EMBOSS: lindna

| ## EMBOSS: lindna

# Program lindna

## Function

Draws linear maps of DNA constructs

## Description

The program 'lindna' draws linear maps of DNA constructs.

It uses the graphical shapes: ticks, ranges, and blocks to represent genetic markers (e.g, genes and ESTs) and places them according to their position in a DNA fragment. The markers can be organized in different groups.

The program reads in one input file in which the user specifies the names and positions of the genetic markers. In this file the user also enters data for controlling the appearance of the markers.

A refined customization of the drawing can be achieved by running the program with '-options' on the command line and changing the values of the desired parameters.

## Usage

Here is a sample session with lindna.

    Graph type [x11]:
    Input file [inputfile]: data.linp
    ticks inside or outside the circle (enter In or Out) [Out]:
    text inside or outside the blocks (enter In or Out) [In]:

## Command line arguments

       Mandatory qualifiers:
       -inputfile          infile     input file containing mapping data
       -graphout           graph      Graph type

       Optional qualifiers:
       -intersymbol        string     type of junctions between blocks (enter
                                      Straight, Up, Down, or No)
       -intercolor         integer    color of junctions between blocks (enter a
                                      color number)
       -interticks         string     do you want horizontal junctions between
                                      ticks (Y or N)
       -gapsize            integer    interval between ticks in the ruler (enter
                                      an integer)
       -ticklines          string     do you want vertical lines at the ruler's
                                      ticks (Y or N)
       -tickheight         float      height of ticks (enter a number to multiply
                                      the default height)
       -blockheight        float      height of blocks (enter a number to multiply
                                      the default height)
       -rangeheight        float      height of range ends (enter a number to
                                      multiply the default height)
       -gapgroup           float      space between groups (enter a number to
                                      multiply the default space)
       -postext            float      space between text and ticks, blocks, and
                                      ranges (enter a number to multiply the
                                      default space)

       Advanced qualifiers: (none)
       General qualifiers:
      -help                bool       report command line options. More
                                      information on associated and general
                                      qualifiers can be found with -help -verbose

Mandatory qualifiers | Allowed values | Default
--- | --- | ---
-inputfile | input file containing mapping data | Input file | inputfile
-graphout | Graph type | EMBOSS has a list of known devices, including postscript, ps, hpgl, hp7470, hp7580, meta, colourps, cps, xwindows, x11, tektronics, tekt, tek4107t, tek, none, null, text, data, xterm, png | EMBOSS_GRAPHICS value, or x11
Optional qualifiers | Allowed values | Default
-intersymbol | type of junctions between blocks (enter Straight, Up, Down, or No) | Any string is accepted | Straight
-intercolor | color of junctions between blocks (enter a color number) | Any integer value | 1
-interticks | do you want horizontal junctions between ticks (Y or N) | Any string is accepted | N
-gapsize | interval between ticks in the ruler (enter an integer) | Any integer value | 500
-ticklines | do you want vertical lines at the ruler's ticks (Y or N) | Any string is accepted | N
-tickheight | height of ticks (enter a number to multiply the default height) | Any integer value | 1
-blockheight | height of blocks (enter a number to multiply the default height) | Any integer value | 1
-rangeheight | height of range ends (enter a number to multiply the default height) | Any integer value | 1
-gapgroup | space between groups (enter a number to multiply the default space) | Any integer value | 1
-postext | space between text and ticks, blocks, and ranges (enter a number to multiply the default space) | Any integer value | 1
Advanced qualifiers | Allowed values | Default
(none)

## Input file format

Here is the input file data.linp for the example run:

    Start   1001
    End     4270

    group
    exons
    label
    Block   1011    1362    3       H
    ex1
    endlabel
    label
    Tick    1610    8       H
    EcoR1
    endlabel
    label
    Block   1647    1815    1       H
    endlabel
    label
    Tick    2459    8       H
    BamH1
    endlabel
    label
    Block   4139    4258    3       H
    ex2
    endlabel
    endgroup

    group
    repeat-regions
    label
    Range   2541    2812    [       ]       5       V
    Alu
    endlabel
    label
    Range   3322    3497    >       <       5       V
    MER13
    endlabel
    endgroup

Blank lines in the input file are ignored.

The file is organized in several fields separated by one or more space or TAB characters.

The first non-blank line gives the start position of the DNA fragment to be drawn after the keyword 'Start'. The end position is on the second line following the keyword 'End'.

Then, one or more groups (up to a maximum of 100) of genetic markers are defined. Each group begins with a line consisting of the keyword 'group' and ends with a line consisting of the keyword 'endgroup'.

If desired, a group name can be given on the very next line. Spaces and tabulations are allowed but only the first 20 characters of that name (including spaces) will be displayed.

Next, the individual markers (up to a maximum of 100) of the group are described. Each marker begins with a line consisting of the keyword 'label' and ends with a line consisting of the keyword 'endlabel'.

Do not start a new marker (by using a 'label' line) before you have closed the previous marker (by using an 'endlabel' line). You must end a previous marker specification before starting a new one. i.e. do not overlap marker specifications in the input file.

For each marker, the line following the 'label' line describes the marker. Three types of markers can be drawn: ticks, blocks, and ranges.

For a tick, the descriptive line begins with the keyword 'Tick', followed by the position of the tick in the DNA fragment, and a number from 0 to 15 specifying the color in which the tick will be drawn (a list of available colors is given below). If desired, one or more names can be written above the tick. In this case an optional letter H or V should be added to the line. H or V indicate whether the text will be horizontal or vertical, respectively. If no letter is specified, H is assumed by default. A list of one or more names can be given on the next lines with one name per line.

For a block, the descriptive line begins with the keyword 'Block', followed by the start and end positions of the block in the DNA fragment, and the number of the block's color. If desired, one or more names can be written above the block. Names are given on the following lines. An optional letter H or V can be added to the end of the descriptive line to specify the orientation of the name(s).

For a range, the descriptive line begins with the keyword 'Range', followed by the start and end positions of the range in the DNA fragment. Next on the line are the types of boundaries that are to be drawn. The user can choose among '>', '<', '[', and ']' for both start and end boundaries. If none of these types is wanted for a given boundary, then a point '.' must be entered. Next is the color number. If desired, one or more names can be written above the range. Names are given on the following lines. An optional letter H or V can be added to the end of the descriptive line to specify the orientation of the name(s).

For any type of markers, try to avoid long names.

The colors defined in the PLPLOT graphics library are:

0 "BLACK", 1 "RED", 2 "YELLOW", 3 "GREEN", 4 "AQUAMARINE", 5 "PINK", 6 "WHEAT", 7 "GREY", 8 "BROWN", 9 "BLUE", 10 "BLUEVIOLET", 11 "CYAN", 12 "TURQUOISE", 13 "MAGENTA", 14 "SALMON", and 15 "WHITE".

This format can also be used for the program "cirdna".

## Output file format

Output is to the specified graphics device.

Click here to see the output of the above example.

## Data files

None.

## Notes

None.

## References

None.

## Warnings

None.

## Diagnostic Error Messages

None.

## Exit status

It always exits with a status of 0.

## Known bugs

None.

## See also

Program name | Description
--- | ---
abiview | Reads ABI file and display the trace
cirdna | Draws circular maps of DNA constructs
pepnet | Displays proteins as a helical net
pepwheel | Shows protein sequences as helices
prettyplot | Displays aligned sequences, with colouring and boxing
prettyseq | Output sequence with translated ranges
remap | Display a sequence with restriction cut sites, translation etc
seealso | Finds programs sharing group names
showalign | Displays a multiple sequence alignment
showdb | Displays information on the currently available databases
showfeat | Show features of a sequence
showseq | Display a sequence with features, translation etc
textsearch | Search sequence documentation text. SRS and Entrez are faster!

cirdna plots representations of circular DNA.

## Author(s)

This application was written by Nicolas Tourasse (nicolas.tourasse@biotek.uio.no) at the Norwegian EMBnet node.

## History

Written (2000) - Nicolas Tourasse

## Target users

This program is intended to be used by everyone and everything, from naive users to embedded scripts.

## Comments