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1 #!/usr/bin/env python
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2
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3 import argparse
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4 import os
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5
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6 import pandas
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7 import matplotlib.pyplot as pyplot
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8 from Bio import SeqIO
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9 from dna_features_viewer import GraphicFeature, GraphicRecord
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10
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11
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12 AMR_COLOR = '#FED976'
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13 INC_GROUPS_COLOR = '#0570B0'
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14 FEATURE_COLORS = [AMR_COLOR, INC_GROUPS_COLOR]
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15 FIGURE_WIDTH = 13
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16
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17
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18 def draw_features(feature_hits_files, contigs, output_dir):
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19 ofh = open('process_log', 'w')
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20 # Read feature_hits_files.
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21 feature_hits = pandas.Series(dtype=object)
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22 feature_plots = pandas.Series(dtype=object)
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23 for feature_hits_file in feature_hits_files:
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24 feature_name = os.path.basename(feature_hits_file)
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25 # Make sure the file is not empty.
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26 if os.path.isfile(feature_hits_file) and os.path.getsize(feature_hits_file) > 0:
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27 best_hits = pandas.read_csv(filepath_or_buffer=feature_hits_file, sep='\t', header=None)
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1
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28 ofh.write("\nFeature file %s will be processed\n" % os.path.basename(feature_hits_file))
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29 else:
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30 ofh.write("\nEmpty feature file %s will NOT be processed\n" % os.path.basename(feature_hits_file))
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31 best_hits = None
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32 feature_hits[feature_name] = best_hits
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33
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34 # Draw one plot per contig for simplicity.
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35 ofh.write("\nProcessing contigs file: %s\n" % str(contigs))
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36 for contig in SeqIO.parse(contigs, 'fasta'):
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37 ofh.write("Processing contig: %s\n" % str(contig))
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38 contig_plot_png = os.path.join(output_dir, '%s.png' % str(contig.id))
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39 feature_sets_to_plot = pandas.Series(dtype=object)
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40 for feature_number in range(len(feature_hits)):
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41 feature_name = feature_hits.index.to_list()[feature_number]
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42 ofh.write("Processing feature name: %s\n" % str(feature_name))
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43 these_features = feature_hits[feature_name]
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44 if these_features is None or these_features.shape[0] == 0:
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45 # No features.
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46 continue
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47 contig_features = these_features.loc[these_features.iloc[:, 0] == contig.id, :]
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48 if contig_features is None or contig_features.shape[0] == 0:
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49 # No features.
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50 continue
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51 features_to_plot = []
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52 for i in range(contig_features.shape[0]):
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53 i = contig_features.iloc[i, :]
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54 features_to_plot += [GraphicFeature(start=i[1], end=i[2], label=i[3], strand=1 * i[5], color=FEATURE_COLORS[feature_number])]
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55 feature_sets_to_plot[feature_name] = features_to_plot
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56 ofh.write("Number of features to plot: %d\n" % len(feature_sets_to_plot))
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57 if len(feature_sets_to_plot) == 0:
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58 # No features.
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59 continue
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60 # Determine each plot height for later scaling
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61 expected_plot_heights = []
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62 for i in range(len(feature_sets_to_plot)):
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63 record = GraphicRecord(sequence_length=len(contig), features=feature_sets_to_plot[i])
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64 if i == len(feature_sets_to_plot) - 1:
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65 with_ruler = True
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66 else:
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67 with_ruler = False
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68 plot, _ = record.plot(figure_width=FIGURE_WIDTH, with_ruler=with_ruler)
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69 expected_plot_heights += [plot.figure.get_size_inches()[1]]
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70 plot_height_sum = sum(expected_plot_heights)
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71 # Make a figure with separate plots for each feature class.
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72 plots = pyplot.subplots(nrows=len(feature_sets_to_plot),
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73 ncols=1,
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74 sharex=True,
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75 figsize=(FIGURE_WIDTH, plot_height_sum * .66666),
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76 gridspec_kw={"height_ratios": expected_plot_heights})
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77 figure = plots[0]
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78 plots = plots[1]
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79 if len(feature_sets_to_plot) == 1:
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80 plots = [plots]
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81 # Add each feature class's plot with the pre-determined height.
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82 for i in range(len(feature_sets_to_plot)):
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83 record = GraphicRecord(sequence_length=len(contig), features=feature_sets_to_plot[i])
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84 if i == len(feature_sets_to_plot) - 1:
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85 with_ruler = True
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86 else:
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87 with_ruler = False
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88 plot, _ = record.plot(ax=plots[i], with_ruler=with_ruler, figure_width=FIGURE_WIDTH)
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89 ymin, ymax = plot.figure.axes[0].get_ylim()
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90 if i == 0:
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91 plot.text(x=0, y=ymax, s=contig.id)
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92 figure.tight_layout()
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93 ofh.write("Saving PNG plot file: %s\n" % str(contig_plot_png))
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94 figure.savefig(contig_plot_png)
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95 feature_plots[contig.id] = contig_plot_png
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96 ofh.close()
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97
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98
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99 if __name__ == '__main__':
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100 parser = argparse.ArgumentParser()
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101
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102 parser.add_argument('--feature_hits_dir', action='store', dest='feature_hits_dir', help='Directory of tabular files containing feature hits')
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103 parser.add_argument('--contigs', action='store', dest='contigs', help='Fasta file of contigs')
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104 parser.add_argument('--output_dir', action='store', dest='output_dir', help='Output directory')
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105
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106 args = parser.parse_args()
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107
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108 # Get thge collection of feature hits files. The collection
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109 # will be sorted alphabetically and will contain 2 files
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110 # named something like AMR_CDS_311_2022_12_20.fasta and
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111 # Incompatibility_Groups_2023_01_01.fasta.
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112 feature_hits_files = []
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113 for file_name in sorted(os.listdir(args.feature_hits_dir)):
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114 file_path = os.path.abspath(os.path.join(args.feature_hits_dir, file_name))
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115 feature_hits_files.append(file_path)
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116
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117 draw_features(feature_hits_files, args.contigs, args.output_dir)
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