evaluateAllFoundersFromInfer.sh

#!/bin/bash

# Arg one is a directory in which there are lists of "1w" fasta files
# named nnnnnnn.list where nnnnnnn is a patient number.  It expects a
# directories within that directory to be called
# hiv_founder_id_processed_nnnnnnn unless a fourth argument is
# provided, in which case it will expect directories to be called
# hiv_founder_id_nnnnnnn. Arg two is the analogous dir for the
# estimates, arg three is the writable dir to put outputs, and the
# fourth argument if present toggles the expec ted dir name (as just
# described in the previous sentence).
#
mkdir ${3}
for patient in  `ls -c1 ${1}/*.list  | egrep --only "[0-9]+\.list" | egrep --only "[0-9]+"  | sort -u`
do
    export outputDir=${3}/${patient}
    mkdir ${outputDir}
   ./evaluateFoundersFromInfer.bash ${1} ${2} ${outputDir} ${patient} ${4} &
done