Mask File Example Format

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Mask File Example Format

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@dschride answered my question in a separate email. I am including the answer here:

cat "simulationInputFile" | msMaskAllRows "maskFileName" | python removeNedOutColumnsFromMsFile.py stdin > "outputFile"

Where simulationInputFile is the path your .ms-style formatted simulation input, and maskFileName is the path to your mask file that you are inquiring about. The masked version will be written to outputFile. I will illustrate the format to the maskFile by example:

"0 0.1 0.2
0 0.3 0.4
//
0 0.05 0.06
0 0.5 0.9
0 0.95 0.99
//"

The above file can be used to mask a simulation file with two replicates. In the first rep, all positions between 0.1 and 0.2 and between 0.3 and 0.4 will be masked (the 0 at the beginning of each line can be ignored). In the second rep (after the first //) we will mask three different stretches of sequence. Note that the lines with numbers are space-separated.