tkmap(1) manual page

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tkmap - a bioTk program for drawing publication quality genetic maps.


tkmap [Tk options]


tkmap is a bioTk script for drawing and printing high quality output of genetic maps. tkmap reads in a framework map file and a confidence interval file in a simple text format and draws the implied map on a Tk canvas. This canvas may be resized, and the font used for drawing the marker labels changed. You can also generate encapsulated postscript from the map, either for printing or importing into a word processing package.


tkmap may understand the usual Tk options, it doesn't yet have any options of it's own.


The framework map file lists the linear map markers one per line, in the correct map order. After each marker (except the last) list the distance from the marker to the next. Comment lines beginning with a ``#'' character and blank lines are ignored. Marker names ending with the ``*'' character are considered to be framework markers and are printed in boldface.

EG0001    0.076
EG0002    0.048
EG0003    0.073
EG0004    0.024
EG0005    0.117
EG0006    0.058

EG0007    0.35
EG0008    0.091
EG0009    0.150
EG0010    0.199
EG0011    0.026
EG0012    0.183
The confidence interval map file also has a list of markers, but instead of each marker being associated with a distance, it is instead associated with an interval between two markers on the framework map. List the two framework map markers at the extremes of the interval to which the new marker is associated.

If several markers are associated to the same interval, you can specify all their names between quotes as the first item in a line.

EG0014	EG0001 EG0008
EG0015	EG0001 EG0003
EG0016	EG0003 EG0010
EG0017	EG0009 EG0013
EG0018	EG0005 EG0007
EG0019	EG0008 EG0012
EG0020	EG0004 EG0008
EG0021	EG0001 EG0007
EG0022	EG0008 EG0011

"EG0023, EG0024"	EG0001 EG0006

"EG0025, EG0026, EG0027, EG0028, EG0029"	EG0010 EG0013


tkmap hardly does any checking of its input data.




Humberto Ortiz Zuazaga, University of Puerto Rico. Internet address Rosemarie Plaetke, University of Alaska at Fairbanks Internet address

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Troglodita approved!

Humberto Ortiz Zuazaga

Most recent change: 2005/2/25 at 22:36
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