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#!/usr/bin/env bash
if [ -z "$foreground" ] && [ -z "$background" ]; then
if (( $# < 2 )); then
echo "please supply two genomes, foreground and background"
exit 1
fi;
: ${foreground=$1}
: ${background=$2}
fi
if [[ ! -f $foreground ]]; then
echo "Could not open $foreground"
exit 1
fi
if [[ ! -f $background ]]; then
echo "Could not open $background"
exit 1
fi
# output directory
: ${output_directory=`basename $foreground`_`basename $background`}
# temp directory
: ${tmp_directory=$output_directory/.tmp}
# directory to store our counts and sorted counts
: ${counts_directory=$tmp_directory}
# range of mers, min and max
: ${min_mer_range=6}
: ${max_mer_range=12}
# max mer distance, the distance between two mers in our selected outputs
: ${max_mer_distance=5000}
# min/maximum kmer meling point
: ${max_melting_temp=30}
: ${min_melting_temp=0}
# minimum mer count
: ${min_mer_count=0}
# maximum mers to pick
: ${max_select=15}
# maximum mers to check
: ${max_check=35}
# mers to specifically IGNORE, space delimited
: ${ignore_mers=''}
# maximum number of mers that are consecutively binding
: ${max_consecutive_binding=4}
export ignore_mers
export min_mer_range
export max_mer_range
export max_select
export min_mer_count
export max_mer_distance
export max_melting_temp
export min_melting_temp
# Make our output directory
if [ ! -d $output_directory ]; then
mkdir $output_directory
fi
# Make our counts directory
if [ ! -d $counts_directory ]; then
mkdir $counts_directory
fi
# Make our temporary directory
if [ ! -d $tmp_directory ]; then
mkdir $tmp_directory
fi
current_run=$output_`date +%s`
mkdir -p $output_directory/$current_run
for fasta_file in $foreground $background; do
counts=$counts_directory/$(basename $fasta_file)
tmp=$tmp_directory/$(basename $fasta_file)
echo pre-processing $fasta_file
# check if our preprocessed file exists
if [[ ! -f $tmp ]]; then
echo "> pre processed $fasta_file" >> $tmp
cat $fasta_file | grep -v "^>" | tr -d '\n' >> $tmp
fi
# run counts if they haven't been created
rm $counts-counts
for mer in `seq $min_mer_range $max_mer_range`; do
if [ ! -e $counts-counts-$mer ]; then
echo checking $mer mers for $fasta_file
kmer_total_count -i $tmp -k $mer -l -n >> $counts-counts-$mer
else
echo "$mer mers already done for $fasta_file"
fi
cat $counts-counts-$mer >> $counts-counts
done
done
fg_counts=$counts_directory/$(basename $foreground)-counts
bg_counts=$counts_directory/$(basename $background)-counts
fg_tmp=$tmp_directory/$(basename $foreground)
bg_tmp=$tmp_directory/$(basename $background)
selected=$output_directory/$current_run/selected-mers
# remove ignored mers
if [ "$ignore_mers" ]; then
echo "removing ignored mers: " + $ignore_mers
for mer in $ignore_mers; do
sed -i '/^'$mer'\t/d' $fg_counts
sed -i '/^'$mer'\t/d' $bg_counts
done
fi
echo "outputing current run parameters"
for var in ignore_mers min_mer_range max_check cpus max_consecutive_binding max_mer_range max_select min_mer_count max_mer_distance max_melting_temp min_melting_temp foreground background; do
echo $var "${!var}" >> $output_directory/$current_run/parameters
done;
echo "checking if mers are within the melting range $min_melting_temp $max_melting_temp"
cat $fg_counts | filter_melting_range $min_melting_temp $max_melting_temp > $output_directory/$current_run/$foreground-counts-non-melting
cat $bg_counts | filter_melting_range $min_melting_temp $max_melting_temp > $output_directory/$current_run/$background-counts-non-melting
echo "filtering out elements that have more consecutive binding mers than allowed by default $max_consecutive_binding"
cat $output_directory/$current_run/$foreground-counts-non-melting | filter_max_consecutive_binding.py $max_consecutive_binding > $output_directory/$current_run/$foreground-counts-filtered-binding
cat $output_directory/$current_run/$background-counts-non-melting | filter_max_consecutive_binding.py $max_consecutive_binding > $output_directory/$current_run/$background-counts-filtered-binding
echo "scoring mer selectivity"
select_mers.py $output_directory/$current_run/$foreground-counts-filtered-binding $fg_tmp $output_directory/$current_run/$background-counts-filtered-binding $bg_tmp > $selected
echo "scoring top mers based on selectivity"
score_mers.py $selected $fg_tmp $bg_tmp $output_directory/$current_run/scores-output
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