comparison cwpair2.py @ 0:507521bf124a draft

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author greg
date Tue, 17 Nov 2015 14:06:28 -0500
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children 430a5bdc55a3
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-1:000000000000 0:507521bf124a
1 """
2 cwpair2.py
3
4 Takes a list of called peaks on both strands and produces a list of matched pairs and a list
5 of unmatched orphans using a specified method for finding matched pairs. Methods for finding
6 matched pairs are mode, closest, largest or all, where the analysis is run for each method
7
8 Input: list of one or more gff format files
9
10 Output: files produced for each input/mode combination:
11 S (simple), D (detailed), O (orphans), P (frequency preview plot), F (final frequency plot),
12 C (statistics graph), statistics.tabular
13 """
14
15 import argparse
16 import csv
17 import cwpair2_util
18
19 if __name__ == '__main__':
20 parser = argparse.ArgumentParser()
21 parser.add_argument('--input', dest='inputs', action='append', nargs=2, help="Input datasets")
22 parser.add_argument('--method', dest='method', default='mode', help='Method of finding match.')
23 parser.add_argument('--up_distance', dest='up_distance', type=int, default=50, help='Distance upstream from a pair.')
24 parser.add_argument('--down_distance', dest='down_distance', type=int, default=100, help='Distance downstream of a pair.')
25 parser.add_argument('--binsize', dest='binsize', type=int, default=1, help='Width of bins for plots and mode.')
26 parser.add_argument('--threshold_format', dest='threshold_format', help='Percentage to filter the 95th percentile.')
27 parser.add_argument('--relative_threshold', dest='relative_threshold', type=float, default=0.0, help='Percentage to filter the 95th percentile.')
28 parser.add_argument('--absolute_threshold', dest='absolute_threshold', type=float, default=0.0, help='Absolute value to filter.')
29 parser.add_argument('--output_files', dest='output_files', default='simple', help='Restrict output dataset collections.')
30 parser.add_argument('--plot_format', dest='plot_format', default=None, help='Format of output graph.')
31 parser.add_argument('--sort_chromosome', dest='sort_chromosome', default='asc', help='Sort output by chromosome.')
32 parser.add_argument('--sort_score', dest='sort_score', default='no', help='Sort output by score.')
33 parser.add_argument('--statistics_output', dest='statistics_output', help='Statistics output file.')
34 args = parser.parse_args()
35
36 cwpair2_util.create_directories(args.method)
37
38 statistics = []
39 if args.absolute_threshold > 0:
40 threshold = args.absolute_threshold
41 elif args.relative_threshold > 0:
42 threshold = args.relative_threshold / 100.0
43 else:
44 threshold = 0
45 for (dataset_path, hid) in args.inputs:
46 stats = cwpair2_util.process_file(dataset_path,
47 hid,
48 args.method,
49 threshold,
50 args.up_distance,
51 args.down_distance,
52 args.binsize,
53 args.output_files,
54 args.plot_format,
55 args.sort_chromosome,
56 args.sort_score)
57 statistics.extend(stats)
58 # Accumulate statistics.
59 by_file = {}
60 for stats in statistics:
61 # Skip "None" statistics from failed files
62 if not stats:
63 continue
64 path = stats['stats_path']
65 if path not in by_file:
66 by_file[path] = []
67 by_file[path].append(stats)
68 # Write tabular statistics file.
69 keys = ['fname', 'final_mode', 'preview_mode', 'perc95', 'paired', 'orphans']
70 statistics_out = csv.writer(open(args.statistics_output, 'wt'), delimiter='\t')
71 statistics_out.writerow(keys)
72 for file_path, statistics in by_file.items():
73 for stats in statistics:
74 statistics_out.writerow([stats[key] for key in keys])