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comparison bigwig_to_wig.sh @ 1:ac8ea1ca115d draft default tip

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/bigwig_to_wig commit 85bdb086a4aa403465844a0b10399440b31b65a7
author artbio
date Fri, 06 Oct 2023 00:19:35 +0000
parents ee2fbee916f7
children
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0:ee2fbee916f7 1:ac8ea1ca115d
52 #make track definition line 52 #make track definition line
53 echo "track type=wiggle_0 name=$mylab description=\"fixedStep format\"" 53 echo "track type=wiggle_0 name=$mylab description=\"fixedStep format\""
54 54
55 #for each chromsome 55 #for each chromsome
56 while read line; do 56 while read line; do
57 57
58 cur_chr=$(echo $line | cut --delimiter=" " -f1) 58 cur_chr=$(echo $line | cut -d " " -f1)
59 cur_length=$(echo $line | cut --delimiter=" " -f2) 59 cur_length=$(echo $line | cut -d " " -f2)
60 60
61 n_bins=$(echo "scale=0; (${cur_length}-${step_size})/${bin_size}" | bc) 61 n_bins=$(echo "scale=0; (${cur_length}-${step_size})/${bin_size}" | bc)
62 62
63 start=1 63 start=1
64 stop=$(echo "$n_bins * $bin_size" | bc) 64 stop=$(echo "$n_bins * $bin_size" | bc)
65 65
66 #write header line for each chromosome 66 #write header line for each chromosome
67 echo "fixedStep chrom=$cur_chr start=$start step=$step_size span=$step_size" 67 echo "fixedStep chrom=$cur_chr start=$start step=$step_size span=$step_size"
68 68
69 #get densities along chr in n_bins with chosen bin_size and step_size (giving overlap in bins) 69 #get densities along chr in n_bins with chosen bin_size and step_size (giving overlap in bins)
70 nice bigWigSummary $bigwig_file $cur_chr $start $stop $n_bins | perl -pe 's/\t/\n/g' | perl -pe "s/n\/a/0/" 70 nice bigWigSummary $bigwig_file $cur_chr $start $stop $n_bins | perl -pe 's/\t/\n/g' | perl -pe "s/n\/a/0/"
71 #gives warning if no data in/for current chromosome 71 #gives warning if no data in/for current chromosome
72 72
73 done < $org_assembly_file 73 done < $org_assembly_file
74 74
75 #rm tmp 75 #rm tmp
76 rm $org_assembly_file 76 rm $org_assembly_file
77 77