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src/b/i/biopython-1.63/Doc/examples/ACT_example.py   biopython(Download)
for f, format in genomes:
    records[f] = SeqIO.read(f, format)
    tracks[f] = gd_diagram.new_track(1, name=f, start=0, end=len(records[f]),
                                     scale_smalltick_interval=1000,
                                     scale_largetick_interval=10000,

src/b/i/biopython-HEAD/Doc/examples/ACT_example.py   biopython(Download)
for f, format in genomes:
    records[f] = SeqIO.read(f, format)
    tracks[f] = gd_diagram.new_track(1, name=f, start=0, end=len(records[f]),
                                     scale_smalltick_interval=1000,
                                     scale_largetick_interval=10000,

src/b/i/biopython-1.63/Doc/examples/Proux_et_al_2002_Figure_6.py   biopython(Download)
    #(empty tracks 2 and 4 add useful white space to emphasise the cross links
    #and also serve to make the tracks vertically more compressed)
    gd_track_for_features = gd_diagram.new_track(5-2*i,
                            name=record.name,
                            greytrack=True, height=0.5,

src/b/i/biopython-HEAD/Doc/examples/Proux_et_al_2002_Figure_6.py   biopython(Download)
    #(empty tracks 2 and 4 add useful white space to emphasise the cross links
    #and also serve to make the tracks vertically more compressed)
    gd_track_for_features = gd_diagram.new_track(5-2*i,
                            name=record.name,
                            greytrack=True, height=0.5,

src/p/i/picobio-HEAD/assembly_comparison/assembly_comparison.py   picobio(Download)
 
gd_diagram = GenomeDiagram.Diagram("Comparison")
gd_track_for_features = gd_diagram.new_track(1,
                                             name="reference",
                                             greytrack=False, height=0.5,
        print("WARNING: Contig %s length %i, reference %i" % (contig_id, contig_len, max_len))
        #Add entire track for the oversized contig...
        gd_track_for_contig = gd_diagram.new_track(3,
                                                   name=contig_id,
                                                   greytrack=False, height=0.5,
            #print "Have %i tracks, adding one more" % len(contig_tracks)
            #1 = references, 2 = gap, 3+ = contigs
            gd_track_for_contig = gd_diagram.new_track(3,
                                                       name=contig_id,
                                                       greytrack=False, height=0.5,
            print("WARNING: Contig %s length %i, reference %i" % (contig_id, contig_len, max_len))
            #Add entire track for the oversized contig...
            gd_track_for_contig = gd_diagram.new_track(max(gd_diagram.tracks) + 1,
                                                       name=contig_id,
                                                       greytrack=False, height=0.5,
            else:
                #print("Having to add another track for %s (len %i bp)" % (contig_id, contig_len))
                gd_track_for_contig = gd_diagram.new_track(max(gd_diagram.tracks) + 1,
                                                           name=contig_id,
                                                           greytrack=False, height=0.5,

src/p/i/picobio-HEAD/assembly_comparison/multi_comparison.py   picobio(Download)
    max_len = max(max_len, track_len)
 
    gd_track = gd_diagram.new_track(1 + 2 * i,
                                    name=assembly_fasta,
                                    greytrack=False, height=0.5,

src/b/i/biopython-1.63/Tests/test_GenomeDiagram.py   biopython(Download)
                      y=0.01, yt=0.01, yb=0.01,
                      x=0.01, xl=0.01, xr=0.01)
        gdt_data = gdd.new_track(1, greytrack=False)
        gds_data = gdt_data.new_set("graph")
        for data_values, name, color in zip([data1, data2, data3],
                      )
        #Add a track of features,
        gdt_features = gdd.new_track(1, greytrack=True,
                                     name="CDS Features",
                                     scale_largetick_interval=1000,
 
        #Add a track of features,
        gdt_features = gdd.new_track(1, greytrack=True,
                                     name="CDS Features", greytrack_labels=0,
                                     height=0.5)
 
        #Now add a graph track...
        gdt_at_gc = gdd.new_track(2, greytrack=True,
                                  name="AT and GC content",
                                  greytrack_labels=True)

src/b/i/biopython-HEAD/Tests/test_GenomeDiagram.py   biopython(Download)
                      y=0.01, yt=0.01, yb=0.01,
                      x=0.01, xl=0.01, xr=0.01)
        gdt_data = gdd.new_track(1, greytrack=False)
        gds_data = gdt_data.new_set("graph")
        for data_values, name, color in zip([data1, data2, data3],
                      )
        #Add a track of features,
        gdt_features = gdd.new_track(1, greytrack=True,
                                     name="CDS Features",
                                     scale_largetick_interval=1000,
 
        #Add a track of features,
        gdt_features = gdd.new_track(1, greytrack=True,
                                     name="CDS Features", greytrack_labels=0,
                                     height=0.5)
 
        #Now add a graph track...
        gdt_at_gc = gdd.new_track(2, greytrack=True,
                                  name="AT and GC content",
                                  greytrack_labels=True)

src/c/l/clusterDbAnalysis-HEAD/src/db_displayExternalClusterHits.py   clusterDbAnalysis(Download)
 
    gd_diagram = GenomeDiagram.Diagram(geneid)
    gd_track_for_gene = gd_diagram.new_track(1, name=geneid)
    gd_feature_set = gd_track_for_gene.new_set()
 
            rps_name += " - Evalue=%s" %(evalue)
 
        gd_track = gd_diagram.new_track(n, name=rps_name)
        gd_feature_set = gd_track.new_set()
        hit_feature = SeqFeature( FeatureLocation(hitstart, hitend), strand=+1, id=rps_name)

src/c/l/clusterDbAnalysis-HEAD/lib/BioPythonGraphics.py   clusterDbAnalysis(Download)
    # Set up an entry genome diagram object                                                                                                                                                                   
    gd_diagram = GenomeDiagram.Diagram("Genome Region")
    gd_track_for_features = gd_diagram.new_track(1, name="Annotated Features")
    gd_feature_set = gd_track_for_features.new_set()
 

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