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annotate bigwig_to_wig.sh @ 0:ee2fbee916f7 draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bigwig_to_wig commit 5baa8e0a6a2bf65e58972c19b636ff4789c25b56
author artbio
date Tue, 25 Sep 2018 17:41:20 -0400
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children ac8ea1ca115d
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ee2fbee916f7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bigwig_to_wig commit 5baa8e0a6a2bf65e58972c19b636ff4789c25b56
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1 #!/bin/bash
ee2fbee916f7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bigwig_to_wig commit 5baa8e0a6a2bf65e58972c19b636ff4789c25b56
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2 #$Id: bigwig2wig 23 2014-01-28 12:09:22Z jens $
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3
ee2fbee916f7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bigwig_to_wig commit 5baa8e0a6a2bf65e58972c19b636ff4789c25b56
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4 #SCRIPT CONVERTS BIGWIG FILE TO FIXED-STEP WIGGLE FORMAT FILE
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5 #RESOLUTION IS CONTROLLED THROUGH THE BIN SIZE
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6
ee2fbee916f7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bigwig_to_wig commit 5baa8e0a6a2bf65e58972c19b636ff4789c25b56
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7 #default bin_size
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8 bin_size=500
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9 mylab="wiggle file"
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10
ee2fbee916f7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bigwig_to_wig commit 5baa8e0a6a2bf65e58972c19b636ff4789c25b56
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11 #parse input
ee2fbee916f7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bigwig_to_wig commit 5baa8e0a6a2bf65e58972c19b636ff4789c25b56
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12 while getopts hf:b:l: myarg
ee2fbee916f7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bigwig_to_wig commit 5baa8e0a6a2bf65e58972c19b636ff4789c25b56
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13 do case "$myarg" in
ee2fbee916f7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bigwig_to_wig commit 5baa8e0a6a2bf65e58972c19b636ff4789c25b56
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14 h) echo "Usage: bigwig_correlation -f <bigwig_file> -b <bin_size>"
ee2fbee916f7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bigwig_to_wig commit 5baa8e0a6a2bf65e58972c19b636ff4789c25b56
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15 echo "Ex: bigwig_correlation -f <MYFILE.bw> -b 600"
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16 exit ;;
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17 f) bigwig_file="$OPTARG" ;; #required
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18 l) mylab="$OPTARG" ;; #optional
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19 b) bin_size="$OPTARG" ;; #optional
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20 [?]) echo "Usage: bigwig_correlation -f <MYFILE.bw> -b <bin_size>"
ee2fbee916f7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bigwig_to_wig commit 5baa8e0a6a2bf65e58972c19b636ff4789c25b56
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21 exit 1 ;;
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22 esac
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23 done
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24
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25 ###################################################
ee2fbee916f7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bigwig_to_wig commit 5baa8e0a6a2bf65e58972c19b636ff4789c25b56
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26 ###VALIDATE INPUT
ee2fbee916f7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bigwig_to_wig commit 5baa8e0a6a2bf65e58972c19b636ff4789c25b56
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27 ###################################################
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29 #make tmp-filename to hold chromosome info
ee2fbee916f7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bigwig_to_wig commit 5baa8e0a6a2bf65e58972c19b636ff4789c25b56
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30 org_assembly_file=$(mktemp -u)
ee2fbee916f7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bigwig_to_wig commit 5baa8e0a6a2bf65e58972c19b636ff4789c25b56
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31 bigWigInfo -chroms $bigwig_file | perl -ne "/^\tchr/ && print" | perl -pe "s/ +/\t/g" | cut -f2,4 > $org_assembly_file
ee2fbee916f7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bigwig_to_wig commit 5baa8e0a6a2bf65e58972c19b636ff4789c25b56
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ee2fbee916f7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bigwig_to_wig commit 5baa8e0a6a2bf65e58972c19b636ff4789c25b56
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33 #check bin_size & define step_size
ee2fbee916f7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bigwig_to_wig commit 5baa8e0a6a2bf65e58972c19b636ff4789c25b56
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34 bin_size_mod=$((bin_size % 2)) #determine modulus
ee2fbee916f7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bigwig_to_wig commit 5baa8e0a6a2bf65e58972c19b636ff4789c25b56
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35 if [ $bin_size_mod -ne 0 ]; then
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36 echo "Chosen bin_size must be an even positive number, added +1 to bin_size"
ee2fbee916f7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bigwig_to_wig commit 5baa8e0a6a2bf65e58972c19b636ff4789c25b56
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37 bin_size=$((bin_size + 1))
ee2fbee916f7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bigwig_to_wig commit 5baa8e0a6a2bf65e58972c19b636ff4789c25b56
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38 fi
ee2fbee916f7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bigwig_to_wig commit 5baa8e0a6a2bf65e58972c19b636ff4789c25b56
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39
ee2fbee916f7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bigwig_to_wig commit 5baa8e0a6a2bf65e58972c19b636ff4789c25b56
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40 if [ $bin_size -lt 100 ]; then
ee2fbee916f7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bigwig_to_wig commit 5baa8e0a6a2bf65e58972c19b636ff4789c25b56
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41 echo "ERROR: Chosen bin_size must be a positive number >=100"
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42 exit 1
ee2fbee916f7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bigwig_to_wig commit 5baa8e0a6a2bf65e58972c19b636ff4789c25b56
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43 fi
ee2fbee916f7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bigwig_to_wig commit 5baa8e0a6a2bf65e58972c19b636ff4789c25b56
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44 #set stetp size equal to bin size i.e. non-overlapping intervals
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45 step_size=$bin_size
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ee2fbee916f7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bigwig_to_wig commit 5baa8e0a6a2bf65e58972c19b636ff4789c25b56
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47 ###################################################
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48 ###EXTRACT DENSITIES FROM NORMALIZED BIGWIG FILES
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49 ###################################################
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51
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52 #make track definition line
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53 echo "track type=wiggle_0 name=$mylab description=\"fixedStep format\""
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54
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55 #for each chromsome
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56 while read line; do
ee2fbee916f7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bigwig_to_wig commit 5baa8e0a6a2bf65e58972c19b636ff4789c25b56
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58 cur_chr=$(echo $line | cut --delimiter=" " -f1)
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59 cur_length=$(echo $line | cut --delimiter=" " -f2)
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61 n_bins=$(echo "scale=0; (${cur_length}-${step_size})/${bin_size}" | bc)
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63 start=1
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64 stop=$(echo "$n_bins * $bin_size" | bc)
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66 #write header line for each chromosome
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67 echo "fixedStep chrom=$cur_chr start=$start step=$step_size span=$step_size"
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68
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69 #get densities along chr in n_bins with chosen bin_size and step_size (giving overlap in bins)
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70 nice bigWigSummary $bigwig_file $cur_chr $start $stop $n_bins | perl -pe 's/\t/\n/g' | perl -pe "s/n\/a/0/"
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71 #gives warning if no data in/for current chromosome
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73 done < $org_assembly_file
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75 #rm tmp
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76 rm $org_assembly_file
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