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1 # -*- coding: utf-8 -*-
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2
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3 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
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8 log = logging.getLogger(__name__)
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9
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10 class GenericMolFile( data.Text ):
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11 file_ext = "mol2/sdf/drf"
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12 def check_filetype( self,filename ):
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13 self.no_mols = commands.getstatusoutput("grep -c \\$\\$\\$\\$ "+filename)
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14 if (self.no_mols[0] == 0) & (self.no_mols[1] > 0):
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15 self.file_ext="sdf"
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16 return True
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17 self.no_mols = commands.getstatusoutput("grep -c @\<TRIPOS\>MOLECULE "+filename)
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18 if (self.no_mols[0] == 0) & (self.no_mols[1] > 0):
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19 self.file_ext="mol2"
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20 return True
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21 self.no_mols = commands.getstatusoutput("grep -c \"ligand id\" "+filename)
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22 if (self.no_mols[0] == 0) & (self.no_mols[1] > 0):
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23 self.file_ext="drf"
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24 return True
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25 self.no_mols = commands.getstatusoutput("grep -c HEADER "+filename)
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26 if (self.no_mols[0] == 0) & (self.no_mols[1] > 0):
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27 self.file_ext="pdb"
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28 return True
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29 return False
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30
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31 def set_peek( self, dataset, is_multi_byte=False ):
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32 if not dataset.dataset.purged:
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33 if(self.check_filetype(dataset.file_name)) :
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34 if (self.no_mols[1] == '1'):
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35 dataset.blurb = "1 molecule"
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36 else:
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37 dataset.blurb = "%s molecules"%self.no_mols[1]
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38 dataset.peek = data.get_file_peek( dataset.file_name, is_multi_byte=is_multi_byte )
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39 else:
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40 dataset.peek = 'file does not exist'
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41 dataset.blurb = 'file purged from disk'
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42
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43 def get_mime(self):
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44 return 'text/plain'
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45
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46
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47 class GenericMultiMolFile( GenericMolFile ):
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48 def set_peek( self, dataset, is_multi_byte=False ):
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49 if not dataset.dataset.purged:
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50 self.sniff(dataset.file_name)
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51 if (self.no_mols[1] == '1'):
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52 dataset.blurb = "1 molecule"
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53 else:
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54 dataset.blurb = "%s molecules"%self.no_mols[1]
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55 dataset.peek = data.get_file_peek( dataset.file_name, is_multi_byte=is_multi_byte )
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56 else:
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57 dataset.peek = 'file does not exist'
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58 dataset.blurb = 'file purged from disk'
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59
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60 class SDF( GenericMultiMolFile ):
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61 file_ext = "sdf"
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62 def sniff( self, filename ):
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63 self.no_mols = commands.getstatusoutput("grep -c \\$\\$\\$\\$ "+filename)
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64 if (self.no_mols[0] == 0) & (self.no_mols[1] > 0):
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65 return True
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66 else:
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67 return False
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68
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69 class MOL2( GenericMultiMolFile ):
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70 file_ext = "mol2"
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71 def sniff( self, filename ):
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72 self.no_mols = commands.getstatusoutput("grep -c @\<TRIPOS\>MOLECULE "+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 DRF( GenericMultiMolFile ):
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79 file_ext = "drf"
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80 def sniff( self, filename ):
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81 self.no_mols = commands.getstatusoutput("grep -c \"ligand id\" "+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 PDB( GenericMolFile ):
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88 file_ext = "pdb"
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89 def sniff( self, filename ):
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90 self.no_mols = commands.getstatusoutput("grep -c HEADER "+filename)
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91 if (self.no_mols[0] == 0) & (self.no_mols[1] > 0):
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92 return True
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93 else:
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94 return False
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95 def set_peek( self, dataset, is_multi_byte=False ):
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96 #def set_peek( self, dataset, line_count=None, is_multi_byte=False ):
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97 if not dataset.dataset.purged:
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98 res = commands.getstatusoutput("lib/galaxy/datatypes/countResidues.sh "+dataset.file_name)
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99 dataset.peek = res[1]
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100 self.sniff(dataset.file_name)
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101 if (self.no_mols[1] == '1'):
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102 dataset.blurb = "1 protein structure"
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103 else:
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104 dataset.blurb = "%s protein structures"%self.no_mols[1]
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105 else:
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106 dataset.peek = 'file does not exist'
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107 dataset.blurb = 'file purged from disk'
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108
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109 class grd ( data.Text ) :
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110 file_ext = "grd"
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111 def set_peek( self, dataset, is_multi_byte=False ):
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112 if not dataset.dataset.purged:
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113 #dataset.peek = ""
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114 dataset.blurb = "score-grids for docking"
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115 else:
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116 dataset.peek = 'file does not exist'
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117 dataset.blurb = 'file purged from disk'
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118
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119 class grdtgz ( data.Text ) :
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120 file_ext = "grd.tgz"
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121 def set_peek( self, dataset, is_multi_byte=False ):
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122 if not dataset.dataset.purged:
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123 #dataset.peek = ""
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124 dataset.blurb = "compressed score-grids for docking"
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125 else:
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126 dataset.peek = 'file does not exist'
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127 dataset.blurb = 'file purged from disk'
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128
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