Example of a script to do Spidermonkey/BGM analysis in the command line

Question

[Mac]

I would like to to perform a co-evolution analysis using spidermonkey on the command line. Does anyone have an example script that I can use to set up the analysis?

Answer 1

[Mac]

I managed to get the script running, I saved it as run_bgm.bf:

inputRedirect = {}; inputRedirect["01"]="Universal"; inputRedirect["02"]="New Analysis"; inputRedirect["03"]="/home/Documents/fastafile_with_NoStopCodons.fasta_gardout_finalout"; inputRedirect["04"]="Default"; inputRedirect["05"]="y"; inputRedirect["06"]="/home/Documents/fastafile_analysis_output.txt"; inputRedirect["07"]="Estimate"; inputRedirect["08"]="BGM co-evolution"; inputRedirect["09"]="Averaged"; inputRedirect["10"]="1"; inputRedirect["11"]="2"; inputRedirect["12"]="10000"; inputRedirect["13"]="100"; inputRedirect["14"]="20"; inputRedirect["15"]="No"; inputRedirect["16"]="/home/Documents/fastafile_analysis_posterior_edge_prb.csv"; inputRedirect["17"]="n"; ExecuteAFile ("/usr/local/lib/hyphy/TemplateBatchFiles/QuickSelectionDetection.bf", inputRedirect);

I then execute the script using: HYPHYMP -np 4 run_bgm.bf