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1 # -*- coding: utf-8 -*-
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2
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3 from galaxy.datatypes import data
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4 import logging
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5 from galaxy.datatypes.sniff import get_headers, get_test_fname
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6 from galaxy.datatypes.data import get_file_peek
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7 from galaxy.datatypes.tabular import Tabular
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8 from galaxy.datatypes.binary import Binary
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9 from galaxy.datatypes.xml import GenericXml
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10 import subprocess
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11 import os
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12 #import pybel
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13 #import openbabel
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14 #openbabel.obErrorLog.StopLogging()
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15
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16 from galaxy.datatypes.metadata import MetadataElement
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17 from galaxy.datatypes import metadata
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18
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19 log = logging.getLogger(__name__)
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20
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21 def count_special_lines( word, filename, invert = False ):
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22 """
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23 searching for special 'words' using the grep tool
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24 grep is used to speed up the searching and counting
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25 The number of hits is returned.
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26 """
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27 try:
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28 cmd = ["grep", "-c"]
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29 if invert:
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30 cmd.append('-v')
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31 cmd.extend([word, filename])
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32 out = subprocess.Popen(cmd, stdout=subprocess.PIPE)
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33 return int(out.communicate()[0].split()[0])
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34 except:
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35 pass
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36 return 0
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37
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38 def count_lines( filename, non_empty = False):
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39 """
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40 counting the number of lines from the 'filename' file
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41 """
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42 try:
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43 if non_empty:
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44 out = subprocess.Popen(['grep', '-cve', '^\s*$', filename], stdout=subprocess.PIPE)
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45 else:
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46 out = subprocess.Popen(['wc', '-l', filename], stdout=subprocess.PIPE)
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47 return int(out.communicate()[0].split()[0])
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48 except:
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49 pass
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50 return 0
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51
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52
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53 class GenericMolFile( data.Text ):
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54 """
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55 abstract class for most of the molecule files
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56 """
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57 MetadataElement( name="number_of_molecules", default=0, desc="Number of molecules", readonly=True, visible=True, optional=True, no_value=0 )
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58
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59 def set_peek( self, dataset, is_multi_byte=False ):
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60 if not dataset.dataset.purged:
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61 dataset.peek = get_file_peek( dataset.file_name, is_multi_byte=is_multi_byte )
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62 if (dataset.metadata.number_of_molecules == 1):
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63 dataset.blurb = "1 molecule"
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64 else:
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65 dataset.blurb = "%s molecules" % dataset.metadata.number_of_molecules
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66 dataset.peek = data.get_file_peek( dataset.file_name, is_multi_byte=is_multi_byte )
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67 else:
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68 dataset.peek = 'file does not exist'
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69 dataset.blurb = 'file purged from disk'
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70
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71 def get_mime(self):
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72 return 'text/plain'
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73
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74 class MOL( GenericMolFile ):
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75 file_ext = "mol"
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76 def sniff( self, filename ):
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77 if count_special_lines("^M\s*END", filename) == 1:
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78 return True
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79 else:
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80 return False
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81
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82 def set_meta( self, dataset, **kwd ):
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83 """
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84 Set the number molecules, in the case of MOL its always one.
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85 """
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86 dataset.metadata.number_of_molecules = 1
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87
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88
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89 class SDF( GenericMolFile ):
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90 file_ext = "sdf"
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91 def sniff( self, filename ):
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92 if count_special_lines("^\$\$\$\$", filename) > 0:
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93 return True
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94 else:
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95 return False
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96
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97 def set_meta( self, dataset, **kwd ):
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98 """
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99 Set the number of molecules in dataset.
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100 """
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101 dataset.metadata.number_of_molecules = count_special_lines("^\$\$\$\$", dataset.file_name)
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102
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103 def split( cls, input_datasets, subdir_generator_function, split_params):
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104 """
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105 Split the input files by molecule records.
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106 """
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107 if split_params is None:
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108 return None
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109
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110 if len(input_datasets) > 1:
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111 raise Exception("SD-file splitting does not support multiple files")
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112 input_files = [ds.file_name for ds in input_datasets]
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113
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114 chunk_size = None
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115 if split_params['split_mode'] == 'number_of_parts':
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116 raise Exception('Split mode "%s" is currently not implemented for SD-files.' % split_params['split_mode'])
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117 elif split_params['split_mode'] == 'to_size':
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118 chunk_size = int(split_params['split_size'])
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119 else:
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120 raise Exception('Unsupported split mode %s' % split_params['split_mode'])
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121
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122 def _read_sdf_records( filename ):
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123 lines = []
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124 with open(filename) as handle:
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125 for line in handle:
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126 lines.append( line )
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127 if line.startswith("$$$$"):
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128 yield lines
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129 lines = []
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130
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131 def _write_part_sdf_file( accumulated_lines ):
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132 part_dir = subdir_generator_function()
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133 part_path = os.path.join(part_dir, os.path.basename(input_files[0]))
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134 part_file = open(part_path, 'w')
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135 part_file.writelines( accumulated_lines )
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136 part_file.close()
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137
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138 try:
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139 sdf_records = _read_sdf_records( input_files[0] )
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140 sdf_lines_accumulated = []
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141 for counter, sdf_record in enumerate( sdf_records, start = 1):
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142 sdf_lines_accumulated.extend( sdf_record )
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143 if counter % chunk_size == 0:
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144 _write_part_sdf_file( sdf_lines_accumulated )
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145 sdf_lines_accumulated = []
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146 if sdf_lines_accumulated:
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147 _write_part_sdf_file( sdf_lines_accumulated )
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148 except Exception, e:
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149 log.error('Unable to split files: %s' % str(e))
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150 raise
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151 split = classmethod(split)
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152
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153
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154 class MOL2( GenericMolFile ):
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155 file_ext = "mol2"
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156 def sniff( self, filename ):
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157 if count_special_lines("@\<TRIPOS\>MOLECULE", filename) > 0:
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158 return True
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159 else:
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160 return False
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161
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162 def set_meta( self, dataset, **kwd ):
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163 """
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164 Set the number of lines of data in dataset.
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165 """
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166 dataset.metadata.number_of_molecules = count_special_lines("@<TRIPOS>MOLECULE", dataset.file_name)#self.count_data_lines(dataset)
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167
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168 def split( cls, input_datasets, subdir_generator_function, split_params):
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169 """
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170 Split the input files by molecule records.
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171 """
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172 if split_params is None:
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173 return None
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174
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175 if len(input_datasets) > 1:
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176 raise Exception("MOL2-file splitting does not support multiple files")
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177 input_files = [ds.file_name for ds in input_datasets]
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178
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179 chunk_size = None
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180 if split_params['split_mode'] == 'number_of_parts':
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181 raise Exception('Split mode "%s" is currently not implemented for MOL2-files.' % split_params['split_mode'])
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182 elif split_params['split_mode'] == 'to_size':
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183 chunk_size = int(split_params['split_size'])
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184 else:
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185 raise Exception('Unsupported split mode %s' % split_params['split_mode'])
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186
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187 def _read_mol2_records( filename ):
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188 lines = []
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189 start = True
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190 with open(filename) as handle:
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191 for line in handle:
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192 if line.startswith("@<TRIPOS>MOLECULE"):
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193 if start:
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194 start = False
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195 else:
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196 yield lines
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197 lines = []
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198 lines.append( line )
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199
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200 def _write_part_mol2_file( accumulated_lines ):
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201 part_dir = subdir_generator_function()
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202 part_path = os.path.join(part_dir, os.path.basename(input_files[0]))
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203 part_file = open(part_path, 'w')
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204 part_file.writelines( accumulated_lines )
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205 part_file.close()
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206
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207 try:
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208 mol2_records = _read_mol2_records( input_files[0] )
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209 mol2_lines_accumulated = []
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210 for counter, mol2_record in enumerate( mol2_records, start = 1):
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211 mol2_lines_accumulated.extend( mol2_record )
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212 if counter % chunk_size == 0:
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213 _write_part_mol2_file( mol2_lines_accumulated )
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214 mol2_lines_accumulated = []
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215 if mol2_lines_accumulated:
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216 _write_part_mol2_file( mol2_lines_accumulated )
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217 except Exception, e:
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218 log.error('Unable to split files: %s' % str(e))
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219 raise
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220 split = classmethod(split)
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221
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222
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223
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224 class FPS( GenericMolFile ):
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225 """
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226 chemfp fingerprint file: http://code.google.com/p/chem-fingerprints/wiki/FPS
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227 """
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228 file_ext = "fps"
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229 def sniff( self, filename ):
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230 header = get_headers( filename, sep='\t', count=1 )
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231 if header[0][0].strip() == '#FPS1':
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232 return True
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233 else:
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234 return False
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235
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236 def set_meta( self, dataset, **kwd ):
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237 """
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238 Set the number of lines of data in dataset.
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239 """
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240 dataset.metadata.number_of_molecules = count_special_lines('^#', dataset.file_name, invert = True)
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241
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242
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243 def split( cls, input_datasets, subdir_generator_function, split_params):
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244 """
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245 Split the input files by fingerprint records.
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246 """
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247 if split_params is None:
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248 return None
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249
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250 if len(input_datasets) > 1:
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251 raise Exception("FPS-file splitting does not support multiple files")
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252 input_files = [ds.file_name for ds in input_datasets]
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253
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254 chunk_size = None
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255 if split_params['split_mode'] == 'number_of_parts':
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256 raise Exception('Split mode "%s" is currently not implemented for MOL2-files.' % split_params['split_mode'])
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257 elif split_params['split_mode'] == 'to_size':
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258 chunk_size = int(split_params['split_size'])
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259 else:
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260 raise Exception('Unsupported split mode %s' % split_params['split_mode'])
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261
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262
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263 def _write_part_fingerprint_file( accumulated_lines ):
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264 part_dir = subdir_generator_function()
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265 part_path = os.path.join(part_dir, os.path.basename(input_files[0]))
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266 part_file = open(part_path, 'w')
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267 part_file.writelines( accumulated_lines )
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268 part_file.close()
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269
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270 try:
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271 header_lines = []
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272 lines_accumulated = []
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273 fingerprint_counter = 0
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274 for line in open( input_files[0] ):
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275 if not line.strip():
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276 continue
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277 if line.startswith('#'):
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278 header_lines.append( line )
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279 else:
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280 fingerprint_counter += 1
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281 lines_accumulated.append( line )
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282 if fingerprint_counter != 0 and fingerprint_counter % chunk_size == 0:
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283 _write_part_fingerprint_file( header_lines + lines_accumulated )
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284 lines_accumulated = []
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285 if lines_accumulated:
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286 _write_part_fingerprint_file( header_lines + lines_accumulated )
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287 except Exception, e:
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288 log.error('Unable to split files: %s' % str(e))
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289 raise
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290 split = classmethod(split)
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291
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292
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293 def merge(split_files, output_file):
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294 """
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295 Merging fps files requires merging the header manually.
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296 We take the header from the first file.
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297 """
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298 if len(split_files) == 1:
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299 #For one file only, use base class method (move/copy)
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300 return data.Text.merge(split_files, output_file)
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301 if not split_files:
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302 raise ValueError("No fps files given, %r, to merge into %s" \
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303 % (split_files, output_file))
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304 out = open(output_file, "w")
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305 first = True
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306 for filename in split_files:
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307 with open(filename) as handle:
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308 for line in handle:
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309 if line.startswith('#'):
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310 if first:
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311 out.write(line)
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312 else:
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313 # line is no header and not a comment, we assume the first header is written to out and we set 'first' to False
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314 first = False
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315 out.write(line)
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316 out.close()
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317 merge = staticmethod(merge)
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318
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319
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320
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321 class OBFS( Binary ):
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322 """OpenBabel Fastsearch format (fs)."""
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323 file_ext = 'fs'
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324 composite_type ='basic'
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325 allow_datatype_change = False
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326
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327 MetadataElement( name="base_name", default='OpenBabel Fastsearch Index',
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328 readonly=True, visible=True, optional=True,)
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329
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330 def __init__(self,**kwd):
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331 """
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332 A Fastsearch Index consists of a binary file with the fingerprints
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333 and a pointer the actual molecule file.
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334 """
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335 Binary.__init__(self, **kwd)
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336 self.add_composite_file('molecule.fs', is_binary = True,
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337 description = 'OpenBabel Fastsearch Index' )
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338 self.add_composite_file('molecule.sdf', optional=True,
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339 is_binary = False, description = 'Molecule File' )
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340 self.add_composite_file('molecule.smi', optional=True,
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341 is_binary = False, description = 'Molecule File' )
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342 self.add_composite_file('molecule.inchi', optional=True,
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343 is_binary = False, description = 'Molecule File' )
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344 self.add_composite_file('molecule.mol2', optional=True,
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345 is_binary = False, description = 'Molecule File' )
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346 self.add_composite_file('molecule.cml', optional=True,
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347 is_binary = False, description = 'Molecule File' )
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348
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349 def set_peek( self, dataset, is_multi_byte=False ):
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350 """Set the peek and blurb text."""
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351 if not dataset.dataset.purged:
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352 dataset.peek = "OpenBabel Fastsearch Index"
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353 dataset.blurb = "OpenBabel Fastsearch Index"
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354 else:
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355 dataset.peek = "file does not exist"
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356 dataset.blurb = "file purged from disk"
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357
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358 def display_peek( self, dataset ):
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359 """Create HTML content, used for displaying peek."""
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360 try:
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361 return dataset.peek
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362 except:
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363 return "OpenBabel Fastsearch Index"
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364
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365 def display_data(self, trans, data, preview=False, filename=None,
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366 to_ext=None, size=None, offset=None, **kwd):
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367 """Apparently an old display method, but still gets called.
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368
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369 This allows us to format the data shown in the central pane via the "eye" icon.
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370 """
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371 return "This is a OpenBabel Fastsearch format. You can speed up your similarity and substructure search with it."
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372
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373 def get_mime(self):
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374 """Returns the mime type of the datatype (pretend it is text for peek)"""
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375 return 'text/plain'
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376
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377 def merge(split_files, output_file, extra_merge_args):
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378 """Merging Fastsearch indices is not supported."""
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379 raise NotImplementedError("Merging Fastsearch indices is not supported.")
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380
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381 def split( cls, input_datasets, subdir_generator_function, split_params):
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382 """Splitting Fastsearch indices is not supported."""
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383 if split_params is None:
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384 return None
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385 raise NotImplementedError("Splitting Fastsearch indices is not possible.")
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386
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387
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388
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389 class DRF( GenericMolFile ):
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390 file_ext = "drf"
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391
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392 def set_meta( self, dataset, **kwd ):
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393 """
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394 Set the number of lines of data in dataset.
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395 """
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396 dataset.metadata.number_of_molecules = count_special_lines('\"ligand id\"', dataset.file_name, invert = True)
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397
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398
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399 class PHAR( GenericMolFile ):
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400 """
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401 Pharmacophore database format from silicos-it.
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402 """
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403 file_ext = "phar"
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404 def set_peek( self, dataset, is_multi_byte=False ):
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405 if not dataset.dataset.purged:
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406 dataset.peek = get_file_peek( dataset.file_name, is_multi_byte=is_multi_byte )
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407 dataset.blurb = "pharmacophore"
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408 else:
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409 dataset.peek = 'file does not exist'
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410 dataset.blurb = 'file purged from disk'
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411
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412
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413 class PDB( GenericMolFile ):
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414 """
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415 Protein Databank format.
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416 http://www.wwpdb.org/documentation/format33/v3.3.html
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417 """
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418 file_ext = "pdb"
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419 def sniff( self, filename ):
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420 headers = get_headers( filename, sep=' ', count=300 )
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421 h = t = c = s = k = e = False
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422 for line in headers:
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423 section_name = line[0].strip()
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424 if section_name == 'HEADER':
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425 h = True
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426 elif section_name == 'TITLE':
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427 t = True
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428 elif section_name == 'COMPND':
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429 c = True
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430 elif section_name == 'SOURCE':
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431 s = True
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432 elif section_name == 'KEYWDS':
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433 k = True
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434 elif section_name == 'EXPDTA':
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435 e = True
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436
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437 if h*t*c*s*k*e == True:
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438 return True
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439 else:
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440 return False
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441
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442 def set_peek( self, dataset, is_multi_byte=False ):
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443 if not dataset.dataset.purged:
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444 atom_numbers = count_special_lines("^ATOM", dataset.file_name)
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445 hetatm_numbers = count_special_lines("^HETATM", dataset.file_name)
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446 dataset.peek = get_file_peek( dataset.file_name, is_multi_byte=is_multi_byte )
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447 dataset.blurb = "%s atoms and %s HET-atoms" % (atom_numbers, hetatm_numbers)
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448 else:
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449 dataset.peek = 'file does not exist'
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450 dataset.blurb = 'file purged from disk'
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451
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452
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453 class grd( data.Text ):
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454 file_ext = "grd"
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455 def set_peek( self, dataset, is_multi_byte=False ):
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456 if not dataset.dataset.purged:
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457 dataset.peek = get_file_peek( dataset.file_name, is_multi_byte=is_multi_byte )
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458 dataset.blurb = "grids for docking"
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459 else:
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460 dataset.peek = 'file does not exist'
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|
461 dataset.blurb = 'file purged from disk'
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462
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463
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464 class grdtgz( Binary ):
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465 file_ext = "grd.tgz"
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466 def set_peek( self, dataset, is_multi_byte=False ):
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467 if not dataset.dataset.purged:
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468 dataset.peek = 'binary data'
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469 dataset.blurb = "compressed grids for docking"
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470 else:
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471 dataset.peek = 'file does not exist'
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|
472 dataset.blurb = 'file purged from disk'
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473
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474
|
|
|
475 class InChI( Tabular ):
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476 file_ext = "inchi"
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|
477 column_names = [ 'InChI' ]
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|
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478 MetadataElement( name="columns", default=2, desc="Number of columns", readonly=True, visible=False )
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|
479 MetadataElement( name="column_types", default=['str'], param=metadata.ColumnTypesParameter, desc="Column types", readonly=True, visible=False )
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|
|
480 MetadataElement( name="number_of_molecules", default=0, desc="Number of molecules", readonly=True, visible=True, optional=True, no_value=0 )
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|
|
481
|
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|
482 def set_meta( self, dataset, **kwd ):
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483 """
|
|
|
484 Set the number of lines of data in dataset.
|
|
|
485 """
|
|
|
486 dataset.metadata.number_of_molecules = self.count_data_lines(dataset)
|
|
|
487
|
|
|
488 def set_peek( self, dataset, is_multi_byte=False ):
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|
489 if not dataset.dataset.purged:
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490 dataset.peek = get_file_peek( dataset.file_name, is_multi_byte=is_multi_byte )
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|
|
491 if (dataset.metadata.number_of_molecules == 1):
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|
|
492 dataset.blurb = "1 molecule"
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|
|
493 else:
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|
|
494 dataset.blurb = "%s molecules" % dataset.metadata.number_of_molecules
|
|
|
495 dataset.peek = data.get_file_peek( dataset.file_name, is_multi_byte=is_multi_byte )
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|
|
496 else:
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|
|
497 dataset.peek = 'file does not exist'
|
|
|
498 dataset.blurb = 'file purged from disk'
|
|
|
499
|
|
|
500 def sniff( self, filename ):
|
|
|
501 """
|
|
|
502 InChI files starts with 'InChI='
|
|
|
503 """
|
|
|
504 inchi_lines = get_headers( filename, sep=' ', count=10 )
|
|
|
505 for inchi in inchi_lines:
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|
|
506 if not inchi[0].startswith('InChI='):
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|
|
507 return False
|
|
|
508 return True
|
|
|
509
|
|
|
510
|
|
|
511 class SMILES( Tabular ):
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|
|
512 file_ext = "smi"
|
|
|
513 column_names = [ 'SMILES', 'TITLE' ]
|
|
|
514 MetadataElement( name="columns", default=2, desc="Number of columns", readonly=True, visible=False )
|
|
|
515 MetadataElement( name="column_types", default=['str','str'], param=metadata.ColumnTypesParameter, desc="Column types", readonly=True, visible=False )
|
|
|
516 MetadataElement( name="number_of_molecules", default=0, desc="Number of molecules", readonly=True, visible=True, optional=True, no_value=0 )
|
|
|
517
|
|
|
518 def set_meta( self, dataset, **kwd ):
|
|
|
519 """
|
|
|
520 Set the number of lines of data in dataset.
|
|
|
521 """
|
|
|
522 dataset.metadata.number_of_molecules = self.count_data_lines(dataset)
|
|
|
523
|
|
|
524 def set_peek( self, dataset, is_multi_byte=False ):
|
|
|
525 if not dataset.dataset.purged:
|
|
|
526 dataset.peek = get_file_peek( dataset.file_name, is_multi_byte=is_multi_byte )
|
|
|
527 if (dataset.metadata.number_of_molecules == 1):
|
|
|
528 dataset.blurb = "1 molecule"
|
|
|
529 else:
|
|
|
530 dataset.blurb = "%s molecules" % dataset.metadata.number_of_molecules
|
|
|
531 dataset.peek = data.get_file_peek( dataset.file_name, is_multi_byte=is_multi_byte )
|
|
|
532 else:
|
|
|
533 dataset.peek = 'file does not exist'
|
|
|
534 dataset.blurb = 'file purged from disk'
|
|
|
535
|
|
|
536
|
|
|
537 '''
|
|
|
538 def sniff( self, filename ):
|
|
|
539 """
|
|
|
540 Its hard or impossible to sniff a SMILES File. We can
|
|
|
541 try to import the first SMILES and check if it is a molecule, but
|
|
|
542 currently its not possible to use external libraries from the toolshed
|
|
|
543 in datatype definition files. TODO
|
|
|
544 """
|
|
|
545 self.molecule_number = count_lines( filename, non_empty = True )
|
|
|
546 word_count = count_lines( filename )
|
|
|
547
|
|
|
548 if self.molecule_number != word_count:
|
|
|
549 return False
|
|
|
550
|
|
|
551 if self.molecule_number > 0:
|
|
|
552 # test first 3 SMILES
|
|
|
553 smiles_lines = get_headers( filename, sep='\t', count=3 )
|
|
|
554 for smiles_line in smiles_lines:
|
|
|
555 if len(smiles_line) > 2:
|
|
|
556 return False
|
|
|
557 smiles = smiles_line[0]
|
|
|
558 try:
|
|
|
559 # if we have atoms, we have a molecule
|
|
|
560 if not len( pybel.readstring('smi', smiles).atoms ) > 0:
|
|
|
561 return False
|
|
|
562 except:
|
|
|
563 # if convert fails its not a smiles string
|
|
|
564 return False
|
|
|
565 return True
|
|
|
566 else:
|
|
|
567 return False
|
|
|
568 '''
|
|
|
569
|
|
|
570
|
|
|
571
|
|
|
572 class CML( GenericXml ):
|
|
|
573 """
|
|
|
574 Chemical Markup Language
|
|
|
575 http://cml.sourceforge.net/
|
|
|
576 """
|
|
|
577 file_ext = "cml"
|
|
|
578 MetadataElement( name="number_of_molecules", default=0, desc="Number of molecules", readonly=True, visible=True, optional=True, no_value=0 )
|
|
|
579
|
|
|
580
|
|
|
581 def set_meta( self, dataset, **kwd ):
|
|
|
582 """
|
|
|
583 Set the number of lines of data in dataset.
|
|
|
584 """
|
|
|
585 dataset.metadata.number_of_molecules = count_special_lines( '^\s*<molecule', dataset.file_name )
|
|
|
586
|
|
|
587 def set_peek( self, dataset, is_multi_byte=False ):
|
|
|
588 if not dataset.dataset.purged:
|
|
|
589 dataset.peek = get_file_peek( dataset.file_name, is_multi_byte=is_multi_byte )
|
|
|
590 if (dataset.metadata.number_of_molecules == 1):
|
|
|
591 dataset.blurb = "1 molecule"
|
|
|
592 else:
|
|
|
593 dataset.blurb = "%s molecules" % dataset.metadata.number_of_molecules
|
|
|
594 dataset.peek = data.get_file_peek( dataset.file_name, is_multi_byte=is_multi_byte )
|
|
|
595 else:
|
|
|
596 dataset.peek = 'file does not exist'
|
|
|
597 dataset.blurb = 'file purged from disk'
|
|
|
598
|
|
|
599 def sniff( self, filename ):
|
|
|
600 """
|
|
|
601 Try to guess if the file is a CML file.
|
|
|
602 TODO: add true positive test, need to submit a CML example
|
|
|
603
|
|
|
604 >>> fname = get_test_fname( 'interval.interval' )
|
|
|
605 >>> CML().sniff( fname )
|
|
|
606 False
|
|
|
607 """
|
|
|
608 handle = open(filename)
|
|
|
609 line = handle.readline()
|
|
|
610 if line.strip() != '<?xml version="1.0"?>':
|
|
|
611 handle.close()
|
|
|
612 return False
|
|
|
613 line = handle.readline()
|
|
|
614 if line.strip().find('http://www.xml-cml.org/schema') == -1:
|
|
|
615 handle.close()
|
|
|
616 return False
|
|
|
617 handle.close()
|
|
|
618 return True
|
|
|
619
|
|
|
620
|
|
|
621 def split( cls, input_datasets, subdir_generator_function, split_params):
|
|
|
622 """
|
|
|
623 Split the input files by molecule records.
|
|
|
624 """
|
|
|
625 if split_params is None:
|
|
|
626 return None
|
|
|
627
|
|
|
628 if len(input_datasets) > 1:
|
|
|
629 raise Exception("CML-file splitting does not support multiple files")
|
|
|
630 input_files = [ds.file_name for ds in input_datasets]
|
|
|
631
|
|
|
632 chunk_size = None
|
|
|
633 if split_params['split_mode'] == 'number_of_parts':
|
|
|
634 raise Exception('Split mode "%s" is currently not implemented for CML-files.' % split_params['split_mode'])
|
|
|
635 elif split_params['split_mode'] == 'to_size':
|
|
|
636 chunk_size = int(split_params['split_size'])
|
|
|
637 else:
|
|
|
638 raise Exception('Unsupported split mode %s' % split_params['split_mode'])
|
|
|
639
|
|
|
640 def _read_cml_records( filename ):
|
|
|
641 lines = []
|
|
|
642 with open(filename) as handle:
|
|
|
643 for line in handle:
|
|
|
644 if line.lstrip().startswith('<?xml version="1.0"?>') or \
|
|
|
645 line.lstrip().startswith('<cml xmlns="http://www.xml-cml.org/schema') or \
|
|
|
646 line.lstrip().startswith('</cml>'):
|
|
|
647 continue
|
|
|
648 lines.append( line )
|
|
|
649 if line.lstrip().startswith('</molecule>'):
|
|
|
650 yield lines
|
|
|
651 lines = []
|
|
|
652
|
|
|
653 header_lines = ['<?xml version="1.0"?>\n', '<cml xmlns="http://www.xml-cml.org/schema">\n']
|
|
|
654 footer_line = ['</cml>\n']
|
|
|
655 def _write_part_cml_file( accumulated_lines ):
|
|
|
656 part_dir = subdir_generator_function()
|
|
|
657 part_path = os.path.join(part_dir, os.path.basename(input_files[0]))
|
|
|
658 part_file = open(part_path, 'w')
|
|
|
659 part_file.writelines( header_lines )
|
|
|
660 part_file.writelines( accumulated_lines )
|
|
|
661 part_file.writelines( footer_line )
|
|
|
662 part_file.close()
|
|
|
663
|
|
|
664 try:
|
|
|
665 cml_records = _read_cml_records( input_files[0] )
|
|
|
666 cml_lines_accumulated = []
|
|
|
667 for counter, cml_record in enumerate( cml_records, start = 1):
|
|
|
668 cml_lines_accumulated.extend( cml_record )
|
|
|
669 if counter % chunk_size == 0:
|
|
|
670 _write_part_cml_file( cml_lines_accumulated )
|
|
|
671 cml_lines_accumulated = []
|
|
|
672 if cml_lines_accumulated:
|
|
|
673 _write_part_cml_file( cml_lines_accumulated )
|
|
|
674 except Exception, e:
|
|
|
675 log.error('Unable to split files: %s' % str(e))
|
|
|
676 raise
|
|
|
677 split = classmethod(split)
|
|
|
678
|
|
|
679
|
|
|
680 def merge(split_files, output_file):
|
|
|
681 """
|
|
|
682 Merging CML files.
|
|
|
683 """
|
|
|
684 if len(split_files) == 1:
|
|
|
685 #For one file only, use base class method (move/copy)
|
|
|
686 return Text.merge(split_files, output_file)
|
|
|
687 if not split_files:
|
|
|
688 raise ValueError("Given no CML files, %r, to merge into %s" \
|
|
|
689 % (split_files, output_file))
|
|
|
690 with open(output_file, "w") as out:
|
|
|
691 for filename in split_files:
|
|
|
692 with open( filename ) as handle:
|
|
|
693 header = handle.readline()
|
|
|
694 if not header:
|
|
|
695 raise ValueError("CML file %s was empty" % f)
|
|
|
696 if not header.lstrip().startswith('<?xml version="1.0"?>'):
|
|
|
697 out.write(header)
|
|
|
698 raise ValueError("%s is not a valid XML file!" % f)
|
|
|
699 line = handle.readline()
|
|
|
700 header += line
|
|
|
701 if not line.lstrip().startswith('<cml xmlns="http://www.xml-cml.org/schema'):
|
|
|
702 out.write(header)
|
|
|
703 raise ValueError("%s is not a CML file!" % f)
|
|
|
704 molecule_found = False
|
|
|
705 for line in handle.readlines():
|
|
|
706 # we found two required header lines, the next line should start with <molecule >
|
|
|
707 if line.lstrip().startswith('</cml>'):
|
|
|
708 continue
|
|
|
709 if line.lstrip().startswith('<molecule'):
|
|
|
710 molecule_found = True
|
|
|
711 if molecule_found:
|
|
|
712 out.write( line )
|
|
|
713 out.write("</cml>\n")
|
|
|
714 merge = staticmethod(merge)
|
|
|
715
|
|
|
716
|
|
|
717 if __name__ == '__main__':
|
|
|
718 """
|
|
|
719 TODO: We need to figure out, how to put example files under /lib/galaxy/datatypes/test/ from a toolshed, so that doctest can work properly.
|
|
|
720 """
|
|
|
721 inchi = get_test_fname('drugbank_drugs.inchi')
|
|
|
722 smiles = get_test_fname('drugbank_drugs.smi')
|
|
|
723 sdf = get_test_fname('drugbank_drugs.sdf')
|
|
|
724 fps = get_test_fname('50_chemfp_fingerprints_FPS1.fps')
|
|
|
725 pdb = get_test_fname('2zbz.pdb')
|
|
|
726 cml = get_test_fname('/home/bag/Downloads/approved.cml')
|
|
|
727
|
|
|
728 print 'CML test'
|
|
|
729 print CML().sniff(cml), 'cml'
|
|
|
730 print CML().sniff(inchi)
|
|
|
731 print CML().sniff(pdb)
|
|
|
732 CML().split()
|
|
|
733 """
|
|
|
734 print 'SMILES test'
|
|
|
735 print SMILES().sniff(smiles), 'smi'
|
|
|
736 print SMILES().sniff(inchi)
|
|
|
737 print SMILES().sniff(pdb)
|
|
|
738 """
|
|
|
739 print 'InChI test'
|
|
|
740 print InChI().sniff(smiles)
|
|
|
741 print InChI().sniff(sdf)
|
|
|
742 print InChI().sniff(inchi), 'inchi'
|
|
|
743
|
|
|
744 print 'FPS test'
|
|
|
745 print FPS().sniff(smiles)
|
|
|
746 print FPS().sniff(sdf)
|
|
|
747 f = FPS()
|
|
|
748 print f.sniff(fps)
|
|
|
749
|
|
|
750 print 'SDF test'
|
|
|
751 print SDF().sniff(smiles)
|
|
|
752 print SDF().sniff(sdf), 'sdf'
|
|
|
753 print SDF().sniff(fps)
|
|
|
754
|
|
|
755 print 'PDB test'
|
|
|
756 print PDB().sniff(smiles)
|
|
|
757 print PDB().sniff(sdf)
|
|
|
758 print PDB().sniff(fps)
|
|
|
759 print PDB().sniff(pdb), 'pdb'
|
