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comparison bigwig_to_wig.sh @ 0:99dc4bdb1d35 draft

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author nikos
date Tue, 05 Aug 2014 07:44:03 -0400
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-1:000000000000 0:99dc4bdb1d35
1 #!/bin/bash
2 #$Id: bigwig2wig 23 2014-01-28 12:09:22Z jens $
3
4 #SCRIPT CONVERTS BIGWIG FILE TO FIXED-STEP WIGGLE FORMAT FILE
5 #RESOLUTION IS CONTROLLED THROUGH THE BIN SIZE
6
7 #default bin_size
8 bin_size=500
9 mylab="wiggle file"
10
11 #parse input
12 while getopts hf:b:l: myarg
13 do case "$myarg" in
14 h) echo "Usage: bigwig_correlation -f <bigwig_file> -b <bin_size>"
15 echo "Ex: bigwig_correlation -f <MYFILE.bw> -b 600"
16 exit ;;
17 f) bigwig_file="$OPTARG" ;; #required
18 l) mylab="$OPTARG" ;; #optional
19 b) bin_size="$OPTARG" ;; #optional
20 [?]) echo "Usage: bigwig_correlation -f <MYFILE.bw> -b <bin_size>"
21 exit 1 ;;
22 esac
23 done
24
25 ###################################################
26 ###VALIDATE INPUT
27 ###################################################
28
29 #make tmp-filename to hold chromosome info
30 org_assembly_file=`mktemp -u`
31 bigWigInfo -chroms $bigwig_file | perl -ne "/^\tchr/ && print" | perl -pe "s/ +/\t/g" | cut -f2,4 > $org_assembly_file
32
33 #check bin_size & define step_size
34 bin_size_mod=`expr $bin_size % 2` #determine modulus
35 if [ $bin_size_mod -ne 0 ]; then
36 echo "Chosen bin_size must be an even positive number, added +1 to bin_size"
37 bin_size=$(($bin_size + 1))
38 fi
39
40 if [ $bin_size -lt 100 ]; then
41 echo "ERROR: Chosen bin_size must be a positive number >=100"
42 exit 1
43 fi
44 #set stetp size equal to bin size i.e. non-overlapping intervals
45 step_size=$bin_size
46
47 ###################################################
48 ###EXTRACT DENSITIES FROM NORMALIZED BIGWIG FILES
49 ###################################################
50
51
52 #make track definition line
53 echo "track type=wiggle_0 name=$mylab description=\"fixedStep format\""
54
55 #for each chromsome
56 cat $org_assembly_file | while read line; do
57
58 cur_chr=`echo $line | cut --delimiter=" " -f1`
59 cur_length=`echo $line | cut --delimiter=" " -f2`
60
61 n_bins=`echo "scale=0; (${cur_length}-${step_size})/${bin_size}" | bc`
62
63 start=1
64 stop=`echo "$n_bins * $bin_size" | bc`
65
66 #write header line for each chromosome
67 echo "fixedStep chrom=$cur_chr start=$start step=$step_size span=$step_size"
68
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/"
71 #gives warning if no data in/for current chromosome
72
73 done
74
75 #rm tmp
76 rm $org_assembly_file
77