# Copyright 2001 by Brad Chapman. All rights reserved. # This code is part of the Biopython distribution and governed by its # license. Please see the LICENSE file that should have been included # as part of this package. """Test the creation of Chromosome Graphics. Provide tests for creating and manipulating pdf pictures of chromosomes. This tests the Graphics.BasicChromosome classes and the Graphics.DisplayRepresentation classes. """ # standard library import os import sys import random from io import StringIO import unittest import warnings from Bio import BiopythonWarning from Bio import MissingPythonDependencyError try: # reportlab from reportlab.lib import colors except ImportError: raise MissingPythonDependencyError( "Install reportlab if you want to use Bio.Graphics." ) from None # local stuff from Bio.SeqFeature import SeqFeature, FeatureLocation from Bio.Graphics import BasicChromosome from Bio.Graphics.DisplayRepresentation import ChromosomeCounts # hold the chromosome info for testing # the info is structured as (label, color, scale) chr1_info = ( ("", None, 1), ("AC30001", None, 1), ("", colors.blue, 2), ("", colors.blue, 1.5), ("", colors.red, 2), ("AC12345", colors.blue, 1), ("", colors.blue, 1), ("", colors.blue, 1), ("", None, 1), ) chr2_info = ( ("", None, 2), ("AC23456", None, 2), ("", colors.blue, 1), ("", colors.blue, 1), ("", colors.red, 1), ("AC00002", colors.blue, 1.5), ("", colors.blue, 1.5), ("", colors.blue, 2), ("", None, 1.5), ("", colors.red, 2), ("", colors.red, 1.5), ("AB0001", None, 1), ("", colors.red, 1), ) chr3_info = ( ("", colors.green, 2), ("", colors.green, 1), ("AD00002", colors.blue, 1), ("", colors.blue, 1), ("", colors.red, 1), ) chr4_info = ( ("", None, 1.5), ("", None, 1), ("AD11111", colors.blue, 2), ("", colors.blue, 1), ("", colors.red, 1.5), ("", colors.blue, 1), ("", colors.blue, 1), ("AC22222", colors.blue, 1), ) all_chr_info = {"I": chr1_info, "II": chr2_info, "III": chr3_info, "IV": chr4_info} def load_chromosome(chr_name): """Load a chromosome and all of its segments.""" cur_chromosome = BasicChromosome.Chromosome(chr_name) chr_segment_info = all_chr_info[chr_name] for seg_info_num in range(len(chr_segment_info)): label, fill_color, scale = chr_segment_info[seg_info_num] # make the top and bottom telomeres if seg_info_num == 0: cur_segment = BasicChromosome.TelomereSegment() elif seg_info_num == len(chr_segment_info) - 1: cur_segment = BasicChromosome.TelomereSegment(1) # otherwise, they are just regular segments else: cur_segment = BasicChromosome.ChromosomeSegment() if label != "": cur_segment.label = label if fill_color is not None: cur_segment.fill_color = fill_color cur_segment.scale = scale cur_chromosome.add(cur_segment) # scale by the size of chromosome 2 cur_chromosome.scale_num = 19 return cur_chromosome # --- stuff for generating random organisms color_choices = (colors.red, colors.blue) letter_choices = "0123456789ABCDEFGHIJKLMNOPQRSTUVWXYZ" num_possible_segments = 500 color_prob = 0.3 id_prob = 0.025 def get_random_id(): """Generate a random id number.""" id = "" for n in range(6): letter = random.choice(letter_choices) id += letter return id def load_random_chromosome(chr_name): """Generate a chromosome with random information about it.""" cur_chromosome = BasicChromosome.Chromosome(chr_name) num_segments = random.randrange(num_possible_segments) for seg in range(num_segments): # make the top and bottom telomeres if seg == 0: cur_segment = BasicChromosome.TelomereSegment() elif seg == num_segments - 1: cur_segment = BasicChromosome.TelomereSegment(1) # otherwise, they are just regular segments else: cur_segment = BasicChromosome.ChromosomeSegment() color_chance = random.random() if color_chance <= color_prob: fill_color = random.choice(color_choices) cur_segment.fill_color = fill_color id_chance = random.random() if id_chance <= id_prob: id = get_random_id() cur_segment.label = id cur_chromosome.add(cur_segment) return cur_chromosome, num_segments class OrganismGraphicTest(unittest.TestCase): """Test the creation of all chromosomes of an organism.""" def setUp(self): self.test_file = os.path.join("Graphics", "organism.pdf") def test_simple_organism(self): """Test the basic functionality of drawing an organism.""" pdf_organism = BasicChromosome.Organism() # add chromosomes for chr_name in ["I", "II", "III", "IV"]: cur_chromosome = load_chromosome(chr_name) pdf_organism.add(cur_chromosome) pdf_organism.draw(self.test_file, "Test organism") def _simple_organism(self, filename, format): """Output a simple organism to given format.""" test_organism = BasicChromosome.Organism(format) test_file = os.path.join("Graphics", filename) # add chromosomes for chr_name in ["I", "II", "III", "IV"]: cur_chromosome = load_chromosome(chr_name) test_organism.add(cur_chromosome) test_organism.draw(test_file, "Test organism") def test_simple_organism_ps(self): """Output a simple organism to a postscript file.""" self._simple_organism("organism.eps", "ps") def test_simple_organism_pdf(self): """Output a simple organism to a PDF file.""" self._simple_organism("organism.pdf", "pdf") def test_simple_organism_svg(self): """Output a simple organism to an SVG file.""" self._simple_organism("organism.svg", "svg") def test_random_organism(self): """Generate an organism with random chromosome info.""" random_file = os.path.join("Graphics", "random_organism.pdf") pdf_organism = BasicChromosome.Organism() all_segs = [] all_chrs = [] num_chrs = random.randrange(1, 15) for chr_name in range(num_chrs): cur_chromosome, num_segs = load_random_chromosome(str(chr_name)) all_chrs.append(cur_chromosome) all_segs.append(num_segs) # scale all of the chromosomes by the maximum number of segments max_segs = max(all_segs) for chr in all_chrs: chr.scale_num = max_segs pdf_organism.add(chr) pdf_organism.draw(random_file, "Randomly generated Organism") def test_widget(self): """Try widget derived functionality.""" test_widget = BasicChromosome.ChromosomeSegment() expected_string = "chr_percent = 0.25" # trick to write the properties to a string save_stdout = sys.stdout new_stdout = StringIO() sys.stdout = new_stdout test_widget.dumpProperties() properties = new_stdout.getvalue() sys.stdout = save_stdout self.assertIn( expected_string, properties, "Unexpected results from dumpProperties: \n %s" % properties, ) properties = test_widget.getProperties() self.assertEqual( properties["label_size"], 6, "Unexpected results from getProperties: %s" % properties, ) test_widget.setProperties({"start_x_position": 12}) self.assertEqual( test_widget.start_x_position, 12, "setProperties doesn't seem to work right: %s" % test_widget.start_x_position, ) class OrganismSubAnnotationsTest(unittest.TestCase): """Test sub-annotations on a segment.""" def test_simple_tRNA_tuples(self): """Test sub-annotations (as tuples) on a genome segment, tRNA for Arabidopsis.""" self.check_simple_tRNA("Graphics/tRNA_chrom.pdf", False) def test_simple_tRNA_seqfeatures(self): """Test sub-annotations (as SeqFeatures) on a genome segment, tRNA for Arabidopsis.""" self.check_simple_tRNA("Graphics/tRNA_chrom_sf.pdf", True) def check_simple_tRNA(self, filename, use_seqfeatures=False): # Turn black code style off # fmt: off f1 = [ (111889, 111961, -1, "G01270"), (306383, 306456, 1, "G01870"), (309274, 309347, -1, "G01890"), (515493, 515566, 1, "G02480"), (552639, 552711, 1, "G02600"), (604401, 604474, 1, "G02760"), (877648, 877720, 1, "G03515"), (892513, 892585, 1, "G03570"), (909809, 909882, -1, "G03640"), (1159021, 1159092, 1, "G04320"), (1324921, 1324959, 1, "G04720"), (1583770, 1583844, -1, "G05390"), (1817398, 1817470, 1, "G05980"), (1978082, 1978156, 1, "G06480"), (2025354, 2025427, 1, "G06610"), (2107396, 2107467, -1, "G06860"), (2111146, 2111217, -1, "G06880"), (2177883, 2177957, 1, "G07100"), (2334818, 2334891, 1, "G07580"), (2406830, 2406902, -1, "G07760"), (2588521, 2588593, 1, "G08240"), (2846538, 2846611, -1, "G08870"), (2879305, 2879377, 1, "G08950"), (2939418, 2939490, 1, "G09110"), (3431185, 3431257, -1, "G10440"), (3676606, 3676644, 1, "G11010"), (3678774, 3678848, -1, "G11030"), (3881528, 3881608, 1, "G11550"), (3914628, 3914700, -1, "G11640"), (4266985, 4267059, -1, "G12510"), (4285884, 4285956, -1, "G12590"), (4440211, 4440284, 1, "G13010"), (4522705, 4522779, -1, "G13240"), (4709631, 4709703, 1, "G13720"), (4741995, 4742068, 1, "G13840"), (4743091, 4743164, 1, "G13850"), (5189681, 5189755, -1, "G15090"), (5309641, 5309713, -1, "G15450"), (5380901, 5380983, 1, "G15650"), (5518055, 5518128, -1, "G16100"), (5619464, 5619537, -1, "G16450"), (6038749, 6038831, 1, "G17570"), (6075812, 6075884, 1, "G17660"), (6075937, 6076011, -1, "G17670"), (6345756, 6345828, 1, "G18430"), (6488645, 6488726, 1, "G18820"), (6948850, 6948934, -1, "G20040"), (6995272, 6995344, -1, "G20170"), (7004504, 7004576, 1, "G20210"), (7016506, 7016579, 1, "G20250"), (7082657, 7082729, 1, "G20420"), (7242749, 7242821, -1, "G20820"), (7499721, 7499793, -1, "G21420"), (7656108, 7656180, -1, "G21800"), (7884405, 7884443, -1, "G22320"), (8520278, 8520352, -1, "G24080"), (9143796, 9143870, 1, "G26430"), (9158169, 9158242, 1, "G26490"), (10089422, 10089494, 1, "G28720"), (10089883, 10089955, 1, "G28730"), (10090353, 10090425, 1, "G28740"), (10090754, 10090826, 1, "G28750"), (10092310, 10092382, 1, "G28770"), (10092786, 10092858, 1, "G28780"), (10093294, 10093366, 1, "G28790"), (10093731, 10093803, 1, "G28800"), (10094158, 10094230, 1, "G28810"), (10096936, 10097008, 1, "G28820"), (10097099, 10097171, 1, "G28830"), (10097703, 10097775, 1, "G28840"), (10098638, 10098710, 1, "G28850"), (10099064, 10099136, 1, "G28860"), (10099410, 10099482, 1, "G28870"), (10099812, 10099884, 1, "G28880"), (10100258, 10100330, 1, "G28890"), (10101013, 10101085, 1, "G28900"), (10101585, 10101657, 1, "G28910"), (10101978, 10102050, 1, "G28920"), (10106075, 10106147, 1, "G28930"), (10106513, 10106585, 1, "G28940"), (10106883, 10106955, 1, "G28950"), (10107634, 10107706, 1, "G28970"), (10108374, 10108446, 1, "G28980"), (10108695, 10108767, 1, "G28990"), (10207291, 10207364, -1, "G29210"), (10756703, 10756776, 1, "G30430"), (10963553, 10963627, -1, "G30830"), (11104093, 11104167, 1, "G31110"), (11797227, 11797265, -1, "G32620"), (12097258, 12097327, -1, "G33370"), (13687637, 13687710, 1, "G36350"), (15733055, 15733127, -1, "G42120"), (16588144, 16588216, -1, "G43820"), (17159046, 17159118, 1, "G45234"), (17159799, 17159871, 1, "G45236"), (17160970, 17161042, 1, "G45238"), (17161418, 17161490, 1, "G45240"), (17162967, 17163039, 1, "G45242"), (17163408, 17163480, 1, "G45244"), (17164461, 17164533, 1, "G45246"), (17735509, 17735582, 1, "G48080"), (18139265, 18139337, -1, "G49020"), (18234146, 18234220, -1, "G49280"), (18312570, 18312607, 1, "G49460"), (18391469, 18391542, 1, "G49690"), (18556666, 18556746, 1, "G50070"), (18561567, 18561647, 1, "G50100"), (19428223, 19428297, 1, "G52170"), (19502087, 19502161, -1, "G52350"), (19688850, 19688887, -1, "G52860"), (19851640, 19851714, 1, "G53220"), (19929506, 19929578, -1, "G53410"), (20416594, 20416667, -1, "G54670"), (20794976, 20795058, 1, "G55625"), (21272451, 21272533, 1, "G56730"), (21272786, 21272823, 1, "G56740"), (21273216, 21273253, 1, "G56750"), (21273960, 21274042, 1, "G56760"), (21274295, 21274332, 1, "G56770"), (21274725, 21274762, 1, "G56780"), (21275469, 21275551, 1, "G56790"), (21275804, 21275841, 1, "G56800"), (21276234, 21276271, 1, "G56810"), (21276978, 21277060, 1, "G56820"), (21277313, 21277350, 1, "G56830"), (21277743, 21277780, 1, "G56840"), (21278487, 21278569, 1, "G56850"), (21278822, 21278859, 1, "G56860"), (21279273, 21279310, 1, "G56870"), (21280016, 21280098, 1, "G56880"), (21280351, 21280388, 1, "G56890"), (21280781, 21280818, 1, "G56900"), (21281525, 21281607, 1, "G56910"), (21281860, 21281897, 1, "G56920"), (21282311, 21282348, 1, "G56930"), (21283054, 21283136, 1, "G56940"), (21283384, 21283421, 1, "G56950"), (21283842, 21283879, 1, "G56960"), (21284586, 21284668, 1, "G56970"), (21284916, 21284953, 1, "G56980"), (21285374, 21285411, 1, "G56990"), (21286118, 21286200, 1, "G57000"), (21286448, 21286485, 1, "G57010"), (21286906, 21286943, 1, "G57020"), (21287650, 21287732, 1, "G57030"), (21287980, 21288017, 1, "G57040"), (21288438, 21288475, 1, "G57050"), (21289183, 21289265, 1, "G57060"), (21289513, 21289550, 1, "G57070"), (21289970, 21290007, 1, "G57080"), (21290714, 21290796, 1, "G57090"), (21291044, 21291081, 1, "G57100"), (21291501, 21291538, 1, "G57110"), (21292245, 21292327, 1, "G57120"), (21292574, 21292611, 1, "G57130"), (21293032, 21293069, 1, "G57140"), (21293776, 21293858, 1, "G57150"), (21294109, 21294146, 1, "G57160"), (21294567, 21294604, 1, "G57170"), (21295125, 21295207, 1, "G57180"), (21295455, 21295492, 1, "G57190"), (21295912, 21295949, 1, "G57200"), (21296656, 21296738, 1, "G57210"), (21296989, 21297026, 1, "G57220"), (21297447, 21297484, 1, "G57230"), (21298005, 21298087, 1, "G57240"), (21298335, 21298372, 1, "G57250"), (21298792, 21298829, 1, "G57260"), (21299536, 21299618, 1, "G57270"), (21299869, 21299906, 1, "G57280"), (21300327, 21300364, 1, "G57290"), (21300885, 21300967, 1, "G57300"), (21301215, 21301252, 1, "G57310"), (21301673, 21301710, 1, "G57320"), (21302417, 21302499, 1, "G57330"), (21302750, 21302787, 1, "G57340"), (21303208, 21303245, 1, "G57350"), (21303766, 21303848, 1, "G57360"), (21304096, 21304133, 1, "G57370"), (21304554, 21304591, 1, "G57380"), (21305298, 21305380, 1, "G57390"), (21305631, 21305668, 1, "G57400"), (21306089, 21306126, 1, "G57410"), (21306647, 21306729, 1, "G57420"), (21306981, 21307018, 1, "G57430"), (21307441, 21307478, 1, "G57440"), (21308184, 21308268, 1, "G57450"), (21308520, 21308557, 1, "G57460"), (21308975, 21309012, 1, "G57470"), (21309719, 21309801, 1, "G57480"), (21310053, 21310090, 1, "G57490"), (21310513, 21310550, 1, "G57500"), (21311256, 21311340, 1, "G57510"), (21311592, 21311629, 1, "G57520"), (21312051, 21312088, 1, "G57530"), (21377983, 21378054, -1, "G57710"), (21887507, 21887589, -1, "G59570"), (22044276, 22044348, -1, "G59880"), (22317078, 22317149, -1, "G60580"), (22398301, 22398372, -1, "G60820"), (22401256, 22401327, -1, "G60840"), (22431831, 22431902, 1, "G60910"), (22481437, 22481511, -1, "G61020"), (22870422, 22870494, -1, "G61880"), (22890754, 22890834, 1, "G61910"), (23562849, 23562921, -1, "G63510"), (23671147, 23671219, -1, "G63790"), (23806215, 23806299, 1, "G64120"), (23936799, 23936872, 1, "G64420"), (24490654, 24490736, -1, "G65830"), (25833316, 25833388, 1, "G68770"), (25890198, 25890272, 1, "G68860"), (25931858, 25931931, 1, "G68950"), (25935739, 25935812, -1, "G68970"), (25944826, 25944898, 1, "G69000"), (25993392, 25993466, 1, "G69130"), (26053140, 26053214, 1, "G69300"), (26385816, 26385888, -1, "G70050"), (26977050, 26977121, 1, "G71700"), (27397046, 27397128, 1, "G72780"), (27792643, 27792715, 1, "G73900"), (28024043, 28024124, -1, "G74570"), (28031620, 28031701, 1, "G74610"), (28188192, 28188264, 1, "G75070"), (28377149, 28377222, -1, "G75570"), (28411644, 28411717, 1, "G75650"), (28444549, 28444621, 1, "G75740"), (28523645, 28523717, -1, "G75970"), (28531427, 28531499, 1, "G76000"), (28639585, 28639667, 1, "G76330"), (28952447, 28952519, -1, "G77040"), (29007098, 29007180, -1, "G77190"), (29147983, 29148055, -1, "G77560"), (29448865, 29448903, -1, "G78250"), (29809015, 29809088, 1, "G79240"), (29838009, 29838081, 1, "G79290"), (29838610, 29838682, 1, "G79300"), (30088888, 30088962, -1, "G79980"), (30178905, 30178977, -1, "G80250"), (30242675, 30242757, 1, "G80430") ] f2 = [ (102063, 102137, 1, "G01160"), (706794, 706867, 1, "G02600"), (846853, 846926, -1, "G02900"), (1054714, 1054787, -1, "G03490"), (1113980, 1114052, -1, "G03660"), (1123386, 1123458, -1, "G03700"), (1154381, 1154454, 1, "G03790"), (3239653, 3239725, -1, "G07742"), (3255828, 3255902, -1, "G07743"), (3268803, 3268883, 1, "G07745"), (3276436, 3276508, 1, "G07746"), (3280859, 3280933, 1, "G07748"), (3290962, 3291034, 1, "G07778"), (3303240, 3303312, -1, "G07752"), (3303350, 3303425, -1, "G07753"), (3303781, 3303819, -1, "G07754"), (3328666, 3328739, -1, "G07755"), (3332674, 3332756, 1, "G07792"), (3369350, 3369437, 1, "G07793"), (3383400, 3383474, -1, "G07794"), (3444359, 3444431, -1, "G07756"), (3452973, 3453060, 1, "G07757"), (3462074, 3462148, 1, "G07758"), (3494378, 3494416, 1, "G07759"), (3494772, 3494847, 1, "G07761"), (3495008, 3495083, 1, "G07762"), (3495438, 3495509, 1, "G07763"), (3496436, 3496508, 1, "G07764"), (3497354, 3497437, 1, "G07765"), (3503518, 3503605, 1, "G07766"), (6953924, 6953961, -1, "G15950"), (7046175, 7046247, 1, "G16240"), (7749793, 7749867, 1, "G17810"), (7962758, 7962832, -1, "G18310"), (9144435, 9144507, 1, "G21360"), (9241319, 9241356, -1, "G21570"), (9273888, 9273969, -1, "G21670"), (9277742, 9277814, -1, "G21700"), (9291113, 9291185, 1, "G21760"), (9400749, 9400823, 1, "G22110"), (9456888, 9456962, -1, "G22220"), (9472660, 9472733, -1, "G22280"), (9509359, 9509433, 1, "G22380"), (9598106, 9598179, 1, "G22580"), (9810296, 9810368, -1, "G23020"), (10066525, 10066597, -1, "G23650"), (10380655, 10380728, 1, "G24380"), (10820917, 10820990, 1, "G25400"), (11122756, 11122837, -1, "G26090"), (11781928, 11782000, -1, "G27560"), (11871230, 11871302, -1, "G27850"), (12336079, 12336151, 1, "G28730"), (12346827, 12346899, 1, "G28770"), (12478849, 12478921, -1, "G29030"), (12645232, 12645305, -1, "G29520"), (12888667, 12888738, 1, "G30180"), (12889810, 12889881, 1, "G30190"), (12983024, 12983095, -1, "G30450"), (13144312, 13144385, -1, "G30850"), (13658350, 13658425, 1, "G32110"), (14054465, 14054503, -1, "G33140"), (14250206, 14250278, 1, "G33650"), (14251774, 14251846, 1, "G33660"), (14357464, 14357536, 1, "G33890"), (14358437, 14358509, 1, "G33900"), (14359269, 14359341, 1, "G33910"), (14360221, 14360293, 1, "G33920"), (14360734, 14360806, 1, "G33930"), (14361176, 14361248, 1, "G33940"), (14362215, 14362287, 1, "G33950"), (14363133, 14363205, 1, "G33960"), (14363599, 14363671, 1, "G33970"), (14750553, 14750627, -1, "G34950"), (14757142, 14757213, 1, "G34985"), (14847685, 14847723, 1, "G35220"), (15175940, 15176014, 1, "G36140"), (15176656, 15176736, 1, "G36150"), (15215480, 15215517, -1, "G36280"), (15327312, 15327395, 1, "G36510"), (15327463, 15327546, -1, "G36520"), (15353238, 15353311, 1, "G36600"), (15477287, 15477324, -1, "G36860"), (15923894, 15923967, 1, "G38030"), (16525641, 16525713, -1, "G39600"), (16525846, 16525918, 1, "G39610"), (16646857, 16646929, -1, "G39860"), (17545780, 17545862, -1, "G42020"), (17667855, 17667926, 1, "G42420"), (17880766, 17880839, 1, "G42970"), (18002649, 18002721, -1, "G43300"), (18317052, 18317134, -1, "G44320"), (18576985, 18577058, 1, "G45020"), (18710751, 18710824, 1, "G45390"), (18963713, 18963786, 1, "G46120"), (19351496, 19351569, 1, "G47100"), (19566924, 19566995, -1, "G47740") ] f3 = [ (259640, 259712, 1, "G01705"), (469666, 469740, 1, "G02315"), (476808, 476880, 1, "G02335"), (586092, 586174, 1, "G02715"), (981975, 982047, 1, "G03845"), (984105, 984177, 1, "G03852"), (1220234, 1220307, 1, "G04525"), (1601343, 1601415, -1, "G05525"), (1707743, 1707815, -1, "G05755"), (1738796, 1738870, 1, "G05835"), (1843329, 1843400, -1, "G06105"), (1920038, 1920110, -1, "G06335"), (2104961, 2105033, -1, "G06665"), (2222251, 2222324, 1, "G07025"), (2232470, 2232506, -1, "G07055"), (2253680, 2253762, -1, "G07115"), (2285607, 2285679, 1, "G07185"), (2918418, 2918492, -1, "G09505"), (2944616, 2944698, 1, "G09585"), (2945700, 2945782, -1, "G09595"), (3090548, 3090631, 1, "G10015"), (3096220, 3096293, 1, "G10035"), (3238371, 3238407, -1, "G10415"), (3535151, 3535224, 1, "G11285"), (3575849, 3575923, 1, "G11395"), (3622697, 3622769, -1, "G11505"), (3942012, 3942084, 1, "G12385"), (3995103, 3995176, -1, "G12585"), (4254534, 4254615, 1, "G13223"), (4330778, 4330850, 1, "G13335"), (4998147, 4998219, 1, "G14855"), (5068300, 5068374, -1, "G15055"), (5275155, 5275228, 1, "G15585"), (5632857, 5632930, 1, "G16552"), (6483945, 6484019, -1, "G18815"), (6540636, 6540673, 1, "G18952"), (6663713, 6663786, 1, "G19235"), (7104314, 7104398, 1, "G20365"), (7224223, 7224296, -1, "G20655"), (7319582, 7319664, -1, "G20885"), (7567399, 7567471, -1, "G21475"), (9373610, 9373684, -1, "G25715"), (9840420, 9840494, 1, "G26747"), (10211564, 10211636, 1, "G27555"), (10319498, 10319570, 1, "G27825"), (10325875, 10325947, 1, "G27845"), (10753667, 10753740, 1, "G28685"), (10760629, 10760702, -1, "G28695"), (11076814, 11076886, 1, "G29095"), (11961645, 11961718, 1, "G30345"), (16438025, 16438097, -1, "G44955"), (16896875, 16896949, 1, "G45935"), (16902623, 16902697, 1, "G45955"), (16905147, 16905221, 1, "G45965"), (17160736, 17160808, 1, "G46585"), (17275564, 17275646, 1, "G46875"), (17905395, 17905467, 1, "G48275"), (17985575, 17985611, -1, "G48515"), (18080062, 18080134, 1, "G48745"), (18518796, 18518870, 1, "G49925"), (18755788, 18755860, -1, "G50505"), (18837020, 18837092, 1, "G50665"), (18907851, 18907924, 1, "G50835"), (18928413, 18928487, 1, "G50895"), (19008621, 19008694, -1, "G51135"), (19044371, 19044443, -1, "G51265"), (19403651, 19403723, -1, "G52285"), (19420345, 19420417, -1, "G52345"), (19511965, 19512045, 1, "G52565"), (19566013, 19566085, 1, "G52765"), (19648105, 19648188, 1, "G52955"), (19935354, 19935426, 1, "G53775"), (19995918, 19995989, 1, "G53965"), (20704664, 20704736, 1, "G55735"), (20720151, 20720223, 1, "G55795"), (20824495, 20824568, -1, "G56085"), (21498293, 21498375, 1, "G58035"), (21553258, 21553329, 1, "G58165"), (21970486, 21970557, 1, "G59415"), (22149699, 22149773, 1, "G59923"), (22149823, 22149895, -1, "G59926"), (22197810, 22197892, -1, "G60075"), (22481215, 22481288, -1, "G60805"), (22622384, 22622465, 1, "G61105"), (22786896, 22786969, 1, "G61545"), (22853496, 22853567, 1, "G61715"), (22871101, 22871174, 1, "G61755"), (22892781, 22892853, 1, "G61825"), (23047854, 23047927, 1, "G62245"), (23062444, 23062517, -1, "G62285"), (23221682, 23221753, 1, "G62735"), (23296567, 23296640, -1, "G63003"), (23296728, 23296801, -1, "G63006") ] f4 = [ (33799, 33872, 1, "G00085"), (424716, 424788, -1, "G00985"), (562560, 562634, -1, "G01355"), (611865, 611932, -1, "G01455"), (808269, 808342, -1, "G01865"), (901175, 901247, 1, "G02055"), (1390894, 1390966, 1, "G03135"), (1442004, 1442076, 1, "G03285"), (1501605, 1501677, 1, "G03405"), (1520781, 1520854, -1, "G03435"), (5268124, 5268210, -1, "G08345"), (6646425, 6646496, 1, "G10815"), (6819287, 6819324, 1, "G11177"), (6837555, 6837639, -1, "G11213"), (6837769, 6837853, -1, "G11216"), (6905479, 6905552, -1, "G11355"), (6944721, 6944793, 1, "G11405"), (7185697, 7185771, 1, "G11985"), (7232792, 7232865, -1, "G12065"), (7256408, 7256481, 1, "G12115"), (7341420, 7341494, -1, "G12405"), (7730956, 7731037, 1, "G13265"), (7814197, 7814270, 1, "G13445"), (8255695, 8255767, 1, "G14345"), (8301720, 8301794, -1, "G14415"), (8979656, 8979729, 1, "G15775"), (9108317, 9108391, 1, "G16105"), (9191590, 9191663, 1, "G16235"), (9287230, 9287304, 1, "G16465"), (9289706, 9289787, 1, "G16475"), (9815215, 9815287, -1, "G17612"), (9873524, 9873596, -1, "G17765"), (9978117, 9978189, -1, "G17975"), (10093077, 10093157, -1, "G18255"), (10302011, 10302084, 1, "G18725"), (10325975, 10326047, -1, "G18815"), (10878733, 10878807, -1, "G20115"), (11774472, 11774508, -1, "G22265"), (11910299, 11910373, 1, "G22635"), (11954751, 11954824, -1, "G22754"), (11974951, 11975032, 1, "G22785"), (12320119, 12320203, 1, "G23635"), (12429608, 12429681, 1, "G23915"), (12486211, 12486282, -1, "G24025"), (12686148, 12686230, 1, "G24565"), (13006243, 13006316, -1, "G25435"), (13058840, 13058922, -1, "G25585"), (13076582, 13076666, -1, "G25635"), (13285431, 13285503, -1, "G26225"), (13336345, 13336419, -1, "G26375"), (13341501, 13341575, -1, "G26385"), (13454562, 13454635, 1, "G26675"), (13704787, 13704860, 1, "G27395"), (13882922, 13882994, -1, "G27875"), (13885196, 13885269, -1, "G27885"), (14032495, 14032567, 1, "G28362"), (14267286, 14267368, 1, "G28915"), (14470283, 14470355, 1, "G29415"), (15120655, 15120728, 1, "G31075"), (15183089, 15183162, 1, "G31265"), (15345717, 15345753, -1, "G31695"), (15430229, 15430303, -1, "G31895"), (15576655, 15576728, 1, "G32265"), (15671398, 15671469, 1, "G32475"), (15804553, 15804635, 1, "G32765"), (16304128, 16304201, 1, "G34035"), (16454700, 16454773, -1, "G34415"), (16556627, 16556700, 1, "G34695"), (16655290, 16655364, 1, "G34975"), (17130054, 17130127, 1, "G36197"), (17149473, 17149545, 1, "G36245"), (17276705, 17276779, -1, "G36635"), (17500800, 17500872, -1, "G37175"), (18254982, 18255018, -1, "G39195"), (18293773, 18293845, 1, "G39345"), (18395021, 18395093, 1, "G39615"), (18411258, 18411332, 1, "G39672"), (18501705, 18501778, -1, "G39865"), (18542164, 18542238, 1, "G39985") ] f5 = [ (150353, 150426, -1, "G01365"), (389889, 389960, -1, "G02025"), (508427, 508500, -1, "G02385"), (530819, 530893, 1, "G02435"), (559327, 559399, -1, "G02505"), (588890, 588964, -1, "G02615"), (614641, 614723, 1, "G02725"), (642397, 642479, -1, "G02815"), (858534, 858571, 1, "G03445"), (862395, 862468, -1, "G03452"), (970797, 970878, -1, "G03705"), (984365, 984448, 1, "G03745"), (998940, 999013, 1, "G03775"), (1742692, 1742765, 1, "G05795"), (1788651, 1788723, 1, "G05945"), (1804616, 1804690, 1, "G05985"), (1853302, 1853382, -1, "G06125"), (2060153, 2060235, -1, "G06685"), (2212678, 2212749, -1, "G07135"), (2309512, 2309549, -1, "G07315"), (2411148, 2411232, 1, "G07625"), (2432263, 2432336, -1, "G07675"), (2587826, 2587899, -1, "G08075"), (2898867, 2898951, -1, "G09345"), (2993327, 2993401, 1, "G09655"), (3030817, 3030890, -1, "G09755"), (3118377, 3118458, 1, "G09975"), (3212351, 3212424, -1, "G10235"), (3287553, 3287635, -1, "G10455"), (3324702, 3324775, 1, "G10525"), (3578295, 3578367, -1, "G11225"), (3617058, 3617130, 1, "G11325"), (3669000, 3669073, -1, "G11475"), (4471050, 4471122, 1, "G13845"), (4530475, 4530548, 1, "G14035"), (4673902, 4673974, 1, "G14495"), (4929562, 4929636, 1, "G15175"), (5157641, 5157715, 1, "G15805"), (5161514, 5161586, 1, "G15815"), (5358918, 5359000, 1, "G16375"), (5962699, 5962771, -1, "G18005"), (5965972, 5966044, -1, "G18015"), (5984378, 5984450, 1, "G18085"), (6258146, 6258218, 1, "G18755"), (6401240, 6401311, 1, "G19095"), (7073531, 7073603, -1, "G20852"), (7073944, 7074016, -1, "G20854"), (7074357, 7074429, -1, "G20856"), (7074773, 7074845, -1, "G20858"), (7222059, 7222131, -1, "G21378"), (7387890, 7387962, 1, "G22315"), (7981400, 7981472, 1, "G23665"), (8906418, 8906502, 1, "G25585"), (8946826, 8946899, -1, "G25625"), (9815405, 9815477, -1, "G27715"), (11802284, 11802356, 1, "G32017"), (13823211, 13823284, -1, "G35605"), (15049737, 15049811, -1, "G37795"), (15242547, 15242621, 1, "G38155"), (15593086, 15593160, 1, "G38905"), (15844253, 15844325, -1, "G39535"), (15993514, 15993587, 1, "G39895"), (16256865, 16256937, -1, "G40545"), (16427812, 16427893, 1, "G40945"), (16524760, 16524832, -1, "G41265"), (16655393, 16655477, 1, "G41605"), (16684663, 16684735, -1, "G41675"), (17476402, 17476475, -1, "G43455"), (17512768, 17512839, -1, "G43535"), (17856811, 17856883, -1, "G44283"), (17894906, 17894979, -1, "G44375"), (18058014, 18058088, 1, "G44705"), (18560206, 18560278, -1, "G45715"), (18576071, 18576143, 1, "G45745"), (18715888, 18715960, -1, "G46105"), (18807534, 18807614, 1, "G46325"), (18924749, 18924821, 1, "G46595"), (19658828, 19658900, 1, "G48465"), (19761400, 19761472, -1, "G48675"), (19820360, 19820398, 1, "G48835"), (20064048, 20064120, 1, "G49435"), (20692447, 20692519, 1, "G50805"), (20758903, 20758940, -1, "G50995"), (20773555, 20773637, 1, "G51055"), (21275059, 21275141, -1, "G52355"), (21318105, 21318189, -1, "G52495"), (21418369, 21418441, 1, "G52815"), (21740339, 21740410, -1, "G53487"), (22091631, 22091704, 1, "G54365"), (22094087, 22094160, 1, "G54375"), (22304851, 22304923, -1, "G54865"), (22355897, 22355970, -1, "G55045"), (22357726, 22357799, -1, "G55055"), (22501995, 22502068, -1, "G55505"), (22845356, 22845430, 1, "G56365"), (22973066, 22973138, 1, "G56745"), (23071996, 23072070, -1, "G56975"), (23463219, 23463291, 1, "G57885"), (23661936, 23662018, 1, "G58495"), (23861431, 23861503, 1, "G59055"), (23971167, 23971239, 1, "G59385"), (23974655, 23974727, 1, "G59395"), (24157171, 24157245, -1, "G59945"), (24279805, 24279886, 1, "G60285"), (24547401, 24547474, 1, "G60963"), (24548892, 24548964, 1, "G60966"), (24684507, 24684579, 1, "G61345"), (24726891, 24726964, 1, "G61445"), (24856205, 24856242, 1, "G61835"), (25347261, 25347333, 1, "G63145"), (25801340, 25801414, 1, "G64505"), (25892619, 25892691, -1, "G64735"), (25942291, 25942372, 1, "G64855"), (25989903, 25989976, 1, "G65015"), (26114755, 26114793, -1, "G65305"), (26174414, 26174496, -1, "G65445"), (26212684, 26212757, 1, "G65535"), (26238859, 26238933, -1, "G65615"), (26573248, 26573322, -1, "G66535"), (26585622, 26585696, 1, "G66568"), (26670495, 26670567, -1, "G66755"), (26699933, 26700004, -1, "G66817"), (26938897, 26938969, 1, "G67455") ] # Turn black code style on # fmt: on entries = [ ("Chr I", "NC_003070", 30432563, f1, colors.red), ("Chr II", "NC_003071", 19705359, f2, colors.green), ("Chr III", "NC_003074", 23470805, f3, colors.blue), ("Chr IV", "NC_003075", 18585042, f4, colors.orange), ("Chr V", "NC_003076", 26992728, f5, colors.purple), ] max_length = max(row[2] for row in entries) chr_diagram = BasicChromosome.Organism() for name, acc, length, features, color in entries: if False: # How I generated the values above... and tested passing in SeqFeatures filename = "/Users/pjcock/Documents/comp_genomics/seed/%s.gbk" % acc import os if not os.path.isfile(filename): continue from Bio import SeqIO record = SeqIO.read(filename, "gb") assert length == len(record) features = [f for f in record.features if f.type == "tRNA"] print(name) # Strip of the first three chars, AT# where # is the chr print( [ ( int(f.location.start), int(f.location.end), f.strand, f.qualifiers["locus_tag"][0][3:], ) for f in features ] ) # Output was copy and pasted to the script, see above. # Continue test using SeqFeature objects! # To test colours from the qualifiers, for i, f in enumerate(features): f.qualifiers["color"] = [str(i % 16)] elif use_seqfeatures: # Features as SeqFeatures features = [ SeqFeature( FeatureLocation(start, end, strand), qualifiers={"name": [label], "color": [color]}, ) for (start, end, strand, label) in features ] else: # Features as 5-tuples features = [ (start, end, strand, label, color) # noqa: C416 for (start, end, strand, label) in features ] # I haven't found a nice source of data for real Arabidopsis # cytobands, so these three are made up at random! cytobands = [] for color in [colors.gray, colors.darkgray, colors.slategray]: start = (length - 1000000) * random.random() end = min(length, start + 1000000) # Draw these with black borders, and a grey fill cytobands.append((start, end, 0, None, colors.black, color)) # Draw these with black borders, and a brown fill: cytobands.append((0, 1000000, 0, "First 1 Mbp", colors.black, colors.brown)) cytobands.append( (length - 1000000, length, 0, "Last 1 Mbp", colors.black, colors.brown) ) # Additional dummy entry to check fill colour on both strands, if name == "Chr III": cytobands.append((11000000, 13000000, -1, "Reverse", "red", "yellow")) elif name == "Chr V": cytobands.append( (9500000, 11000000, +1, "Forward", colors.red, colors.yellow) ) # Create the drawing object for the chromosome cur_chromosome = BasicChromosome.Chromosome(name) # Set the length, adding an extra 20 percent for the tolomeres etc: cur_chromosome.scale_num = max_length * 1.2 cur_chromosome.label_sep_percent = 0.15 # Add a dummy segment for allocating vertical space # which can be used for feature label placement spacer = BasicChromosome.SpacerSegment() spacer.scale = 0.03 * max_length cur_chromosome.add(spacer) # Add an opening telomere start = BasicChromosome.TelomereSegment() start.scale = 0.02 * max_length start.fill_color = colors.lightgrey cur_chromosome.add(start) # Add a body - using bp as the scale length here. # Note we put the cytobands a start of combined list, # as want them drawn underneath the tRNA markers. body = BasicChromosome.AnnotatedChromosomeSegment( length, cytobands + features ) body.scale = length cur_chromosome.add(body) # Add a closing telomere end = BasicChromosome.TelomereSegment(inverted=True) end.scale = 0.02 * max_length end.fill_color = colors.lightgrey cur_chromosome.add(end) # Another spacer spacer = BasicChromosome.SpacerSegment() spacer.scale = 0.03 * max_length cur_chromosome.add(spacer) # This chromosome is done chr_diagram.add(cur_chromosome) with warnings.catch_warnings(): # BiopythonWarning: Too many labels to avoid overlap warnings.simplefilter("ignore", BiopythonWarning) chr_diagram.draw(filename, "Arabidopsis thaliana tRNA") class ChromosomeCountTest(unittest.TestCase): """Test the display representation for simple counts on a chromosome.""" def setUp(self): self.names = ["Bob", "Dylan", "Doesn't", "Like", "Spam"] self.count_display = ChromosomeCounts(self.names) def test_add_count(self): """Add counts to specific chromosome segments.""" self.count_display.add_count(self.names[1]) self.count_display.add_count(self.names[2], 5) try: self.count_display.add_count("Non-existent") raise AssertionError("Didn't raise a KeyError on a fake key") except KeyError: pass def test_add_label(self): """Add labels to chromosome segments.""" self.count_display.add_label(self.names[1], "Rules") try: self.count_display.add_label("Non-existent", "Elephant") raise AssertionError("Didn't raise a KeyError on a fake key") except KeyError: pass def test_set_scale(self): """Set the scale for a chromosome segment.""" self.count_display.set_scale(self.names[1], 1.5) try: self.count_display.set_scale("Non-existant", 5) raise AssertionError("Didn't raise a KeyError on a fake key.") except KeyError: pass def test_color_from_count(self): """Retrieve a color from a count number with the default color scheme.""" test_color = self.count_display._color_from_count(3) assert test_color == colors.blue, "Unexpected color %s" % test_color test_color = self.count_display._color_from_count(9) assert test_color == colors.red, "Unexpected color %s" % test_color try: self.count_display._color_from_count(200) raise AssertionError("Didn't raise an error for bad count.") except ValueError: pass def test_fill_chromosome(self): """Test filling out the information on a chromosome.""" test_chr = BasicChromosome.Chromosome("1") self.count_display.add_count(self.names[2], 5) self.count_display.add_count(self.names[1], 2) self.count_display.add_label(self.names[3], "Test-Label") new_chr = self.count_display.fill_chromosome(test_chr) def test_get_segment_info(self): """Test retrieval of segment information.""" test_count_num = 1 test_count_value = 5 test_label_num = 3 test_label_value = "BigBird" self.count_display.add_count(self.names[test_count_num], test_count_value) self.count_display.add_label(self.names[test_label_num], test_label_value) seg_info = self.count_display.get_segment_info() self.assertEqual( seg_info[test_count_num][0], test_count_value, "Did not set and retrieve counts correctly.", ) self.assertEqual( seg_info[test_label_num][1], test_label_value, "Did not set and retrieve label correctly.", ) if __name__ == "__main__": runner = unittest.TextTestRunner(verbosity=2) unittest.main(testRunner=runner)