Mercurial > repos > devteam > subtract_query
comparison subtract_query.py @ 1:df4bce472400 draft
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
author | devteam |
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date | Tue, 13 Oct 2015 12:51:35 -0400 |
parents | 8a3448727cec |
children | f58ba0382c26 |
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0:8a3448727cec | 1:df4bce472400 |
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4 """ | 4 """ |
5 Subtract an entire query from another query | 5 Subtract an entire query from another query |
6 usage: %prog in_file_1 in_file_2 begin_col end_col output | 6 usage: %prog in_file_1 in_file_2 begin_col end_col output |
7 --ignore-empty-end-cols: ignore empty end columns when subtracting | 7 --ignore-empty-end-cols: ignore empty end columns when subtracting |
8 """ | 8 """ |
9 import sys, re | 9 import sys |
10 from bx.cookbook import doc_optparse | 10 from bx.cookbook import doc_optparse |
11 | 11 |
12 # Older py compatibility | 12 # Older py compatibility |
13 try: | 13 try: |
14 set() | 14 set() |
15 except: | 15 except: |
16 from sets import Set as set | 16 from sets import Set as set |
17 | 17 |
18 assert sys.version_info[:2] >= ( 2, 4 ) | 18 assert sys.version_info[:2] >= ( 2, 4 ) |
19 | |
19 | 20 |
20 def get_lines(fname, begin_col='', end_col='', ignore_empty_end_cols=False): | 21 def get_lines(fname, begin_col='', end_col='', ignore_empty_end_cols=False): |
21 lines = set([]) | 22 lines = set([]) |
22 i = 0 | 23 i = 0 |
23 for i, line in enumerate(file(fname)): | 24 for i, line in enumerate(file(fname)): |
25 if line and not line.startswith('#'): | 26 if line and not line.startswith('#'): |
26 if begin_col and end_col: | 27 if begin_col and end_col: |
27 """Both begin_col and end_col must be integers at this point.""" | 28 """Both begin_col and end_col must be integers at this point.""" |
28 try: | 29 try: |
29 line = line.split('\t') | 30 line = line.split('\t') |
30 line = '\t'.join([line[j] for j in range(begin_col-1, end_col)]) | 31 line = '\t'.join([line[j] for j in range(begin_col - 1, end_col)]) |
31 if ignore_empty_end_cols: | 32 if ignore_empty_end_cols: |
32 # removing empty fields, we do not compare empty fields at the end of a line. | 33 # removing empty fields, we do not compare empty fields at the end of a line. |
33 line = line.rstrip() | 34 line = line.rstrip() |
34 lines.add( line ) | 35 lines.add( line ) |
35 except: pass | 36 except: |
37 pass | |
36 else: | 38 else: |
37 if ignore_empty_end_cols: | 39 if ignore_empty_end_cols: |
38 # removing empty fields, we do not compare empty fields at the end of a line. | 40 # removing empty fields, we do not compare empty fields at the end of a line. |
39 line = line.rstrip() | 41 line = line.rstrip() |
40 lines.add( line ) | 42 lines.add( line ) |
41 if i: return (i+1, lines) | 43 if i: |
42 else: return (i, lines) | 44 return (i + 1, lines) |
45 else: | |
46 return (i, lines) | |
47 | |
43 | 48 |
44 def main(): | 49 def main(): |
45 | |
46 # Parsing Command Line here | 50 # Parsing Command Line here |
47 options, args = doc_optparse.parse( __doc__ ) | 51 options, args = doc_optparse.parse( __doc__ ) |
48 | 52 |
49 try: | 53 try: |
50 inp1_file, inp2_file, begin_col, end_col, out_file = args | 54 inp1_file, inp2_file, begin_col, end_col, out_file = args |
51 except: | 55 except: |
52 doc_optparse.exception() | 56 doc_optparse.exception() |
53 | 57 |
54 begin_col = begin_col.strip() | 58 begin_col = begin_col.strip() |
55 end_col = end_col.strip() | 59 end_col = end_col.strip() |
56 | 60 |
57 if begin_col != 'None' or end_col != 'None': | 61 if begin_col != 'None' or end_col != 'None': |
58 """ | 62 """ |
59 The user selected columns for restriction. We'll allow default | 63 The user selected columns for restriction. We'll allow default |
60 values for both begin_col and end_col as long as the user selected | 64 values for both begin_col and end_col as long as the user selected |
61 at least one of them for restriction. | 65 at least one of them for restriction. |
73 begin_col = tmp_col | 77 begin_col = tmp_col |
74 else: | 78 else: |
75 begin_col = end_col = '' | 79 begin_col = end_col = '' |
76 | 80 |
77 try: | 81 try: |
78 fo = open(out_file,'w') | 82 fo = open(out_file, 'w') |
79 except: | 83 except: |
80 print >> sys.stderr, "Unable to open output file" | 84 print >> sys.stderr, "Unable to open output file" |
81 sys.exit() | 85 sys.exit() |
82 | 86 |
83 """ | 87 """ |
86 diff1 is the number of duplicate lines removed from inp1_file | 90 diff1 is the number of duplicate lines removed from inp1_file |
87 """ | 91 """ |
88 len1, lines1 = get_lines(inp1_file, begin_col, end_col, options.ignore_empty_end_cols) | 92 len1, lines1 = get_lines(inp1_file, begin_col, end_col, options.ignore_empty_end_cols) |
89 diff1 = len1 - len(lines1) | 93 diff1 = len1 - len(lines1) |
90 len2, lines2 = get_lines(inp2_file, begin_col, end_col, options.ignore_empty_end_cols) | 94 len2, lines2 = get_lines(inp2_file, begin_col, end_col, options.ignore_empty_end_cols) |
91 | 95 |
92 lines1.difference_update(lines2) | 96 lines1.difference_update(lines2) |
93 """lines1 is now the set of unique lines in inp1_file - the set of unique lines in inp2_file""" | 97 """lines1 is now the set of unique lines in inp1_file - the set of unique lines in inp2_file""" |
94 | 98 |
95 for line in lines1: | 99 for line in lines1: |
96 print >> fo, line | 100 print >> fo, line |
97 | 101 |
98 fo.close() | 102 fo.close() |
99 | 103 |
100 info_msg = 'Subtracted %d lines. ' %((len1 - diff1) - len(lines1)) | 104 info_msg = 'Subtracted %d lines. ' % ((len1 - diff1) - len(lines1)) |
101 | 105 |
102 if begin_col and end_col: | 106 if begin_col and end_col: |
103 info_msg += 'Restricted to columns c' + str(begin_col) + ' thru c' + str(end_col) + '. ' | 107 info_msg += 'Restricted to columns c' + str(begin_col) + ' thru c' + str(end_col) + '. ' |
104 | 108 |
105 if diff1 > 0: | 109 if diff1 > 0: |
106 info_msg += 'Eliminated %d duplicate/blank/comment/invalid lines from first query.' %diff1 | 110 info_msg += 'Eliminated %d duplicate/blank/comment/invalid lines from first query.' % diff1 |
107 | 111 |
108 print info_msg | 112 print info_msg |
109 | 113 |
110 if __name__ == "__main__": | 114 if __name__ == "__main__": |
111 main() | 115 main() |