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src/b/i/biopython-1.63/Doc/examples/ACT_example.py   biopython(Download)
 
from Bio.Blast.Applications import NcbitblastxCommandline
from Bio.Graphics.GenomeDiagram import Diagram, CrossLink
from Bio.SeqFeature import SeqFeature, FeatureLocation
from Bio import SeqIO
#Create diagram with tracks, each with a feature set
assert len(genomes) >= 2 and len(genomes) == len(comparisons)+1
gd_diagram = Diagram(name, track_size=0.35, circular=False)
tracks = dict()
feature_sets = dict()

src/b/i/biopython-HEAD/Doc/examples/ACT_example.py   biopython(Download)
 
from Bio.Blast.Applications import NcbitblastxCommandline
from Bio.Graphics.GenomeDiagram import Diagram, CrossLink
from Bio.SeqFeature import SeqFeature, FeatureLocation
from Bio import SeqIO
#Create diagram with tracks, each with a feature set
assert len(genomes) >= 2 and len(genomes) == len(comparisons)+1
gd_diagram = Diagram(name, track_size=0.35, circular=False)
tracks = dict()
feature_sets = dict()

src/b/i/biopython-1.63/Doc/examples/Proux_et_al_2002_Figure_6.py   biopython(Download)
    raise KeyError(id)
 
gd_diagram = GenomeDiagram.Diagram(name)
feature_sets = {}
max_len = 0

src/b/i/biopython-HEAD/Doc/examples/Proux_et_al_2002_Figure_6.py   biopython(Download)
    raise KeyError(id)
 
gd_diagram = GenomeDiagram.Diagram(name)
feature_sets = {}
max_len = 0

src/b/i/biopython-1.63/Tests/test_GenomeDiagram.py   biopython(Download)
 
# Bio.Graphics.GenomeDiagram
from Bio.Graphics.GenomeDiagram import FeatureSet, GraphSet, Track, Diagram
from Bio.Graphics.GenomeDiagram import CrossLink
#from Bio.Graphics.GenomeDiagram.Utilities import *
        data3 = [2*math.sin(2*x*scale) for x in range(points)]
 
        gdd = Diagram('Test Diagram', circular=False,
                      y=0.01, yt=0.01, yb=0.01,
                      x=0.01, xl=0.01, xr=0.01)
    def setUp(self):
        self.gdd = Diagram('Test Diagram', circular=False,
                           y=0.01, yt=0.01, yb=0.01,
                           x=0.01, xl=0.01, xr=0.01)
 
    def setUp(self):
        self.gdd = Diagram('Test Diagram', circular=False,
                           y=0.01, yt=0.01, yb=0.01,
                           x=0.01, xl=0.01, xr=0.01)
 
    def test_write_arguments(self):
        """Check how the write methods respond to output format arguments."""
        gdd = Diagram('Test Diagram')
        gdd.drawing = None  # Hack - need the ReportLab drawing object to be created.
        filename = os.path.join("Graphics", "error.txt")

src/b/i/biopython-HEAD/Tests/test_GenomeDiagram.py   biopython(Download)
 
# Bio.Graphics.GenomeDiagram
from Bio.Graphics.GenomeDiagram import FeatureSet, GraphSet, Track, Diagram
from Bio.Graphics.GenomeDiagram import CrossLink
#from Bio.Graphics.GenomeDiagram.Utilities import *
        data3 = [2*math.sin(2*x*scale) for x in range(points)]
 
        gdd = Diagram('Test Diagram', circular=False,
                      y=0.01, yt=0.01, yb=0.01,
                      x=0.01, xl=0.01, xr=0.01)
    def setUp(self):
        self.gdd = Diagram('Test Diagram', circular=False,
                           y=0.01, yt=0.01, yb=0.01,
                           x=0.01, xl=0.01, xr=0.01)
 
    def setUp(self):
        self.gdd = Diagram('Test Diagram', circular=False,
                           y=0.01, yt=0.01, yb=0.01,
                           x=0.01, xl=0.01, xr=0.01)
 
    def test_write_arguments(self):
        """Check how the write methods respond to output format arguments."""
        gdd = Diagram('Test Diagram')
        gdd.drawing = None  # Hack - need the ReportLab drawing object to be created.
        filename = os.path.join("Graphics", "error.txt")

src/p/i/picobio-HEAD/assembly_comparison/multi_comparison.py   picobio(Download)
 
max_len = 0
gd_diagram = GenomeDiagram.Diagram("Comparison")
reference_fasta = None
ref_offsets = dict()

src/p/i/picobio-HEAD/assembly_comparison/assembly_comparison.py   picobio(Download)
    fasta_saved_count = 0
 
gd_diagram = GenomeDiagram.Diagram("Comparison")
gd_track_for_features = gd_diagram.new_track(1,
                                             name="reference",

src/c/l/clusterDbAnalysis-HEAD/src/db_displayExternalClusterHits.py   clusterDbAnalysis(Download)
    annotation = geneinfo[0][9]
 
    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()

src/c/l/clusterDbAnalysis-HEAD/lib/GenomeCircleDiagrams.py   clusterDbAnalysis(Download)
    '''
 
    gd_diagram = GenomeDiagram.Diagram(genomeDiagramName)
    tracknum = 0
    for name in sorted(seqFeatureNameToList.keys()):

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