diff options
| author | Calvin Morrison <mutantturkey@gmail.com> | 2014-01-29 11:53:30 -0500 |
|---|---|---|
| committer | Calvin Morrison <mutantturkey@gmail.com> | 2014-01-29 11:53:30 -0500 |
| commit | 94d04a1e503121a98b403f882c18a4f0799267d7 (patch) | |
| tree | 0d2cf5586b31bddc9bca99b4b07ebb4b993f1130 /SelectiveGenomeAmplification | |
| parent | 73531da5cdf33f9bde7d4db0e4ce96f1e41f581b (diff) | |
add filtering based on consecutive mer lengths
Diffstat (limited to 'SelectiveGenomeAmplification')
| -rwxr-xr-x | SelectiveGenomeAmplification | 16 |
1 files changed, 9 insertions, 7 deletions
diff --git a/SelectiveGenomeAmplification b/SelectiveGenomeAmplification index 543f90b..fcbd5dd 100755 --- a/SelectiveGenomeAmplification +++ b/SelectiveGenomeAmplification @@ -41,6 +41,8 @@ fi : ${max_select=15} # 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 @@ -124,16 +126,16 @@ for var in ignore_mers min_mer_range max_mer_range max_select min_mer_count max_ echo $var "${!var}" >> $output_directory/$current_run/parameters done; -echo "checking if mers are below melting temperature in the foreground" -rm $fg_counts-non-melting -melting_range $min_melting_temp $max_melting_temp < $fg_counts > $fg_counts-non-melting +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 > $fg_counts-non-melting +cat $bg_counts | filter_melting_range $min_melting_temp $max_melting_temp > $bg_counts-non-melting -echo "checking if mers are below melting temperature in the background" -rm $bg_counts-non-melting -melting_range $min_melting_temp $max_melting_temp < $bg_counts > $bg_counts-non-melting +echo "filtering out elements that have more consecutive binding mers than allowed by default $max_consecutive_binding" +cat $fg_counts-non-melting | filter_max_consecutive_binding.py $max_consecutive_binding > $fg_counts-filtered-binding +cat $bg_counts-non-melting | filter_max_consecutive_binding.py $max_consecutive_binding > $bg_counts-filtered-binding echo "scoring mer selectivity" -select_mers.py $fg_counts-non-melting $fg_tmp $bg_counts-non-melting $bg_tmp > $selected +select_mers.py $fg_counts-filtered-binding $fg_tmp $bg_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 |