things list
Specify a list of one or more code characters in the
order in which you wish things to be displayed one above the other 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 this is left blank, then
the sequence case is left alone. 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 this is left
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 A file of ranges to colour (one range per
line) can be specified as '@filename'.
-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'.
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 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: *
-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
-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
SEE ALSO¶
showpep 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.
