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| author | Calvin Morrison <mutantturkey@gmail.com> | 2014-08-13 16:59:37 -0400 |
|---|---|---|
| committer | Calvin Morrison <mutantturkey@gmail.com> | 2014-08-13 16:59:37 -0400 |
| commit | d4ec5459d0fc141d20a4bbbf0a7dc40742e0372f (patch) | |
| tree | 17d8797427b2534b538b00ed0660ac1781cd3c58 /SelectiveWholeGenomeAmplification | |
| parent | 972add88040cac2f0a969e99c533051be7220ccc (diff) | |
add filter max bg mers
Diffstat (limited to 'SelectiveWholeGenomeAmplification')
| -rwxr-xr-x | SelectiveWholeGenomeAmplification | 10 |
1 files changed, 9 insertions, 1 deletions
diff --git a/SelectiveWholeGenomeAmplification b/SelectiveWholeGenomeAmplification index 7a3d46b..8304387 100755 --- a/SelectiveWholeGenomeAmplification +++ b/SelectiveWholeGenomeAmplification @@ -182,6 +182,9 @@ done # bg_ratio : ${min_bg_ratio=0} +# max_bg_mers +: ${max_bg_mers=-1} + export ignore_mers export min_mer_range export max_mer_range @@ -246,6 +249,7 @@ ignore_all_mers_counts="$output_directory/$current_run/passes-filter/2-$fg_basen average_binding="$output_directory/$current_run/passes-filter/3-$fg_basename-average-binding" non_melting="$output_directory/$current_run/passes-filter/4-$fg_basename-non-melting" consecutive_binding="$output_directory/$current_run/passes-filter/5-$fg_basename-consecutive-binding" +bg_filtered="$output_directory/$current_run/passes-filter/6-$fg_basename-bg-filtered" # Make our output directory if [[ ! -d "$output_directory" ]]; then @@ -342,7 +346,11 @@ if [[ -n "$step_filters" ]] || [[ -n "$all" ]]; then filter_max_consecutive_binding.py "$max_consecutive_binding" < "$non_melting" > "$consecutive_binding" || exit 1 check_non_empty "$consecutive_binding" "consecutive binding" - cp $consecutive_binding $final_fg_counts + echo " filtering mers that have more bg mers than allowed ($max_bg_mers)" + filter_max_bg_mers.py "$max_bg_mers" "$bg_counts" < "$consecutive_binding" > "$bg_filtered" || exit 1 + check_non_empty "$bg_filtered" "background filtered" + + cp $bg_filtered $final_fg_counts fi if [[ -n "$step_select" ]] || [[ -n "$all" ]]; then |