Emboss - Software Development

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MMDrawer is a simple program developed to draw chromosome maps from the output of MapMaker EXP. The output format is a Enhanced Metafile, which can be imported into most Windows-based presentation or document editing programs.

The current version is still under development, but is fully functional. There are no known bugs in the output, but the interface is still not totally intuitive. Also, if there are a large number of uncertainly-placed markers, the program output may need a bit of manual "post-processing" to make the result more readable.

Delphi source code is freely available upon request. This software is available under the MIT licence.

Complete customisation of drawing options: page height/width, margins, bar width, text padding, ...
Automatic psuedointercross detection and marking in italics, and detection of unmapped markers.
Colouring any number of ranges of markers to any colour.
Marker position output to aid in sorting of markers in the input file.
Automatic scaling of groups of chromosomes so that the bar length corresponds to the cM length of the chromosome.
Minimal formatting required to prepare the data.

Sample output:
Note: These files are not "real", in the sense that processing indata.txt with mapmaker will not generate outdata.txt. However, indata.txt in only used for marker names and psuedointercross detection, so the important file is outdata.txt, which could come from any indata.txt file.

Input files to MMDrawer:
data type f2 intercross
8 8 0

*mark1 A A A A A A A A
*mark2 A A A A A A A A
*mark3 A A A A A A A A
*mark4 A A A A A A A A
*mark5 C A B D D H H H
*mark5 C A B D D H H H
*mark7 A A A A A A A A
*mark8 A A A A A A A A

To process this file in mapmaker and generate the output file, execute the following script:
make chromosome chr1
s mark1 mark2 mark3 mark4 mark5 mark6 mark7 mark8
photo tempdata.txt
photo off
The "s" line can also be used to select a chromosome that has had markers placed on it though "group", "attach", "assign", etc.

To get outdata.txt, just take the final map output from in tempdata.txt and copy/paste it into outdata.txt. The format of this file is very loose: All that is required is that the lines "Map:" and "Markers placed relative to above map:" are copied in, and nothing is changed between "Map:" and the end of the relative placement list.

Chromosome 1:

  Markers          Distance
    2  mark2         3.7 cM
    3  mark3         7.5 cM
    8  mark8         3.3 cM
    4  mark4      ----------
                    13.5 cM   4 markers   log-likelihood= -98.25

Markers placed relative to above map:
          2    3    8    4
   1 3 **.:....:....:....:...
   5 3 ...:.**.:....:....:...
   6 3 ...:.**.:....:....:...
   7 3 ...:....:.**.:....:...

Output map image:

see the giant list of genetics programs for many other MapMaker related programs.