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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 *
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6 import commands
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7 import pybel
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8 import openbabel
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9 openbabel.obErrorLog.StopLogging()
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10
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11 from galaxy.datatypes.metadata import MetadataElement
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12 from galaxy.datatypes import metadata
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13
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14 log = logging.getLogger(__name__)
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15
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16 class GenericMolFile( data.Text ):
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17
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18 MetadataElement( name="molecules", default=0, desc="Number of molecules", readonly=True, visible=False, optional=True, no_value=0 )
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19
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20 file_ext = "mol2/sdf/drf"
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21 def check_filetype( self,filename ):
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22 self.no_mols = commands.getstatusoutput("grep -c \\$\\$\\$\\$ "+filename)
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23 if (self.no_mols[0] == 0) & (self.no_mols[1] > 0):
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24 self.file_ext="sdf"
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25 return True
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26 self.no_mols = commands.getstatusoutput("grep -c @\<TRIPOS\>MOLECULE "+filename)
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27 if (self.no_mols[0] == 0) & (self.no_mols[1] > 0):
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28 self.file_ext="mol2"
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29 return True
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30 self.no_mols = commands.getstatusoutput("grep -c \"ligand id\" "+filename)
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31 if (self.no_mols[0] == 0) & (self.no_mols[1] > 0):
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32 self.file_ext="drf"
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33 return True
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34 self.no_mols = commands.getstatusoutput("grep -c HEADER "+filename)
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35 if (self.no_mols[0] == 0) & (self.no_mols[1] > 0):
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36 self.file_ext="pdb"
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37 return True
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38 return False
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39
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40 def set_peek( self, dataset, is_multi_byte=False ):
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41 if not dataset.dataset.purged:
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42 if(self.check_filetype(dataset.file_name)) :
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43 if (self.no_mols[1] == '1'):
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44 dataset.blurb = "1 molecule"
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45 else:
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46 dataset.blurb = "%s molecules" % self.no_mols[1]
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47 dataset.peek = data.get_file_peek( dataset.file_name, is_multi_byte=is_multi_byte )
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48 else:
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49 dataset.peek = 'file does not exist'
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50 dataset.blurb = 'file purged from disk'
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51
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52 def get_mime(self):
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53 return 'text/plain'
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54
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55
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56 class GenericMultiMolFile( GenericMolFile ):
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57 def set_peek( self, dataset, is_multi_byte=False ):
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58 if not dataset.dataset.purged:
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59 self.sniff(dataset.file_name)
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60 if (self.no_mols[1] == '1'):
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61 dataset.blurb = "1 molecule"
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62 else:
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63 dataset.blurb = "%s molecules" % self.no_mols[1]
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64 dataset.peek = data.get_file_peek( dataset.file_name, is_multi_byte=is_multi_byte )
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65 else:
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66 dataset.peek = 'file does not exist'
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67 dataset.blurb = 'file purged from disk'
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68
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69 class SDF( GenericMultiMolFile ):
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70 file_ext = "sdf"
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71 def sniff( self, filename ):
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72 self.no_mols = commands.getstatusoutput("grep -c \\$\\$\\$\\$ "+filename)
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73 if (self.no_mols[0] == 0) & (self.no_mols[1] > 0):
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74 return True
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75 else:
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76 return False
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77
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78 class MOL2( GenericMultiMolFile ):
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79 file_ext = "mol2"
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80 def sniff( self, filename ):
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81 self.no_mols = commands.getstatusoutput("grep -c @\<TRIPOS\>MOLECULE "+filename)
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82 if (self.no_mols[0] == 0) & (self.no_mols[1] > 0):
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83 return True
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84 else:
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85 return False
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86
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87 class FPS( GenericMultiMolFile ):
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88 file_ext = "fps"
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89 def sniff( self, filename ):
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90 self.no_mols = commands.getstatusoutput("grep -c -v '^#' "+filename)
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91 with open(filename) as in_handle:
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92 for line_counter, line in enumerate(in_handle):
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93 line = line.strip()
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94 if line.startswith('#FPS1'):
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95 return True
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96 if line_counter > 10:
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97 return False
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98
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99 class DRF( GenericMultiMolFile ):
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100 file_ext = "drf"
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101 def sniff( self, filename ):
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102 self.no_mols = commands.getstatusoutput("grep -c \"ligand id\" "+filename)
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103 if (self.no_mols[0] == 0) & (self.no_mols[1] > 0):
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104 return True
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105 else:
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106 return False
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107
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108
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109 class PHAR( GenericMultiMolFile ):
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110 MetadataElement( name="base_name", desc="base name", default='Phar',
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111 readonly=True, set_in_upload=True)
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112 file_ext = "phar"
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113 def sniff( self, filename ):
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114 self.no_mols = commands.getstatusoutput("grep -c -v '^#' "+filename)
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115 return False
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116
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117 class PDB( GenericMolFile ):
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118 file_ext = "pdb"
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119 def sniff( self, filename ):
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120 self.no_mols = commands.getstatusoutput("grep -c HEADER "+filename)
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121 if (self.no_mols[0] == 0) & (self.no_mols[1] > 0):
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122 return True
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123 else:
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124 return False
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125 def set_peek( self, dataset, is_multi_byte=False ):
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126 #def set_peek( self, dataset, line_count=None, is_multi_byte=False ):
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127 if not dataset.dataset.purged:
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128 res = commands.getstatusoutput("lib/galaxy/datatypes/countResidues.sh "+dataset.file_name)
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129 dataset.peek = res[1]
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130 self.sniff(dataset.file_name)
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131 if (self.no_mols[1] == '1'):
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132 dataset.blurb = "1 protein structure"
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133 else:
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134 dataset.blurb = "%s protein structures"%self.no_mols[1]
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135 else:
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136 dataset.peek = 'file does not exist'
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137 dataset.blurb = 'file purged from disk'
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138
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139 class grd ( data.Text ) :
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140 file_ext = "grd"
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141 def set_peek( self, dataset, is_multi_byte=False ):
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142 if not dataset.dataset.purged:
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143 #dataset.peek = ""
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144 dataset.blurb = "score-grids for docking"
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145 else:
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146 dataset.peek = 'file does not exist'
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147 dataset.blurb = 'file purged from disk'
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148
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149 class grdtgz ( data.Text ) :
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150 file_ext = "grd.tgz"
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151 def set_peek( self, dataset, is_multi_byte=False ):
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152 if not dataset.dataset.purged:
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153 #dataset.peek = ""
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154 dataset.blurb = "compressed score-grids for docking"
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155 else:
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156 dataset.peek = 'file does not exist'
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157 dataset.blurb = 'file purged from disk'
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158
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159
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160 class InChI( GenericMultiMolFile ):
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161 file_ext = "inchi"
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162 def sniff( self, filename ):
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163 self.no_mols = commands.getstatusoutput("grep -c '^InChI=' "+filename)
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164 word_count = commands.getoutput("wc -w "+filename).split()[0]
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165
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166 if self.no_mols[1] != word_count:
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167 return False
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168
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169 if (self.no_mols[0] == 0) & (self.no_mols[1] > 0):
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170 return True
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171 else:
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172 return False
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173
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174 def set_meta( self, dataset, **kwd ):
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175 """
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176 Set the number of sequences and the number of data lines
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177 in dataset.
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178 """
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179 if self.max_optional_metadata_filesize >= 0 and dataset.get_size() > self.max_optional_metadata_filesize:
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180 dataset.metadata.data_lines = None
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181 dataset.metadata.sequences = None
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182 return
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183 #word_count = commands.getoutput("wc -w "+filename).split()[0]
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184 # word_count are the lines of the file, if word_count and molecule count
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185 # are the same, that must hold to be an InChI File, then that should be
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186 # the same number as all non-empty lines
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187 #dataset.metadata.data_lines = word_count
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188 #int(commands.getoutput("grep -cve '^\s*$' "+filename))
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189 #dataset.metadata.molecules = word_count
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190
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191
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192 class SMILES( GenericMultiMolFile ):
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193 file_ext = "smi"
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194 def sniff( self, filename ):
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195 """
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196 Its hard or impossible to sniff a SMILES File. All what i know is the
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197 word_count must be the same as the non-empty line count. And that i can
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198 try to import the first SMILES and check if it is a molecule.
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199 """
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200
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201 # that corresponds to non-empty line count
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202 self.no_mols = commands.getstatusoutput("grep -cve '^\s*$' "+filename)
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203 word_count = int(commands.getoutput("wc -w "+filename).split()[0])
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204
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205 if int(self.no_mols[1]) != word_count:
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206 return False
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207
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208 if (self.no_mols[0] == 0) & (int(self.no_mols[1]) > 0):
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209 for line in open(filename):
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210 line = line.strip()
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211 if line:
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212 # if we have atoms, we have a molecule
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213 try:
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214 if len(pybel.readstring('smi', line).atoms) > 0:
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215 return True
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216 else:
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217 return False
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218 except:
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219 # if convert fails its not a smiles string
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220 return False
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221 return True
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222 else:
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223 return False
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224
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225 def set_meta( self, dataset, **kwd ):
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226 """
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227 Set the number of sequences and the number of data lines
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228 in dataset.
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229 """
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230 if self.max_optional_metadata_filesize >= 0 and dataset.get_size() > self.max_optional_metadata_filesize:
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231 dataset.metadata.data_lines = None
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232 dataset.metadata.sequences = None
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233 return
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234
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235 #word_count = int(commands.getoutput("wc -w "+filename).split()[0])
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236 # word_count are the lines of the file, if word_count and molecule count
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237 # are the same, that must hold to be an InChI File, then that should be
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238 # the same number as all non-empty lines
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239 #dataset.metadata.data_lines = word_count
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240 #dataset.metadata.molecules = word_count
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241
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242
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