Scripts used in genetic mapping

MAPMAKER

Eric Lander's MAPMAKER program adapted by Russell Malmberg to run in a windows command prompt environment.

try.py

'try.py' places markers in the position identified by the MAPMAKER 'try' command.  When two markers map to the same interval, the marker with the biggest difference in likelihood between the most likely position and second-best position will be placed first.  To place the second marker, a second round of MAPMAKER 'try' and 'try.py' needs to be run.  Provide the MAPMAKER 'try' output as input (see 'lg1.txt' as example).  The script generates an ordered sequence (see 'ordered_lg1.txt' as example) which can be used as input for MAPMAKER 'try'.  Continue running until all markers are ordered.

ripple.py

'ripple.try' uses MAPMAKER's 'ripple' command to check marker orders.  If necessary, markers will be reordered, and this will be automatically followed by another round of 'ripple'.  Reordering and rippling will continue until the most likely map order has been established.  Provide the MAPMAKER raw data file (see 'mapmaker_lg1.txt' as example) and marker order (see 'ripple_order_lg1.txt' as example) as inputs.  The final order will be found in the file that starts with 'Rippled'.

Example files

lg1.txt

ordered_lg1.txt

mapmaker_lg1.txt

ripple_order_lg1.txt