| Next changeset 1:e1a9ad05dced (2014-06-03) |
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Commit message:
Uploaded tool tarball. |
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added:
hilbertvis.sh hilbertvis.xml test-data/hvis_mkar_chr22.pdf test-data/hvis_mkar_chr22.tab tool_dependencies.xml |
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| diff -r 000000000000 -r 0e80ffa5b7f7 hilbertvis.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/hilbertvis.sh Wed Sep 25 11:23:48 2013 -0400 |
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| @@ -0,0 +1,109 @@ +#!/usr/bin/env bash + +input_file="$1" +output_file="$2" +chromInfo_file="$3" +chrom="$4" +score_col="$5" +hilbert_curve_level="$6" +summarization_mode="$7" +chrom_col="$8" +start_col="$9" +end_col="${10}" +strand_col="${11}" + +## use first sequence if chrom filed is empty +if [ -z "$chrom" ]; then + chrom=$( head -n 1 "$input_file" | cut -f$chrom_col ) +fi + +## get sequence length +if [ ! -r "$chromInfo_file" ]; then + echo "Unable to read chromInfo_file $chromInfo_file" 1>&2 + exit 1 +fi + +chrom_len=$( awk '$1 == chrom {print $2}' chrom=$chrom $chromInfo_file ) + +## error if we can't find the chrom_len +if [ -z "$chrom_len" ]; then + echo "Can't find length for sequence \"$chrom\" in chromInfo_file $chromInfo_file" 1>&2 + exit 1 +fi + +## make sure chrom_len is positive +if [ $chrom_len -le 0 ]; then + echo "sequence \"$chrom\" length $chrom_len <= 0" 1>&2 + exit 1 +fi + +## modify R script depending on the inclusion of a score column, strand information +input_cols="\$${start_col}, \$${end_col}" +col_types='beg=0, end=0, strand=""' + +# if strand_col == 0 (strandCol metadata is not set), assume everything's on the plus strand +if [ $strand_col -ne 0 ]; then + input_cols="${input_cols}, \$${strand_col}" +else + input_cols="${input_cols}, \\\"+\\\"" +fi + +# set plot value (either from data or use a constant value) +if [ $score_col -eq -1 ]; then + value=1 +else + input_cols="${input_cols}, \$${score_col}" + col_types="${col_types}, score=0" + value='chunk$score[i]' +fi + +R --vanilla &> /dev/null <<endOfCode +library(HilbertVis); + +chrom_len <- ${chrom_len}; +chunk_size <- 1000; +interval_count <- 0; +invalid_strand <- 0; + +awk_cmd <- paste( + "awk 'BEGIN{FS=\"\t\";OFS=\"\t\"}", + "\$${chrom_col} == \"${chrom}\"", + "{print ${input_cols}}' ${input_file}" +); + +col_types <- list(${col_types}); +vec <- vector(mode="numeric", length=chrom_len); +conn <- pipe(description=awk_cmd, open="r"); + +repeat { + chunk <- scan(file=conn, what=col_types, sep="\t", nlines=chunk_size, quiet=TRUE); + + if ((rows <- length(chunk\$beg)) == 0) + break; + + interval_count <- interval_count + rows; + + for (i in 1:rows) { + if (chunk\$strand[i] == '+') { + start <- chunk\$beg[i] + 1; + stop <- chunk\$end[i]; + } else if (chunk\$strand[i] == '-') { + start <- chrom_len - chunk\$end[i] - 1; + stop <- chrom_len - chunk\$beg[i]; + } else { + invalid_strand <- invalid_strand + 1; + interval_count <- interval_count - 1; + next; + } + vec[start:stop] <- ${value}; + } +} + +close(conn); + +hMat <- hilbertImage(vec, level=$hilbert_curve_level, mode="$summarization_mode"); +pdf(file="$output_file", onefile=TRUE, width=8, height=10.5, paper="letter"); +showHilbertImage(hMat); +dev.off(); +endOfCode + |
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| diff -r 000000000000 -r 0e80ffa5b7f7 hilbertvis.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/hilbertvis.xml Wed Sep 25 11:23:48 2013 -0400 |
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| @@ -0,0 +1,120 @@ +<tool id="hgv_hilbertvis" name="HVIS" version="1.0.0"> + <description>visualization of genomic data with the Hilbert curve</description> + <requirements> + <requirement type="package" version="2.11.0">R</requirement> + <requirement type="package" version="1.18.0">bioc_hilbertvis</requirement> + </requirements> + <command interpreter="bash"> + hilbertvis.sh $input $output $chromInfo "$chrom" $plot_value.score_col $level $mode + #if isinstance( $input.datatype, $__app__.datatypes_registry.get_datatype_by_extension('gff').__class__) + 1 4 5 7 + #else + ${input.metadata.chromCol} ${input.metadata.startCol} ${input.metadata.endCol} ${input.metadata.strandCol} + #end if + </command> + + <inputs> + <param name="input" type="data" format="interval,gff" label="Dataset"> + <validator type="unspecified_build"/> + <validator type="metadata" check="chromCol" message="chromCol missing"/> + <validator type="metadata" check="startCol" message="startCol missing"/> + <validator type="metadata" check="endCol" message="endCol missing"/> + </param> + <param name="chrom" type="text" label="Sequence to plot" help="Name of sequence (from the chromosome column in the dataset) to plot. If left blank, the first sequence in the dataset will be plotted."/> + <conditional name="plot_value"> + <param name="choice" type="select" label="Value to plot"> + <option value="score" selected="true">Score column from dataset</option> + <option value="exist">Same value for each base (existence)</option> + </param> + <when value="score"> + <param name="score_col" type="data_column" data_ref="input" numerical="true" label="Score column"/> + </when> + <when value="exist"> + <param name="score_col" type="hidden" value="-1"/> + </when> + </conditional> + <param name="level" type="integer" value="9" label="Level" help="Level of Hilbert curve. The resulting image will have 2<sup>level</sup> by 2<sup>level</sup> pixels."> + <validator type="in_range" min="1" message="The level must be an integer >= 1."/> + </param> + <param name="mode" type="select" label="Summarization mode" help="Method used to determine a value for a point in the plot which covers multiple values in the input."> + <option value="max">Maximal value in each bin</option> + <option value="min">Minimal value in each bin</option> + <option value="absmax" selected="true">Maximal absolute value in each bin</option> + <option value="mean">Mean value of each bin</option> + </param> + </inputs> + + <outputs> + <data name="output" format="pdf"/> + </outputs> + + <tests> + <test> + <param name="input" value="hvis_mkar_chr22.tab"/> + <param name="chrom" value="chr22"/> + <param name="choice" value="score"/> + <param name="score_col" value="15"/> + <param name="level" value="9"/> + <param name="mode" value="absmax"/> + <output name="output" file="hvis_mkar_chr22.pdf" compare="sim_size" delta="7168"/> + </test> + </tests> + + <help> +**Dataset formats** + +The input format is interval_, and the output is an image in PDF format. +(`Dataset missing?`_) + +.. _interval: ${static_path}/formatHelp.html#interval +.. _Dataset missing?: ${static_path}/formatHelp.html + +----- + +**What it does** + +HilbertVis uses the Hilbert space-filling curve to visualize the structure of +position-dependent data. It maps the traditional one-dimensional line +visualization onto a two-dimensional square. For example, here is a diagram +showing the path of a level-2 Hilbert curve. + +.. image:: ${static_path}/images/hilbertvisDiagram.png + +The shade of each pixel represents the value for the corresponding bin of +consecutive genomic positions, calculated according to the specified +summarization mode. The pixels are arranged so that bins that are close +to each other on the data vector are represented by pixels that are close +to each other in the plot. In particular, adjacent bins are mapped to +adjacent pixels. Hence, dark spots in a figure represent a peak; the area +of the spot in the two-dimensional plot is proportional to the width of the +peak in the one-dimensional data, and the darkness of the spot corresponds to +the height of the peak. + +The input file is in interval format, and typically contains a column with +scores or other numbers, such as conservation scores, SNP density, the +coverage of aligned reads from ChIP-Seq data, etc. + +Website: http://www.ebi.ac.uk/huber-srv/hilbert/ + +----- + +**Examples** + +Here are some examples from the HilbertVis homepage, using ChIP-Seq data. + +.. image:: ${static_path}/images/hilbertvis1.png + +----- + +.. image:: ${static_path}/images/hilbertvis2.png + +----- + +**Reference** + +Anders S. (2009) +Visualization of genomic data with the Hilbert curve. +Bioinformatics. 25(10):1231-5. Epub 2009 Mar 17. + + </help> +</tool> |
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| diff -r 000000000000 -r 0e80ffa5b7f7 test-data/hvis_mkar_chr22.pdf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/hvis_mkar_chr22.pdf Wed Sep 25 11:23:48 2013 -0400 |
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| diff -r 000000000000 -r 0e80ffa5b7f7 test-data/hvis_mkar_chr22.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/hvis_mkar_chr22.tab Wed Sep 25 11:23:48 2013 -0400 |
| b |
| b'@@ -0,0 +1,28863 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49476000\t20\t117\t0.170940\t6\t29\t0.206897\t0.826211\t20.709302\t116.290698\t5.290698\t29.709302\t0.7916051321\n+chr22\t49467000\t49477000\t16\t86\t0.186047\t7\t34\t0.205882\t0.903654\t16.405594\t85.594406\t6.594406\t34.405594\t0.8064236219\n+chr22\t49468000\t49478000\t10\t34\t0.294118\t7\t44\t0.159091\t1.848739\t7.873684\t36.126316\t9.126316\t41.873684\t0.2917184446\n+chr22\t49469000\t49479000\t4\t24\t0.166667\t14\t51\t0.274510\t0.607143\t5.419355\t22.580645\t12.580645\t52.419355\t0.5700385455\n+chr22\t49470000\t49480000\t6\t26\t0.230769\t16\t51\t0.313725\t0.735577\t7.111111\t24.888889\t14.888889\t52.111111\t0.6165078993\n+chr22\t49471000\t49481000\t9\t30\t0.300000\t16\t53\t0.301887\t0.993750\t9.027778\t29.972222\t15.972222\t53.027778\t1.0000000000\n+chr22\t49472000\t49482000\t10\t30\t0.333333\t16\t55\t0.290909\t1.145833\t9.369369\t30.630631\t16.630631\t54.369369\t0.8174766567\n+chr22\t49473000\t49483000\t8\t32\t0.250000\t14\t42\t0.333333\t0.750000\t9.166667\t30.833333\t12.833333\t43.166667\t0.6287868790\n+chr22\t49474000\t49484000\t12\t32\t0.375000\t14\t42\t0.333333\t1.125000\t11.440000\t32.560000\t14.560000\t41.440000\t0.8218179393\n+chr22\t49475000\t49485000\t14\t36\t0.388889\t13\t34\t0.382353\t1.017094\t13.917526\t36.082474\t13.082474\t33.917526\t1.0000000000\n+chr22\t49476000\t49486000\t15\t38\t0.394737\t10\t34\t0.294118\t1.342105\t13.659794\t39.340206\t11.340206\t32.659794\t0.6427291231\n+chr22\t49477000\t49487000\t18\t48\t0.375000\t9\t29\t0.310345\t1.208333\t17.134615\t48.865385\t9.865385\t28.134615\t0.8174337525\n+chr22\t49478000\t49488000\t20\t53\t0.377358\t10\t26\t0.384615\t0.981132\t20.091743\t52.908257\t9.908257\t26.091743\t1.0000000000\n+chr22\t49479000\t49489000\t23\t61\t0.377049\t3\t21\t0.142857\t2.639344\t20.222222\t63.777778\t5.777778\t18.222222\t0.1788144309\n+chr22\t49480000\t49490000\t27\t65\t0.415385\t1\t19\t0.052632\t7.892308\t23.000000\t69.000000\t5.000000\t15.000000\t0.0228178904\n+chr22\t49482000\t49492000\t30\t61\t0.491803\t2\t15\t0.133333\t3.688525\t26.962963\t64.037037\t5.037037\t11.962963\t0.0906328328\n+chr22\t49483000\t49493000\t33\t62\t0.532258\t5\t18\t0.277778\t1.916129\t30.593220\t64.406780\t7.406780\t15.593220\t0.3211810702\n+chr22\t49484000\t49494000\t31\t60\t0.516667\t9\t25\t0.360000\t1.435185\t29.120000\t61.880000\t10.880000\t23.120000\t0.5197826507\n+chr22\t49485000\t49495000\t29\t62\t0.467742\t9\t29\t0.310345\t1.507168\t26.806202\t64.193798\t11.193798\t26.806202\t0.4026259795\n+chr22\t49486000\t49496000\t31\t70\t0.442857\t9\t24\t0.375000\t1.180952\t30.149254\t70.850746\t9.850746\t23.149254\t0.8278306450\n+chr22\t49487000\t49497000\t30\t82\t0.365854\t9\t24\t0.375000\t0.975610\t30.124138\t81.875862\t8.875862\t24.124138\t1.0000000000\n+chr22\t49488000\t49498000\t32\t85\t0.376471\t8\t17\t0.470588\t0.800000\t32.957746\t84.042254\t7.042254\t17.957746\t0.6313420873\n+chr22\t49489000\t49499000\t34\t82\t0.414634\t9\t18\t0.500000\t0.829268\t34.881119\t81.118881\t8.118881\t18.881119\t0.8160427665\n+chr22\t49490000\t49500000\t32\t88\t0.363636\t9\t20\t0.450000\t0.808081\t33.020134\t86.979866\t7.979866\t21.020134\t0.6476674445\n+chr22\t49491000\t49501000\t34\t93\t0.365591\t9\t20\t0.450000\t0.812425\t35.006410\t91.993590\t7.993590\t21.006410\t0.6497917361\n+chr22\t49492000\t49502000\t32\t85\t0.376471\t8\t24\t0.333333\t1.129412\t31.409396\t85.590604\t8.590604\t23.409396\t1.0000000000\n+chr22\t49493000\t49503000\t31\t88\t0.352273\t6\t24\t0.250000\t1.409091\t29.550336\t89.449664\t7.449664\t22.550336\t0.6378617992\n+chr22\t49547000\t49557000\t6\t32\t0.187500\t7\t52\t0.134615\t1.392857\t5.092784\t32.907216\t7.907216\t51.092784\t0.7612004699\n+chr22\t49549000\t49559000\t6\t35\t0.171429\t7\t46\t0.152174\t1.126531\t5.670213\t35.329787\t7.329787\t45.670213\t1.0000000000\n+chr22\t49550000\t49560000\t6\t38\t0.157895\t6\t38\t0.157895\t1.000000\t6.000000\t38.000000\t6.000000\t38.000000\t1.0000000000\n+chr22\t49551000\t49561000\t8\t54\t0.148148\t7\t36\t0.194444\t0.761905\t8.857143\t53.142857\t6.142857\t36.857143\t0.7778037535\n' |
| b |
| diff -r 000000000000 -r 0e80ffa5b7f7 tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Wed Sep 25 11:23:48 2013 -0400 |
| b |
| @@ -0,0 +1,9 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="R" version="2.11.0"> + <repository changeset_revision="8d0a55bf7aaf" name="package_r_2_11_0" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" /> + </package> + <package name="bioc_hilbertvis" version="1.18.0"> + <repository changeset_revision="ce15999e50b1" name="package_bioc_hilbertvis_1_18_0" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" /> + </package> +</tool_dependency> |