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src/b/i/biopython-1.63/Doc/examples/Proux_et_al_2002_Figure_6.py   biopython(Download)
gd_diagram.draw(format="linear", pagesize='A4', fragments=1,
                start=0, end=max_len)
gd_diagram.write(name + ".pdf", "PDF")
gd_diagram.write(name + ".eps", "EPS")
gd_diagram.write(name + ".svg", "SVG")

src/b/i/biopython-HEAD/Doc/examples/Proux_et_al_2002_Figure_6.py   biopython(Download)
gd_diagram.draw(format="linear", pagesize='A4', fragments=1,
                start=0, end=max_len)
gd_diagram.write(name + ".pdf", "PDF")
gd_diagram.write(name + ".eps", "EPS")
gd_diagram.write(name + ".svg", "SVG")

src/b/i/biopython-1.63/Doc/examples/ACT_example.py   biopython(Download)
gd_diagram.draw(format="linear", fragments=3,
                orientation="landscape", pagesize=(20*cm, 10*cm))
gd_diagram.write(name + ".pdf", "PDF")
 
gd_diagram.draw(format="circular",
                orientation="landscape", pagesize=(20*cm, 20*cm))
gd_diagram.write(name + "_c.pdf", "PDF")

src/b/i/biopython-HEAD/Doc/examples/ACT_example.py   biopython(Download)
gd_diagram.draw(format="linear", fragments=3,
                orientation="landscape", pagesize=(20*cm, 10*cm))
gd_diagram.write(name + ".pdf", "PDF")
 
gd_diagram.draw(format="circular",
                orientation="landscape", pagesize=(20*cm, 20*cm))
gd_diagram.write(name + "_c.pdf", "PDF")

src/m/g/mgtaxa-HEAD/MGT/Proj/CrisprMooreApp.py   mgtaxa(Download)
        gd_diagram.draw(format="linear", pagesize=(3000,400), fragments=1,
                        start=0, end=len(seqRec))
        gd_diagram.write(outGraphFileRoot+".pdf", "PDF")
        gd_diagram.write(outGraphFileRoot+".svg", "SVG")
 

src/c/l/clusterDbAnalysis-HEAD/src/db_displayExternalClusterHits.py   clusterDbAnalysis(Download)
    gd_diagram.draw(format="linear", start=start, end=end, fragments=1)
    pathname = os.path.join( options.outdir, sanitizeString(geneid, False) + ".svg" )
    gd_diagram.write(pathname, "SVG")
    sys.stderr.write("Image file for gene %s written to %s\n" %(geneid, pathname))
 

src/p/i/picobio-HEAD/assembly_comparison/assembly_comparison.py   picobio(Download)
gd_diagram.draw(format="circular", circular=True, circle_core=0.5,
                pagesize=page, start=0, end=max_len)
gd_diagram.write(diagram_pdf, "PDF")
print("Saved %r" % diagram_pdf)
 

src/p/i/picobio-HEAD/assembly_comparison/multi_comparison.py   picobio(Download)
gd_diagram.draw(format="linear", fragments=1,
                pagesize=page, start=0, end=max_len)
gd_diagram.write(diagram_pdf, "PDF")
print("Saved %r" % diagram_pdf)
 

src/c/l/clusterDbAnalysis-HEAD/lib/BioPythonGraphics.py   clusterDbAnalysis(Download)
    gd_diagram.draw(format="linear", start=start, end=end, fragments=1, pagesize=(ht, pagew_px), xl=(loffset/pagew_px), xr=(roffset/pagew_px), yt=yt, yb=yb )
 
    gd_diagram.write(imgfileloc, "PNG")
 
    #flip for reversed genes

src/b/i/biopython-1.63/Tests/test_GenomeDiagram.py   biopython(Download)
                 fragments=1,
                 start=0, end=points)
        gdd.write(os.path.join('Graphics', "line_graph.pdf"), "pdf")
        #Circular diagram
        gdd.draw(tracklines=False,
                 pagesize=(15*cm, 15*cm),
                 circular=True,  # Data designed to be periodic
                 start=0, end=points, circle_core=0.5)
        gdd.write(os.path.join('Graphics', "line_graph_c.pdf"), "pdf")
        for output in ["XXX", "xxx", None, 123, 5.9]:
            try:
                gdd.write(filename, output)
                assert False, \
                       "Should have rejected %s as an output format" % output
                 start=start, end=end)
        output_filename = os.path.join('Graphics', 'GD_region_linear.pdf')
        gdd.write(output_filename, 'PDF')
 
        #Also check the write_to_string method matches,
 
        output_filename = os.path.join('Graphics', 'GD_region_linear.svg')
        gdd.write(output_filename, 'SVG')
 
        #Circular with a particular start/end is a bit odd, but by setting

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