Commands

POPout can be run using our Python script with the following command:

./POPout.py trait1.pop trait2.pop.... 

The following commands are supported:

Names (--names)

By default the file prefixes are used as trait names, to use custom trait names the user can provide a list of names equal in length to the number of POP files, for example:

./POPout.py trait1.pop trait2.pop --names traitA traitB  

Output Prefix (--out)

The default output prefix is "out" but it can be changed as follows:

./POPout.py trait1.pop trait2.pop --names traitA traitB  --out customOutput 

Plot Format (--plotFormat)

The default format for plots is "pdf" but this can be changed to png as follows:

./POPout.py trait1.pop trait2.pop --names traitA traitB  --out customOutput --plotFormat png 

Tail Size (--tailSize)

By default POPout considers the lower and upper 1% as the trait tails. This can be changed as follows*:

./POPout.py trait1.pop trait2.pop --names traitA traitB  --out customOutput --plotFormat png --tailSize 5  

*Note that for this option, values between 1 and 25 are valid as are the values 0.5 (half a percent), 0.25 (a quarter percent), and 0.1 (a tenth of a percent).