diff options
| author | Calvin Morrison <mutantturkey@gmail.com> | 2014-02-17 10:18:06 -0500 |
|---|---|---|
| committer | Calvin Morrison <mutantturkey@gmail.com> | 2014-02-17 10:18:06 -0500 |
| commit | 474d8f0de34dbe1f502784a22284f535ee4a2513 (patch) | |
| tree | 13dbc8a150a24496539a5ad59b68b6648e3a580a | |
| parent | 926e829f7c62906d9b10961d31dd30893c3e7f59 (diff) | |
output filters into output directory not temp to enable multiple runs at once
| -rwxr-xr-x | SelectiveGenomeAmplification | 10 |
1 files changed, 5 insertions, 5 deletions
diff --git a/SelectiveGenomeAmplification b/SelectiveGenomeAmplification index d03ff96..ef9aa8d 100755 --- a/SelectiveGenomeAmplification +++ b/SelectiveGenomeAmplification @@ -127,15 +127,15 @@ for var in ignore_mers min_mer_range max_consecutive_binding max_mer_range max_s 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 > $output_directory/$foreground-counts-non-melting -cat $bg_counts | filter_melting_range $min_melting_temp $max_melting_temp > $output_directory/$background-counts-non-melting +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 $output_directory/$foreground-counts-non-melting | filter_max_consecutive_binding.py $max_consecutive_binding > $output_directory/$foreground-counts-filtered-binding -cat $output_directory/$background-counts-non-melting | filter_max_consecutive_binding.py $max_consecutive_binding > $output_directory/$background-counts-filtered-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 $output_directory/$foreground-counts-filtered-binding $fg_tmp $output_directory/$background-counts-filtered-binding $bg_tmp > $selected +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 |