showpep

Function

Description

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.

Usage

Command line arguments

Input file format

showpep reads one or more protein sequences.

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: 

          
# this is my set of ranges
12   23         red
 4   5          darkturquoise
67   10348      #FFE4E1

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: 

# this is my set of ranges
12   23         exon 1
 4   5          CAP site
67   10348      exon 2

Output file format

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.

Data files

Notes

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:

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

Alternatively, there is a selection of pre-defined formats to choose from. The codes from above used in the list of standard formats are:

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

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.

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