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python-biopython  1.60
Variables
ACT_example Namespace Reference

Variables

string input_folder = "/Applications/Artemis/Artemis.app/Contents/artemis/etc"
string name = "af063097_v_b132222"
string file_a = "af063097.embl"
string file_b = "b132222.embl"
string format_a = "embl"
string format_b = "embl"
string file_a_vs_b = "af063097_v_b132222.crunch"
list genomes
list comparisons = [os.path.join(input_folder, file_a_vs_b)]
tuple gd_diagram = Diagram(name, track_size=0.35, circular=False)
tuple tracks = dict()
tuple feature_sets = dict()
tuple records = dict()
int scale_smalltick_interval = 1000
int scale_largetick_interval = 10000
int greytrack = 0
list q = genomes[i+1]
list s = genomes[i]
list q_set = feature_sets[q]
list s_set = feature_sets[s]
tuple handle = open(crunch_file)
tuple parts = line.rstrip("\n")
 flip = False
tuple c = colors.Color(0, 0, 1, alpha=0.25)
 b = False
tuple q_feature
tuple s_feature
list record = records[f]
list feature_set = feature_sets[f]
 color = colors.lightblue,
 border = colors.blue)
string orientation = "landscape"

Variable Documentation

ACT_example.b = False

Definition at line 84 of file ACT_example.py.

ACT_example.border = colors.blue)

Definition at line 109 of file ACT_example.py.

tuple ACT_example.c = colors.Color(0, 0, 1, alpha=0.25)

Definition at line 83 of file ACT_example.py.

ACT_example.color = colors.lightblue,

Definition at line 108 of file ACT_example.py.

Definition at line 33 of file ACT_example.py.

Definition at line 102 of file ACT_example.py.

tuple ACT_example.feature_sets = dict()

Definition at line 39 of file ACT_example.py.

string ACT_example.file_a = "af063097.embl"

Definition at line 17 of file ACT_example.py.

string ACT_example.file_a_vs_b = "af063097_v_b132222.crunch"

Definition at line 21 of file ACT_example.py.

string ACT_example.file_b = "b132222.embl"

Definition at line 18 of file ACT_example.py.

Definition at line 75 of file ACT_example.py.

string ACT_example.format_a = "embl"

Definition at line 19 of file ACT_example.py.

string ACT_example.format_b = "embl"

Definition at line 20 of file ACT_example.py.

tuple ACT_example.gd_diagram = Diagram(name, track_size=0.35, circular=False)

Definition at line 37 of file ACT_example.py.

Initial value:
00001 [
00002     (os.path.join(input_folder, file_a), format_a),
00003     (os.path.join(input_folder, file_b), format_b),
00004 ]

Definition at line 29 of file ACT_example.py.

Definition at line 46 of file ACT_example.py.

tuple ACT_example.handle = open(crunch_file)

Definition at line 55 of file ACT_example.py.

string ACT_example.input_folder = "/Applications/Artemis/Artemis.app/Contents/artemis/etc"

Definition at line 14 of file ACT_example.py.

string ACT_example.name = "af063097_v_b132222"

Definition at line 16 of file ACT_example.py.

string ACT_example.orientation = "landscape"

Definition at line 112 of file ACT_example.py.

tuple ACT_example.parts = line.rstrip("\n")

Definition at line 59 of file ACT_example.py.

list ACT_example.q = genomes[i+1]

Definition at line 51 of file ACT_example.py.

Initial value:
00001 q_set.add_feature(SeqFeature(FeatureLocation(q_start-1, q_end)),
00002                                                  color=c, border=b)

Definition at line 88 of file ACT_example.py.

Definition at line 53 of file ACT_example.py.

Definition at line 101 of file ACT_example.py.

tuple ACT_example.records = dict()

Definition at line 40 of file ACT_example.py.

Definition at line 52 of file ACT_example.py.

Initial value:
00001 s_set.add_feature(SeqFeature(FeatureLocation(s_start-1, s_end)),
00002                                                  color=c, border=b)

Definition at line 90 of file ACT_example.py.

Definition at line 54 of file ACT_example.py.

Definition at line 45 of file ACT_example.py.

Definition at line 44 of file ACT_example.py.

tuple ACT_example.tracks = dict()

Definition at line 38 of file ACT_example.py.