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| author | Calvin Morrison <mutantturkey@gmail.com> | 2014-03-31 13:27:06 -0400 |
|---|---|---|
| committer | Calvin Morrison <mutantturkey@gmail.com> | 2014-03-31 13:27:06 -0400 |
| commit | 5a5d89d3881cb0d9014168845d96e5eebeb2bd42 (patch) | |
| tree | 72ad2c1cb7aad7a9100c640b81741db96786fa48 /SelectiveGenomeAmplification | |
| parent | 59ac62e890a7a1c11c6e316f12fd284b31c0c4ab (diff) | |
Add feature to have a top-scores file. closes issue #21
Diffstat (limited to 'SelectiveGenomeAmplification')
| -rwxr-xr-x | SelectiveGenomeAmplification | 13 |
1 files changed, 12 insertions, 1 deletions
diff --git a/SelectiveGenomeAmplification b/SelectiveGenomeAmplification index 44fdb90..9793293 100755 --- a/SelectiveGenomeAmplification +++ b/SelectiveGenomeAmplification @@ -144,6 +144,9 @@ done # primer_weight, how much weight to give to sets with a higher number of primers. (between 0 and 1) : ${primer_weight=0} +# output_top_nb, How many scored sets would you like in the top_scored_sets output file (Default = 10000)? +: ${output_top_nb=10000} + export ignore_mers export min_mer_range export max_mer_range @@ -315,5 +318,13 @@ if [[ -n "$step_score" ]] || [[ -n "$all" ]]; then fi echo "Step 4: Scoring top mers based on selectivity" - score_wrapper.sh "$selected" "$foreground" "$background" "$output_directory/$current_run/scores-output" || exit 1 + score_wrapper.sh "$selected" "$foreground" "$background" "$output_directory/$current_run/all-scores" || exit 1 + + # output our sorted scores + echo "sorting and outputting top $output_top_nb scores" + echo "top scores output file: $output_directory/$current_run/top-scores" + head -n 1 $output_directory/$current_run/all-scores > $output_directory/$current_run/top-scores + tail -n +2 $output_directory/$current_run/all-scores | sort -r $output_directory/$current_run/all-scores -t $'\t' -nk 3 | head -n $output_top_nb >> $output_directory/$current_run/top-scores fi + + |