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comparison infernal.py @ 0:652f9d550531 draft

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author bgruening
date Tue, 22 Apr 2014 13:56:22 -0400
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children 2c2c5e5e495b
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-1:000000000000 0:652f9d550531
1 # -*- coding: utf-8 -*-
2
3 from galaxy.datatypes.data import Text
4 from galaxy.datatypes.sniff import get_headers, get_test_fname
5 from galaxy.datatypes.data import get_file_peek
6 import subprocess
7 import os
8
9 from galaxy.datatypes.metadata import MetadataElement
10 from galaxy.datatypes import metadata
11
12 def count_special_lines( word, filename, invert = False ):
13 """
14 searching for special 'words' using the grep tool
15 grep is used to speed up the searching and counting
16 The number of hits is returned.
17 """
18 try:
19 cmd = ["grep", "-c"]
20 if invert:
21 cmd.append('-v')
22 cmd.extend([word, filename])
23 out = subprocess.Popen(cmd, stdout=subprocess.PIPE)
24 return int(out.communicate()[0].split()[0])
25 except:
26 pass
27 return 0
28
29 def count_lines( filename, non_empty = False):
30 """
31 counting the number of lines from the 'filename' file
32 """
33 try:
34 if non_empty:
35 out = subprocess.Popen(['grep', '-cve', '^\s*$', filename], stdout=subprocess.PIPE)
36 else:
37 out = subprocess.Popen(['wc', '-l', filename], stdout=subprocess.PIPE)
38 return int(out.communicate()[0].split()[0])
39 except:
40 pass
41 return 0
42
43
44 class Infernal_CM_1_1( Text ):
45 file_ext = "cm"
46
47 MetadataElement( name="number_of_models", default=0, desc="Number of covariance models", readonly=True, visible=True, optional=True, no_value=0 )
48
49 def set_peek( self, dataset, is_multi_byte=False ):
50 if not dataset.dataset.purged:
51 dataset.peek = get_file_peek( dataset.file_name, is_multi_byte=is_multi_byte )
52 if (dataset.metadata.number_of_models == 1):
53 dataset.blurb = "1 model"
54 else:
55 dataset.blurb = "%s models" % dataset.metadata.number_of_models
56 dataset.peek = data.get_file_peek( dataset.file_name, is_multi_byte=is_multi_byte )
57 else:
58 dataset.peek = 'file does not exist'
59 dataset.blurb = 'file purged from disc'
60
61 def sniff( self, filename ):
62 if count_special_lines("^INFERNAL1/a", filename) > 0:
63 return True
64 else:
65 return False
66
67 def set_meta( self, dataset, **kwd ):
68 """
69 Set the number of models in dataset.
70 """
71 dataset.metadata.number_of_models = count_special_lines("^INFERNAL1/a", dataset.file_name)
72
73 def split( cls, input_datasets, subdir_generator_function, split_params):
74 """
75 Split the input files by model records.
76 """
77 if split_params is None:
78 return None
79
80 if len(input_datasets) > 1:
81 raise Exception("CM-file splitting does not support multiple files")
82 input_files = [ds.file_name for ds in input_datasets]
83
84 chunk_size = None
85 if split_params['split_mode'] == 'number_of_parts':
86 raise Exception('Split mode "%s" is currently not implemented for CM-files.' % split_params['split_mode'])
87 elif split_params['split_mode'] == 'to_size':
88 chunk_size = int(split_params['split_size'])
89 else:
90 raise Exception('Unsupported split mode %s' % split_params['split_mode'])
91
92 def _read_cm_records( filename ):
93 lines = []
94 with open(filename) as handle:
95 for line in handle:
96 if line.startswith("INFERNAL1/a") and lines:
97 yield lines
98 lines = [line]
99 else:
100 lines.append( line )
101 yield lines
102
103 def _write_part_cm_file( accumulated_lines ):
104 part_dir = subdir_generator_function()
105 part_path = os.path.join( part_dir, os.path.basename( input_files[0] ) )
106 part_file = open( part_path, 'w' )
107 part_file.writelines( accumulated_lines )
108 part_file.close()
109
110 try:
111 cm_records = _read_cm_records( input_files[0] )
112 cm_lines_accumulated = []
113 for counter, cm_record in enumerate( cm_records, start = 1):
114 cm_lines_accumulated.extend( cm_record )
115 if counter % chunk_size == 0:
116 _write_part_cm_file( cm_lines_accumulated )
117 cm_lines_accumulated = []
118 if cm_lines_accumulated:
119 _write_part_cm_file( cm_lines_accumulated )
120 except Exception, e:
121 log.error('Unable to split files: %s' % str(e))
122 raise
123 split = classmethod(split)
124
125 if __name__ == '__main__':
126 Infernal_CM_1_1()
127 Stockholm_1_0()
128