showpep displays one or more protein sequences, with features, in a style suitable for publication. The output is sent to screen by default but can be written to file. You may pick a format from a list, alternatively, use the many options to control what is output and in what format. Optionally, the sequence feature table can be displayed. There are various other options for controlling how the sequence is displayed and numbered and the output can be formatted for HTML.
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You can specify a file of ranges to display in uppercase by giving the '-uppercase' qualifier the value '@' followed by the name of the file containing the ranges. (eg: '-upper @myfile').
The format of the range file is:
An example range file is:
# this is my set of ranges 12 23 4 5 this is like 12-23, but smaller 67 10348 interesting region
You can specify a file of ranges to highlight in a different colour when outputting in HTML format (using the '-html' qualifier) by giving the '-highlight' qualifier the value '@' followed by the name of the file containing the ranges. (eg: '-highlight @myfile').
The format of this file is very similar to the format of the above
uppercase range file, except that the text after the start and end
positions is used as the HTML colour name. This colour name is used 'as
is' when specifying the colour in HTML in a ''
construct, (where 'xxx' is the name of the colour).
The standard names of HTML font colours are given in
http://http://www.w3.org/TR/REC-html40/types.html#h-6.5
An example highlight range file is:
You can specify a file of ranges to annotate
by giving
the '-annotate' qualifier the value '@' followed by the name of the
file containing the ranges. (eg: '-annotate @myfile').
The format of this file is very similar to the format of the above
highlight range file, except that the text after the start and end
positions is used as the displayed text of the annotated region.
An example annotation range file is:
Most of the variants of the output format have already been described in
the 'Description' and 'Usage' sections, but here is some more just to
fill out this section.
The output format is extremely variable and under the control of the
qualifiers used.
The sequence can be formatted for HTML display by using the '-html'
qualifier. The top and tail html tags <HEAD>, <BODY> etc. are not
included as it is expected that the output of this program will be
included in a more extensive HTML page and so these parts are left to
the user to provide.
The name of the sequence is displayed, followed by the description of
the sequence. These can be turned off with the '-noname' and
'-nodescription' qualifiers.
Then the sequence is output, one line at a time. Any associated
information to be displayed is also output above and below the sequence
line, as specified by the '-format' and or '-things' qualifiers. (See
the 'Description' section for detals).
The margins around the sequence are specified by the use of the
'-margin' qaulifier and any numbering of the sequence and its
translations are placed in the margin.
One or more things may be selected for display from a menu
(-things option). The order of specified characters (upper
or lower case) determines the order in the output: Alternatively, there is a selection of pre-defined formats to
choose from. The codes from above used in the list of standard formats
are: The default standard format displays the following: for every new
line that the sequence starts to write, the output display will
contain first a blank line (b), then the position numbers of
the ticks (n) then the ticks every 10 characters (t)
then the sequence itself (s) then any user-supplied
annotation (a) then the features from the feature table
(f). Subsequent lines of the sequence output will repeat this
format. The output can be formatted for HTML. If the output is being
formatted for HTML, then specified regions of the sequence can be
displayed in any valid HTML colours. If the sequence is in SwissProt format, the
feature table of the sequence can be displayed with the sequence. GFF
file features can also be displayed if they are included on the
command line using -ufo=file.
Other display options include: The displayed sequence can be numbered
either by numbering the start and ending positions, or by placing a
ruler with ticks above or below the sequence. An initial position to
start the numbering from can be set. The width of a line, and width
of a margin around the sequence reserved for numbering can be set.
Specified regions of the sequence can be displayed in uppercase to
highlight them.
# this is my set of ranges
12 23 red
4 5 darkturquoise
67 10348 #FFE4E1
# this is my set of ranges
12 23 exon 1
4 5 CAP site
67 10348 exon 2
Output file format
Data files
Notes
s Sequence
b Blank line
t Ticks line
n Number ticks line
f Features (from the feature table or from a command line -ufo file)
a User Annotation
Sequence only: S A
Default sequence: B N T S A F
Pretty sequence: B N T S A
Baroque: B N T S T A F
References
None.
Warnings
None.
Diagnostic Error Messages
None.
Exit status
It always exits with status 0.
Known bugs
None known.
Author(s)
History
Target users
Comments