# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User rc # Date 1282769169 14400 # Node ID 95915784818931029539fd058c328e45470d34c2 # Parent b1a9700382738ba805c20047f40541b06d33b04b (no commit message)
--- a/tools/mutation/visualize.xml +++ b/tools/mutation/visualize.xml @@ -1,9 +1,16 @@ <tool id="mutation_visualize" name="Mutation Visualization" version="1.0.0"><description></description> - <command interpreter="python">visualize.py --input-file=$input --output-file=$out_file1 $header_row</command> + <command interpreter="python">visualize.py --input-file=$input --output-file=$out_file1 --zoom=$zoom_value $header_row</command><inputs><param format="tabular" name="input" type="data" label="Compare sequences in"></param><param name="header_row" type="boolean" label="Header in dataset?" checked="yes" truevalue="" falsevalue="--noheaders"/> + <param name="zoom_value" type="select" label="Zoom"> + <option value="1">1x</option> + <option value="2">2x</option> + <option value="3">3x</option> + <option value="4">4x</option> + <option value="5">5x</option> + </param></inputs><outputs><data format="svg" name="out_file1" />
--- a/tools/mutation/visualize.py +++ b/tools/mutation/visualize.py @@ -17,21 +17,21 @@ import svgfig as svg COLS_PER_SAMPLE = 7 HEADER_COLS = 4
-SPACE_PAIRS = 0.8 -SPACE_SAMPLES = 1 +HEIGHT = 6 +WIDTH = 12 +BAR_WIDTH = 1.5 +GAP = 2
-HEIGHT = 4 -WIDTH = 8
colors = {'A':'blue', 'C':'green', 'G':'orange', 'T':'red'} bases = ['A', 'C', 'G', 'T' ]
def mainsvg(opts): - s = svg.SVG('g') + s = svg.SVG('g', transform="translate(20,0)")
# display legend - for i, b in enumerate(bases): + for i, b in enumerate( bases ): bt = svg.SVG("tspan", b, style="font-family:Verdana;font-size:3") s.append(svg.SVG("text", bt, x=12+(i*10), y=8, stroke="none", fill="black")) s.append(svg.SVG("rect", x=13+(i*10), y=5, width=4, height=3, @@ -71,10 +71,10 @@ def mainsvg(opts): #print 'position', position, ref, count
# display positions - bt = svg.SVG("tspan", str(position), style="font-family:Verdana;font-size:3") - s.append(svg.SVG("text", bt, x=9, y=33+(count*5), stroke="none", fill="black")) - s.append(svg.SVG("rect", x=4, y=30+(count*5), width=10, height=4, - stroke='none', fill=colors[ref.upper()], fill_opacity=0.3)) + bt = svg.SVG("tspan", str(position), style="font-family:Verdana;font-size:4") + s.append(svg.SVG("text", bt, x=7, y=34+(count*(HEIGHT+GAP)), stroke="none", fill="black")) + s.append(svg.SVG("rect", x=0, y=30+(count*(HEIGHT+GAP)), width=14, height=HEIGHT, + stroke='none', fill=colors[ref.upper()], fill_opacity=0.2))
for sample_index in range(int((len(row)-HEADER_COLS)/COLS_PER_SAMPLE)): start_col = HEADER_COLS+(COLS_PER_SAMPLE*sample_index) @@ -88,10 +88,10 @@ def mainsvg(opts):
#print 'sample_index', sample_index, total if total: - x = 16+(sample_index*10) - y = 30+(count*5) + x = 16+(sample_index*(WIDTH+GAP)) + y = 30+(count*(HEIGHT+GAP)) width = WIDTH - height = 4 + height = HEIGHT
if imp == 1: fill_opacity = 0.1 @@ -104,18 +104,21 @@ def mainsvg(opts): stroke='none', fill='grey', fill_opacity=fill_opacity)) for base, value in enumerate([n_a, n_c, n_g, n_t]): width = int(math.ceil(value / total * WIDTH)) - s.append(svg.SVG("rect", x=x, y=y, width=width, height=1, + s.append(svg.SVG("rect", x=x, y=y, width=width, height=BAR_WIDTH, stroke='none', fill=colors[bases[base]], fill_opacity=0.6)) - y = y + 1 + y = y + BAR_WIDTH #print base, value, total, x, y, width
count=count+1 - - w = str(int(700)) + "px" - h = str(int(1000)) + "px" - canv = svg.canvas(s, width=w, height=h, viewBox="0 0 200 300") + + #print x, y + + zoom = int(opts.zoom) + w = "%ipx" % (x*(10+zoom)) + h = "%ipx" % (y*(2+zoom)) + canv = svg.canvas(s, width=w, height=h, viewBox="0 0 %i %i" %(x+100, y+100)) canv.save(opts.output_file)
@@ -123,6 +126,7 @@ if __name__ == '__main__': parser = optparse.OptionParser() parser.add_option('-i', '--input-file', dest='input_file', action='store') parser.add_option('-o', '--output-file', dest='output_file', action='store') + parser.add_option('-z', '--zoom', dest='zoom', action='store', default='1') parser.add_option('-n', '--noheaders', dest='header_row', action='store_false', default=True) (opts, args) = parser.parse_args() mainsvg(opts)
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