Giovanni Marco Dall'Olio avatar Giovanni Marco Dall'Olio committed cc9f9ef

BEDS: adding the central_snp_position column to bed files. This is important, otherwise I wont be able to retrieve the exact position of the top scores

The upstream and downstream positions are needed in order to correctly filter all the windows that fall within a masked region.

However, I want to retrieve the top scores only for the central SNP.

Comments (0)

Files changed (1)

src/results_to_bed.sh

 ## Average Degree (23)
 echo "Av degree"
 #echo results/tables/whole_chromosomes/w11/chr*_w11.csv.gz | gawk '{print "chr"$6, $9-1, $8, $5, $23 > "results/beds/results_bed/av_degree_"$2".bed"}'
-gunzip -c results/tables/whole_chromosomes/w11/chr*_w11.csv.gz | gawk '{print "chr"$6, $9-1, $8, $5, $23 > "results/beds/results_bed/av_degree_"$2".bed"}'
+gunzip -c results/tables/whole_chromosomes/w11/chr*_w11.csv.gz | gawk '{print "chr"$6, $9-1, $8, $5, $23, $7 > "results/beds/results_bed/av_degree_"$2".bed"}'
 find results/beds/results_bed/ -iname "av_degree*.bed" | parallel "cat {} | starch - > {}.starch"
 
 # N vertices (15)
 echo "N Vertices"
-gunzip -c results/tables/whole_chromosomes/w11/chr*_w11.csv.gz | gawk '{print "chr"$6, $9-1, $8, $5, $15 > "results/beds/results_bed/n_vertices_"$2".bed"}'
+gunzip -c results/tables/whole_chromosomes/w11/chr*_w11.csv.gz | gawk '{print "chr"$6, $9-1, $8, $5, $15, $7> "results/beds/results_bed/n_vertices_"$2".bed"}'
 
 # N components (17)
 echo "N components"
-gunzip -c results/tables/whole_chromosomes/w11/chr*_w11.csv.gz | gawk '{print "chr"$6, $9-1, $8, $5, $17 > "results/beds/results_bed/n_components_"$2".bed"}'
+gunzip -c results/tables/whole_chromosomes/w11/chr*_w11.csv.gz | gawk '{print "chr"$6, $9-1, $8, $5, $17, $7> "results/beds/results_bed/n_components_"$2".bed"}'
 
 # Average Path Length (18)
 echo "Av Path Length"
-gunzip -c results/tables/whole_chromosomes/w11/chr*_w11.csv.gz | gawk '{print "chr"$6, $9-1, $8, $5, $18 > "results/beds/results_bed/av_path_length"$2".bed"}'
+gunzip -c results/tables/whole_chromosomes/w11/chr*_w11.csv.gz | gawk '{print "chr"$6, $9-1, $8, $5, $18, $7 > "results/beds/results_bed/av_path_length"$2".bed"}'
 
 # Average Closeness (29)
 echo "Av Closeness"
-gunzip -c results/tables/whole_chromosomes/w11/chr*_w11.csv.gz | gawk '{print "chr"$6, $9-1, $8, $5, $29 > "results/beds/results_bed/av_closeness_"$2".bed"}'
+gunzip -c results/tables/whole_chromosomes/w11/chr*_w11.csv.gz | gawk '{print "chr"$6, $9-1, $8, $5, $29, $7 > "results/beds/results_bed/av_closeness_"$2".bed"}'
 
 
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