Mercurial > repos > greg > cwpair2
comparison cwpair2.py @ 0:507521bf124a draft
Uploaded
author | greg |
---|---|
date | Tue, 17 Nov 2015 14:06:28 -0500 |
parents | |
children | 430a5bdc55a3 |
comparison
equal
deleted
inserted
replaced
-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]) |