diff options
| -rwxr-xr-x | select_kmers.sh | 40 |
1 files changed, 35 insertions, 5 deletions
diff --git a/select_kmers.sh b/select_kmers.sh index 11ee124..3d10bcd 100755 --- a/select_kmers.sh +++ b/select_kmers.sh @@ -2,24 +2,37 @@ # range of mers, min and max : ${min_mer_range=6} : ${max_mer_range=10} +# max mer distance, the distance between two mers in our selected outputs +: ${max_mer_distance=5000} # directory to store our counts and sorted counts : ${counts_directory=$PWD/counts} # temp directory : ${tmp_directory=$PWD/tmp} -# maximum kmer melting point -: ${max_melting_temp=20} +# min/maximum kmer melting point +: ${max_melting_temp=18} +: ${min_melting_temp=0} # minimum mer count # ! you can supply either a percentage like this .5 # ! or you can supply a raw number (100) : ${min_mer_count=1000} # maximum mers to pick : ${max_select=15} +# mers to specifically IGNORE, space delimited +: ${ignore_mers=''} +export ignore_mers export min_mer_range export max_mer_range + export max_select + export min_mer_count +export max_mer_distance + +export max_melting_temp +export min_melting_temp +PATH=$PATH:`pwd` if [ ! -d $counts_directory ]; then mkdir $counts_directory @@ -77,10 +90,27 @@ bg_counts=$counts_directory/$(basename $background)-counts fg_tmp=$tmp_directory/$(basename $foreground) bg_tmp=$tmp_directory/$(basename $background) -echo "checking if mers are below melting temperature in the foreground" +# remove ignored mers +if [ "$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 "checking if mers are below melting temperature in the foreground" rm $fg_counts-fg-non-melting +melting_range $min_melting_temp $max_melting_temp < $fg_counts > $fg_counts-fg-non-melting & + +echo "checking if mers are below melting temperature in the background" +rm $bg_counts-bg-non-melting +melting_range $min_melting_temp $max_melting_temp < $bg_counts > $bg_counts-bg-non-melting -python below_melting_temperature.py $max_melting_temp < $fg_counts > $fg_counts-fg-non-melting +# echo "scoring mer selectivity" +# python ./mer_selectivity.py $fg_counts-fg-non-melting $bg_counts-bg-non-melting -python ./select_mers.py $fg_counts-fg-non-melting $fg_tmp $bg_counts $bg_tmp # > $(basename $foreground)_$(basename $background)_final_mers +echo "" +echo "scoring mers" +python ./select_mers.py $fg_counts-fg-non-melting $fg_tmp $bg_counts-bg-non-melting $bg_tmp # > $(basename $foreground)_$(basename $background)_final_mers |