diff options
| author | Calvin Morrison <mutantturkey@gmail.com> | 2014-01-21 15:42:53 -0500 |
|---|---|---|
| committer | Calvin Morrison <mutantturkey@gmail.com> | 2014-01-21 15:42:53 -0500 |
| commit | 42f2b64fffdbc16912c17c599e0f4fb417e4dcbe (patch) | |
| tree | 74e3a1abec5718912986ffb05054220508673b16 /SelectiveGenomeAmplification | |
| parent | 24d17ba72d27162653f4be6ddc47e64f99e35067 (diff) | |
split out score and selection
Diffstat (limited to 'SelectiveGenomeAmplification')
| -rwxr-xr-x | SelectiveGenomeAmplification | 22 |
1 files changed, 13 insertions, 9 deletions
diff --git a/SelectiveGenomeAmplification b/SelectiveGenomeAmplification index 1f495eb..4e14ecb 100755 --- a/SelectiveGenomeAmplification +++ b/SelectiveGenomeAmplification @@ -107,6 +107,8 @@ bg_counts=$counts_directory/$(basename $background)-counts fg_tmp=$tmp_directory/$(basename $foreground) bg_tmp=$tmp_directory/$(basename $background) +selected=$tmp_directory/$(basename $foreground)$(basename $background)-selected + # remove ignored mers if [ "$ignore_mers" ]; then echo "removing ignored mers: " + $ignore_mers @@ -118,16 +120,18 @@ 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 & +rm $fg_counts-non-melting +melting_range $min_melting_temp $max_melting_temp < $fg_counts > $fg_counts-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 +rm $bg_counts-non-melting +melting_range $min_melting_temp $max_melting_temp < $bg_counts > $bg_counts-non-melting -# echo "scoring mer selectivity" -# python ./mer_selectivity.py $fg_counts-fg-non-melting $bg_counts-bg-non-melting +#echo "scoring mer selectivity" +# python ./mer_selectivity.py $fg_counts-non-melting $bg_counts-non-melting +mer_selectivity.py $fg_counts-non-melting $fg_tmp $bg_counts-non-melting $bg_tmp > $selected + -echo "" -echo "scoring mers" -select_mers.py $fg_counts-fg-non-melting $fg_tmp $bg_counts-bg-non-melting $bg_tmp $output_directory/output_`date +%s` +# echo "scoring top 100 mers based on selectivity" +# select_mers.py $selected $output_directory/output_`date +%s` +select_mers.py $selected $fg_tmp $bg_tmp $output_directory/output_`date +%s` |