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1 # -*- coding: utf-8 -*-
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2
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3 from galaxy.datatypes.data import Text
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4 from galaxy.datatypes.sniff import get_headers, get_test_fname
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5 from galaxy.datatypes.data import get_file_peek
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6 import subprocess
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7 import os
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8
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9 from galaxy.datatypes.metadata import MetadataElement
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10 from galaxy.datatypes import metadata
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11
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12 def count_special_lines( word, filename, invert = False ):
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13 """
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14 searching for special 'words' using the grep tool
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15 grep is used to speed up the searching and counting
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16 The number of hits is returned.
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17 """
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18 try:
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19 cmd = ["grep", "-c"]
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20 if invert:
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21 cmd.append('-v')
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22 cmd.extend([word, filename])
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23 out = subprocess.Popen(cmd, stdout=subprocess.PIPE)
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24 return int(out.communicate()[0].split()[0])
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25 except:
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26 pass
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27 return 0
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28
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29 class Stockholm_1_0( Text ):
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30 file_ext = "stockholm"
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31
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32 MetadataElement( name="number_of_alignments", default=0, desc="Number of multiple alignments", readonly=True, visible=True, optional=True, no_value=0 )
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33
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34 def set_peek( self, dataset, is_multi_byte=False ):
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35 if not dataset.dataset.purged:
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36 dataset.peek = get_file_peek( dataset.file_name, is_multi_byte=is_multi_byte )
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37 if (dataset.metadata.number_of_models == 1):
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38 dataset.blurb = "1 alignment"
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39 else:
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40 dataset.blurb = "%s alignments" % dataset.metadata.number_of_models
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41 dataset.peek = data.get_file_peek( dataset.file_name, is_multi_byte=is_multi_byte )
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42 else:
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43 dataset.peek = 'file does not exist'
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44 dataset.blurb = 'file purged from disc'
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45
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46 def sniff( self, filename ):
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47 if count_special_lines('^#[[:space:]+]STOCKHOLM[[:space:]+]1.0', filename) > 0:
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48 return True
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49 else:
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50 return False
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51
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52 def set_meta( self, dataset, **kwd ):
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53 """
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54
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55 Set the number of models in dataset.
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56 """
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57 dataset.metadata.number_of_models = count_special_lines('^#[[:space:]+]STOCKHOLM[[:space:]+]1.0', dataset.file_name)
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58
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59 def split( cls, input_datasets, subdir_generator_function, split_params):
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60 """
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61
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62 Split the input files by model records.
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63 """
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64 if split_params is None:
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65 return None
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66
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67 if len(input_datasets) > 1:
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68 raise Exception("STOCKHOLM-file splitting does not support multiple files")
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69 input_files = [ds.file_name for ds in input_datasets]
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70
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71 chunk_size = None
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72 if split_params['split_mode'] == 'number_of_parts':
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73 raise Exception('Split mode "%s" is currently not implemented for STOCKHOLM-files.' % split_params['split_mode'])
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74 elif split_params['split_mode'] == 'to_size':
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75 chunk_size = int(split_params['split_size'])
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76 else:
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77 raise Exception('Unsupported split mode %s' % split_params['split_mode'])
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78
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79 def _read_stockholm_records( filename ):
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80 lines = []
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81 with open(filename) as handle:
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82 for line in handle:
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83 lines.append( line )
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84 if line.strip() == '//':
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85 yield lines
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86 lines = []
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87
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88 def _write_part_stockholm_file( accumulated_lines ):
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89 part_dir = subdir_generator_function()
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90 part_path = os.path.join( part_dir, os.path.basename( input_files[0] ) )
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91 part_file = open( part_path, 'w' )
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92 part_file.writelines( accumulated_lines )
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93 part_file.close()
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94
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95 try:
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96
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97 stockholm_records = _read_stockholm_records( input_files[0] )
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98 stockholm_lines_accumulated = []
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99 for counter, stockholm_record in enumerate( stockholm_records, start = 1):
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100 stockholm_lines_accumulated.extend( stockholm_record )
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101 if counter % chunk_size == 0:
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102 _write_part_stockholm_file( stockholm_lines_accumulated )
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103 stockholm_lines_accumulated = []
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104 if stockholm_lines_accumulated:
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105 _write_part_stockholm_file( stockholm_lines_accumulated )
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106 except Exception, e:
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107 log.error('Unable to split files: %s' % str(e))
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108 raise
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109 split = classmethod(split)
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110
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