Mercurial > repos > greg > draw_features

comparison draw_features.py @ 7:c5555f1c8f49 draft

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author greg
date Thu, 23 Mar 2023 17:20:23 +0000
parents 7d47800ee5ac
children 67520145696f
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6:d5a5d145cfce 7:c5555f1c8f49
1 #!/usr/bin/env python 1 #!/usr/bin/env python
2 2
3 import argparse 3 import argparse
4 import os 4 import os
5 import random
5 6
7 import matplotlib.pyplot as pyplot
6 import pandas 8 import pandas
7 import matplotlib.pyplot as pyplot
8 from Bio import SeqIO 9 from Bio import SeqIO
9 from dna_features_viewer import GraphicFeature, GraphicRecord 10 from dna_features_viewer import GraphicFeature, GraphicRecord
10 11
11 12
12 AMR_COLOR = '#FED976' 13 AMR_COLOR = '#FED976'
13 INC_GROUPS_COLOR = '#0570B0' 14 INC_GROUPS_COLOR = '#0570B0'
14 FEATURE_COLORS = [AMR_COLOR, INC_GROUPS_COLOR] 15 FEATURE_COLORS = [AMR_COLOR, INC_GROUPS_COLOR]
15 FIGURE_WIDTH = 13 16 FIGURE_WIDTH = 13
17
18
19 def get_random_color():
20 number_of_colors = 16
21 colors = ['#%s' % ' '.join([random.choice('0123456789ABCDEF') for j in range(6)]) for i in range(number_of_colors)]
22 return random.choice(colors)
16 23
17 24
18 def draw_features(feature_hits_files, contigs, output_dir): 25 def draw_features(feature_hits_files, contigs, output_dir):
19 ofh = open('process_log', 'w') 26 ofh = open('process_log', 'w')
20 # Read feature_hits_files. 27 # Read feature_hits_files.
49 # No features. 56 # No features.
50 continue 57 continue
51 features_to_plot = [] 58 features_to_plot = []
52 for i in range(contig_features.shape[0]): 59 for i in range(contig_features.shape[0]):
53 i = contig_features.iloc[i, :] 60 i = contig_features.iloc[i, :]
54 features_to_plot += [GraphicFeature(start=i[1], end=i[2], label=i[3], strand=1 * i[5], color=FEATURE_COLORS[feature_number])] 61 if feature_number <= len(FEATURE_COLORS):
62 color = FEATURE_COLORS[feature_number]
63 else:
64 color = get_random_color()
65 features_to_plot += [GraphicFeature(start=i[1], end=i[2], label=i[3], strand=1 * i[5], color=color)]
55 feature_sets_to_plot[feature_name] = features_to_plot 66 feature_sets_to_plot[feature_name] = features_to_plot
56 ofh.write("Number of features to plot: %d\n" % len(feature_sets_to_plot)) 67 ofh.write("Number of features to plot: %d\n" % len(feature_sets_to_plot))
57 if len(feature_sets_to_plot) == 0: 68 if len(feature_sets_to_plot) == 0:
58 # No features. 69 # No features.
59 continue 70 continue