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comparison genetrack_util.py @ 7:a7da50a23270 draft

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author greg
date Tue, 24 Nov 2015 08:14:42 -0500
parents a952b6740fb9
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6:fa85ca6c9cf8 7:a7da50a23270
7 import tempfile 7 import tempfile
8 8
9 GFF_EXT = 'gff' 9 GFF_EXT = 'gff'
10 SCIDX_EXT = 'scidx' 10 SCIDX_EXT = 'scidx'
11 11
12 ROMAN = ['0', 'I', 'II', 'III', 'IV', 'V', 'VI', 'VII', 'VIII', 'IX', 'X',
13 'XI', 'XII', 'XIII', 'XIV', 'XV', 'XVI', 'XVII', 'XVIII', 'XIX', 'XX',
14 'XXI', 'XXII', 'XXIII', 'XXIV', 'XXV', 'XXVI', 'XXVII', 'XXVIII', 'XXIX',
15 'XXX']
16
17 12
18 def noop(data): 13 def noop(data):
19 return data 14 return data
20 15
21 16
25 20
26 def numeric_to_zeropad(data): 21 def numeric_to_zeropad(data):
27 return re.sub(r'chr(\d([^\d]|$))', r'chr0\1', data) 22 return re.sub(r'chr(\d([^\d]|$))', r'chr0\1', data)
28 23
29 24
30 def roman_to_numeric(data): 25 FORMATS = ['zeropad', 'numeric']
31 def convert(match): 26 IN_CONVERT = {'zeropad': zeropad_to_numeric, 'numeric': noop}
32 """ 27 OUT_CONVERT = {'zeropad': numeric_to_zeropad, 'numeric': noop}
33 Converts a single roman numeral to a number
34 """
35 numeral = match.group(1)
36 numeral = numeral.upper()
37 if numeral not in ROMAN:
38 # Unable to convert detected Roman numeral
39 return match.group(0)
40 return 'chr'+str(ROMAN.index(numeral))+(match.group(2) or '')
41 r = re.compile('chr([IVX]+)([^IVX]|$)', flags=re.IGNORECASE)
42 data = r.sub(convert, data)
43 return data
44
45
46 def numeric_to_roman(data):
47 def convert(match):
48 """
49 Converts a number to a roman numeral
50 """
51 number = int(match.group(1))
52 if number >= len(ROMAN):
53 # Number is out of range to convert to a Roman numeral
54 return match.group(0)
55 return 'chr'+ROMAN[number]+(match.group(2) or '')
56 r = re.compile('chr(\d+)([^\d]|$)')
57 data = r.sub(convert, data)
58 return data
59
60 FORMATS = ['zeropad', 'numeric', 'roman']
61 IN_CONVERT = {'zeropad': zeropad_to_numeric, 'roman': roman_to_numeric, 'numeric': noop}
62 OUT_CONVERT = {'zeropad': numeric_to_zeropad, 'roman': numeric_to_roman, 'numeric': noop}
63 28
64 29
65 def conversion_functions(in_fmt, out_fmt): 30 def conversion_functions(in_fmt, out_fmt):
66 """ 31 """
67 Returns the proper list of functions to apply to perform a conversion 32 Returns the proper list of functions to apply to perform a conversion
68 """ 33 """
69 return [IN_CONVERT[in_fmt], OUT_CONVERT[out_fmt]] 34 return [IN_CONVERT[in_fmt], OUT_CONVERT[out_fmt]]
70 35
71 36
72 def autodetect_format(data):
73 if re.search('chr0\d', data):
74 fmt = 'zeropad'
75 elif re.search('chr[IVXivx]', data):
76 fmt = 'roman'
77 else:
78 fmt = 'numeric'
79 return fmt
80
81
82 def convert_data(data, in_fmt, out_fmt): 37 def convert_data(data, in_fmt, out_fmt):
83 if in_fmt == 'autodetect':
84 in_fmt = autodetect_format(data)
85 for fn in conversion_functions(in_fmt, out_fmt): 38 for fn in conversion_functions(in_fmt, out_fmt):
86 data = fn(data) 39 data = fn(data)
87 return data 40 return data
88 41
89 42
423 for peak in reverse_peaks: 376 for peak in reverse_peaks:
424 if process_bounds[0] < peak.index < process_bounds[1]: 377 if process_bounds[0] < peak.index < process_bounds[1]:
425 write(cname, '-', peak) 378 write(cname, '-', peak)
426 379
427 380
428 def sort_chromosome_reads_by_index( input_path ): 381 def sort_chromosome_reads_by_index(input_path):
429 """ 382 """
430 Return a gff file with chromosome reads sorted by index. 383 Return a gff file with chromosome reads sorted by index.
431 """ 384 """
432 # Will this sort produce different results across platforms? 385 # Will this sort produce different results across platforms?
433 output_path = tempfile.NamedTemporaryFile( delete=False ).name 386 output_path = tempfile.NamedTemporaryFile(delete=False).name
434 command = 'sort -k 1,1 -k 4,4n "%s" > "%s"' % (input_path, output_path) 387 command = 'sort -k 1,1 -k 4,4n "%s" > "%s"' % (input_path, output_path)
435 p = subprocess.Popen(command, shell=True) 388 p = subprocess.Popen(command, shell=True)
436 p.wait() 389 p.wait()
437 return output_path 390 return output_path