Mercurial > repos > devteam > hgv_hilbertvis

comparison hilbertvis.sh @ 0:0e80ffa5b7f7 draft

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author devteam
date Wed, 25 Sep 2013 11:23:48 -0400
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-1:000000000000 0:0e80ffa5b7f7
1 #!/usr/bin/env bash
2
3 input_file="$1"
4 output_file="$2"
5 chromInfo_file="$3"
6 chrom="$4"
7 score_col="$5"
8 hilbert_curve_level="$6"
9 summarization_mode="$7"
10 chrom_col="$8"
11 start_col="$9"
12 end_col="${10}"
13 strand_col="${11}"
14
15 ## use first sequence if chrom filed is empty
16 if [ -z "$chrom" ]; then
17 chrom=$( head -n 1 "$input_file" | cut -f$chrom_col )
18 fi
19
20 ## get sequence length
21 if [ ! -r "$chromInfo_file" ]; then
22 echo "Unable to read chromInfo_file $chromInfo_file" 1>&2
23 exit 1
24 fi
25
26 chrom_len=$( awk '$1 == chrom {print $2}' chrom=$chrom $chromInfo_file )
27
28 ## error if we can't find the chrom_len
29 if [ -z "$chrom_len" ]; then
30 echo "Can't find length for sequence \"$chrom\" in chromInfo_file $chromInfo_file" 1>&2
31 exit 1
32 fi
33
34 ## make sure chrom_len is positive
35 if [ $chrom_len -le 0 ]; then
36 echo "sequence \"$chrom\" length $chrom_len <= 0" 1>&2
37 exit 1
38 fi
39
40 ## modify R script depending on the inclusion of a score column, strand information
41 input_cols="\$${start_col}, \$${end_col}"
42 col_types='beg=0, end=0, strand=""'
43
44 # if strand_col == 0 (strandCol metadata is not set), assume everything's on the plus strand
45 if [ $strand_col -ne 0 ]; then
46 input_cols="${input_cols}, \$${strand_col}"
47 else
48 input_cols="${input_cols}, \\\"+\\\""
49 fi
50
51 # set plot value (either from data or use a constant value)
52 if [ $score_col -eq -1 ]; then
53 value=1
54 else
55 input_cols="${input_cols}, \$${score_col}"
56 col_types="${col_types}, score=0"
57 value='chunk$score[i]'
58 fi
59
60 R --vanilla &> /dev/null <<endOfCode
61 library(HilbertVis);
62
63 chrom_len <- ${chrom_len};
64 chunk_size <- 1000;
65 interval_count <- 0;
66 invalid_strand <- 0;
67
68 awk_cmd <- paste(
69 "awk 'BEGIN{FS=\"\t\";OFS=\"\t\"}",
70 "\$${chrom_col} == \"${chrom}\"",
71 "{print ${input_cols}}' ${input_file}"
72 );
73
74 col_types <- list(${col_types});
75 vec <- vector(mode="numeric", length=chrom_len);
76 conn <- pipe(description=awk_cmd, open="r");
77
78 repeat {
79 chunk <- scan(file=conn, what=col_types, sep="\t", nlines=chunk_size, quiet=TRUE);
80
81 if ((rows <- length(chunk\$beg)) == 0)
82 break;
83
84 interval_count <- interval_count + rows;
85
86 for (i in 1:rows) {
87 if (chunk\$strand[i] == '+') {
88 start <- chunk\$beg[i] + 1;
89 stop <- chunk\$end[i];
90 } else if (chunk\$strand[i] == '-') {
91 start <- chrom_len - chunk\$end[i] - 1;
92 stop <- chrom_len - chunk\$beg[i];
93 } else {
94 invalid_strand <- invalid_strand + 1;
95 interval_count <- interval_count - 1;
96 next;
97 }
98 vec[start:stop] <- ${value};
99 }
100 }
101
102 close(conn);
103
104 hMat <- hilbertImage(vec, level=$hilbert_curve_level, mode="$summarization_mode");
105 pdf(file="$output_file", onefile=TRUE, width=8, height=10.5, paper="letter");
106 showHilbertImage(hMat);
107 dev.off();
108 endOfCode
109