Mercurial > repos > matces > carpet_toolsuite
comparison carpet-src-1/tools/CARPET/TSS_distance.py @ 0:cdd489d98766
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
author | matces |
---|---|
date | Tue, 07 Jun 2011 16:50:41 -0400 |
parents | |
children |
comparison
equal
deleted
inserted
replaced
-1:000000000000 | 0:cdd489d98766 |
---|---|
1 #!/usr/bin/env python | |
2 | |
3 # Copyright 2009 Matteo Cesaroni, Lucilla Luzi | |
4 # | |
5 # This program is free software; ; you can redistribute it and/or modify | |
6 # it under the terms of the GNU Lesser General Public License as published by | |
7 # the Free Software Foundation; either version 3 of the License, or (at your | |
8 # option) any later version. | |
9 # | |
10 # This program is distributed in the hope that it will be useful, | |
11 # but WITHOUT ANY WARRANTY; without even the implied warranty of | |
12 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the | |
13 # GNU General Public License for more details. | |
14 | |
15 | |
16 import sys | |
17 from rpy import * | |
18 | |
19 | |
20 def stop_err(msg): | |
21 sys.stderr.write(msg) | |
22 sys.exit() | |
23 | |
24 def main(): | |
25 | |
26 # Handle input params | |
27 in_fname = sys.argv[1] | |
28 out_fname = sys.argv[2] | |
29 try: | |
30 column = int( sys.argv[3] ) - 1 | |
31 except: | |
32 stop_err( "..Column not specified, your query does not contain a column of numerical data." ) | |
33 title = sys.argv[4] | |
34 xlab = sys.argv[5] | |
35 breaks = int( sys.argv[6] ) | |
36 if breaks == 0: breaks = "Sturges" | |
37 if sys.argv[7] == "true": density = True | |
38 else: density = False | |
39 | |
40 | |
41 | |
42 matrix = [] | |
43 skipped_lines = 0 | |
44 first_invalid_line = 0 | |
45 invalid_value = '' | |
46 | |
47 for i, line in enumerate( file( in_fname ) ): | |
48 valid = True | |
49 line = line.rstrip('\r\n') | |
50 # Skip comments | |
51 if line and not line.startswith( '#' ): | |
52 # Extract values and convert to floats | |
53 row = [] | |
54 try: | |
55 fields = line.split( "\t" ) | |
56 val = fields[column] | |
57 if val.lower() == "na": | |
58 row.append( float( "nan" ) ) | |
59 if float(val) > float(xlab): | |
60 val = (float(xlab)+2000) | |
61 | |
62 row.append( float( val ) ) | |
63 except: | |
64 valid = False | |
65 skipped_lines += 1 | |
66 if not first_invalid_line: | |
67 first_invalid_line = i+1 | |
68 else: | |
69 try: | |
70 row.append( float( val ) ) | |
71 except ValueError: | |
72 valid = False | |
73 skipped_lines += 1 | |
74 if not first_invalid_line: | |
75 first_invalid_line = i+1 | |
76 invalid_value = fields[column] | |
77 else: | |
78 valid = False | |
79 skipped_lines += 1 | |
80 if not first_invalid_line: | |
81 first_invalid_line = i+1 | |
82 | |
83 if valid: | |
84 matrix.append( row ) | |
85 | |
86 if skipped_lines < i: | |
87 print "..on columnn %s" %sys.argv[3] | |
88 try: | |
89 a = array( matrix ) | |
90 r.pdf( out_fname, 8, 8 ) | |
91 r.hist( a, probability=True, main=title, xlab="TSS distance", breaks=breaks ) | |
92 if density: | |
93 r.lines( r.density( a ) ) | |
94 r.dev_off() | |
95 except exc: | |
96 stop_err("Building histogram resulted in error: %s." %str( exc )) | |
97 else: | |
98 print "..all values in column %s are non-numeric." %sys.argv[3] | |
99 | |
100 if skipped_lines > 0: | |
101 print "..skipped %d invalid lines starting with line #%d. Value '%s' is not numeric." % ( skipped_lines, first_invalid_line, invalid_value ) | |
102 | |
103 r.quit( save="no" ) | |
104 | |
105 if __name__ == "__main__": | |
106 main() |