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Giovanni Marco Dall'Olio committed 021df7a Merge

MERGE

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  • Parent commits 5eddf89, 89e1db3

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Files changed (10)

 end
 
 
-desc "Get top scores"
-#task :get_topscores  => get_top_avdegree_EUR 
-task :get_topscores do
-do
-    puts("getting top scores")
-#    system("./bin/parallel -P1 -u --arg-sep ::: 'Rscript src/get_topscores_byproperty.R 2>&1 --property {} | tee logs/topscores/{}' ::: av_closeness n_components av_path_length n_verticesav_degree")
-puts("option Temporanely disabled")
-    puts("Top scores generated")
-end
+#desc "Get top scores"
+##task :get_topscores  => get_top_avdegree_EUR 
+#task :get_topscores do
+#do
+#    puts("getting top scores")
+##    system("./bin/parallel -P1 -u --arg-sep ::: 'Rscript src/get_topscores_byproperty.R 2>&1 --property {} | tee logs/topscores/{}' ::: av_closeness n_components av_path_length n_verticesav_degree")
+#puts("option Temporanely disabled")
+#    puts("Top scores generated")
+#end
 
 desc "Convert to BED"
 task :convert_to_bed do

jobs/get_topscores.q

+#/!usr/bin/env bash
+# Get Top Scores
+#
+#$ -cwd
+#$ -V
+#$ -l h_vmem=200M
+#$ -t 1-9
+#$ -j y
+#$ -o logs/bed/
+#$ -N topscores
+
+#SGE_TASK_ID=9
+
+case $$SGE_TASK_ID in 
+
+1)
+    gawk '$$5 > 4    {print $$1, $$6-1, $$6, $$4}' results/beds/results_bed/filtered/av_degree_EUR.bed > results/beds/results_bed/top_regions/avdegree_EUR_4.bed
+    ;;
+2)
+    gawk '$$5 > 4.5  {print $$1, $$6-1, $$6, $$4}' results/beds/results_bed/filtered/av_degree_EUR.bed > results/beds/results_bed/top_regions/avdegree_EUR_45.bed
+    ;;
+3)
+    gawk '$$5 > 0.7  {print $$1, $$6-1, $$6, $$4}' results/beds/results_bed/filtered/av_closeness_EUR.bed > results/beds/results_bed/top_regions/avcloseness_EUR_7.bed
+    ;;
+4)
+    gawk '$$5 > 0.75 {print $$1, $$6-1, $$6, $$4}' results/beds/results_bed/filtered/av_closeness_EUR.bed > results/beds/results_bed/top_regions/avcloseness_EUR_75.bed
+    ;;
+5)
+    gawk '$$5 > 20   {print $$1, $$6-1, $$6, $$4}' results/beds/results_bed/filtered/n_components_EUR.bed > results/beds/results_bed/top_regions/ncomponents_EUR_20.bed
+    ;;
+6)
+    gawk '$$5 > 30   {print $$1, $$6-1, $$6, $$4}' results/beds/results_bed/filtered/n_components_EUR.bed > results/beds/results_bed/top_regions/ncomponents_EUR_30.bed
+    ;;
+7)
+    gawk '$$5 > 3.5  {print $$1, $$6-1, $$6, $$4}' results/beds/results_bed/filtered/av_path_length_EUR.bed > results/beds/results_bed/top_regions/avpathlength_EUR_35.bed
+    ;;
+8)
+    gawk '$$5 > 4    {print $$1, $$6-1, $$6, $$4}' results/beds/results_bed/filtered/av_path_length_EUR.bed > results/beds/results_bed/top_regions/avpathlength_EUR_4.bed
+    ;;
+9)
+    gawk '$$5 > 4.5  {print $$1, $$6-1, $$6, $$4}' results/beds/results_bed/filtered/av_path_length_EUR.bed > results/beds/results_bed/top_regions/avpathlength_EUR_45.bed
+    ;;
+esac

logs/vcf_to_binary_convert.log

 DEBUG:root:Finished parsing file data/vcf_filtered/DUT.recode.vcf.gz
 DEBUG:root:parsing data/vcf_filtered/DUT.recode.vcf.gz
 DEBUG:root:Finished parsing file data/vcf_filtered/DUT.recode.vcf.gz
+DEBUG:root:parsing data/vcf_filtered/chr2p.recode.vcf.gz
+DEBUG:root:parsing data/vcf_filtered/chr2q.recode.vcf.gz