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1 """
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2 Proteomics format classes
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3 """
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4 import logging
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5 import re
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6 from galaxy.datatypes.data import *
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7 from galaxy.datatypes.xml import *
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8 from galaxy.datatypes.sniff import *
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9 from galaxy.datatypes.binary import *
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10
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11 log = logging.getLogger(__name__)
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12
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13
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14 class Xls( Binary ):
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15 """Class describing a binary excel spreadsheet file"""
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16 file_ext = "xls"
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17
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18 def set_peek( self, dataset, is_multi_byte=False ):
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19 if not dataset.dataset.purged:
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20 dataset.peek = "Excel Spreadsheet file"
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21 dataset.blurb = data.nice_size( dataset.get_size() )
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22 else:
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23 dataset.peek = 'file does not exist'
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24 dataset.blurb = 'file purged from disk'
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25 def display_peek( self, dataset ):
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26 try:
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27 return dataset.peek
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28 except:
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29 return "Binary xls file (%s)" % ( data.nice_size( dataset.get_size() ) )
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30
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31 class ProteomicsXml(GenericXml):
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32 """ An enhanced XML datatype used to reuse code across several
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33 proteomic/mass-spec datatypes. """
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34
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35 def sniff(self, filename):
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36 """ Determines whether the file is the correct XML type. """
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37 with open(filename, 'r') as contents:
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38 while True:
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39 line = contents.readline()
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40 if line == None or not line.startswith('<?'):
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41 break
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42 pattern = '^<(\w*:)?%s' % self.root # pattern match <root or <ns:root for any ns string
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43 return line != None and re.match(pattern, line) != None
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44
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45 def set_peek( self, dataset, is_multi_byte=False ):
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46 """Set the peek and blurb text"""
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47 if not dataset.dataset.purged:
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48 dataset.peek = data.get_file_peek( dataset.file_name, is_multi_byte=is_multi_byte )
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49 dataset.blurb = self.blurb
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50 else:
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51 dataset.peek = 'file does not exist'
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52 dataset.blurb = 'file purged from disk'
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53
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54 class PepXml(ProteomicsXml):
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55 """pepXML data"""
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56 file_ext = "pepxml"
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57 blurb = 'pepXML data'
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58 root = "msms_pipeline_analysis"
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59
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60
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61 class MzML(ProteomicsXml):
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62 """mzML data"""
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63 file_ext = "mzml"
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64 blurb = 'mzML Mass Spectrometry data'
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65 root = "(mzML|indexedmzML)"
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66
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67
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68 class ProtXML(ProteomicsXml):
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69 """protXML data"""
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70 file_ext = "protxml"
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71 blurb = 'prot XML Search Results'
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72 root = "protein_summary"
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73
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74
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75 class MzXML(ProteomicsXml):
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76 """mzXML data"""
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77 file_ext = "mzXML"
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78 blurb = "mzXML Mass Spectrometry data"
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79 root = "mzXML"
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80
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81 ## PSI datatypes
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82 class MzIdentML(ProteomicsXml):
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83 file_ext = "mzid"
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84 blurb = "XML identified peptides and proteins."
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85 root = "MzIdentML"
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86
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87
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88 class TraML(ProteomicsXml):
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89 file_ext = "traML"
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90 blurb = "TraML transition list"
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91 root = "TraML"
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92
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93
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94 class MzQuantML(ProteomicsXml):
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95 file_ext = "mzq"
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96 blurb = "XML quantification data"
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97 root = "MzQuantML"
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98
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99
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100 class Mgf( Text ):
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101 """Mascot Generic Format data"""
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102 file_ext = "mgf"
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103
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104 def set_peek( self, dataset, is_multi_byte=False ):
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105 """Set the peek and blurb text"""
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106 if not dataset.dataset.purged:
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107 dataset.peek = data.get_file_peek( dataset.file_name, is_multi_byte=is_multi_byte )
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108 dataset.blurb = 'mgf Mascot Generic Format'
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109 else:
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110 dataset.peek = 'file does not exist'
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111 dataset.blurb = 'file purged from disk'
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112
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113
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114 def sniff( self, filename ):
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115 mgf_begin_ions = "BEGIN IONS"
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116 max_lines=100
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117
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118 for i, line in enumerate( file( filename ) ):
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119 line = line.rstrip( '\n\r' )
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120 if line==mgf_begin_ions:
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121 return True
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122 if i>max_lines:
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123 return False
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124
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125
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126 class MascotDat( Text ):
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127 """Mascot search results """
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128 file_ext = "mascotdat"
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129
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130 def set_peek( self, dataset, is_multi_byte=False ):
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131 """Set the peek and blurb text"""
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132 if not dataset.dataset.purged:
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133 dataset.peek = data.get_file_peek( dataset.file_name, is_multi_byte=is_multi_byte )
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134 dataset.blurb = 'mascotdat Mascot Search Results'
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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
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140 def sniff( self, filename ):
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141 mime_version = "MIME-Version: 1.0 (Generated by Mascot version 1.0)"
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142 max_lines=10
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143
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144 for i, line in enumerate( file( filename ) ):
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145 line = line.rstrip( '\n\r' )
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146 if line==mime_version:
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147 return True
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148 if i>max_lines:
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149 return False
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150
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151
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152 class RAW( Binary ):
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153 """Class describing a Thermo Finnigan binary RAW file"""
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154 file_ext = "raw"
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155 def sniff( self, filename ):
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156 # Thermo Finnigan RAW format is proprietary and hence not well documented.
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157 # Files start with 2 bytes that seem to differ followed by F\0i\0n\0n\0i\0g\0a\0n
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158 # This combination represents 17 bytes, but to play safe we read 20 bytes from
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159 # the start of the file.
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160 try:
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161 header = open( filename ).read(20)
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162 hexheader = binascii.b2a_hex( header )
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163 finnigan = binascii.hexlify( 'F\0i\0n\0n\0i\0g\0a\0n' )
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164 if hexheader.find(finnigan) != -1:
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165 return True
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166 return False
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167 except:
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168 return False
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169 def set_peek( self, dataset, is_multi_byte=False ):
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170 if not dataset.dataset.purged:
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171 dataset.peek = "Thermo Finnigan RAW file"
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172 dataset.blurb = data.nice_size( dataset.get_size() )
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173 else:
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174 dataset.peek = 'file does not exist'
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175 dataset.blurb = 'file purged from disk'
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176 def display_peek( self, dataset ):
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177 try:
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178 return dataset.peek
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179 except:
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180 return "Thermo Finnigan RAW file (%s)" % ( data.nice_size( dataset.get_size() ) )
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181
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182
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183 if hasattr(Binary, 'register_sniffable_binary_format'):
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184 Binary.register_sniffable_binary_format('RAW', 'RAW', RAW)
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185
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186
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187 class Msp(Text):
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188 """ Output of NIST MS Search Program chemdata.nist.gov/mass-spc/ftp/mass-spc/PepLib.pdf """
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189 file_ext = "msp"
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190
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191 @staticmethod
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192 def next_line_starts_with(contents, prefix):
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193 next_line = contents.readline()
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194 return next_line != None and next_line.startswith(prefix)
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195
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196 def sniff(self, filename):
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197 """ Determines whether the file is a NIST MSP output file.
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198
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199 >>> fname = get_test_fname('test.msp')
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200 >>> Msp().sniff(fname)
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201 True
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202 >>> fname = get_test_fname('test.mzXML')
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203 >>> Msp().sniff(fname)
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204 False
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205 """
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206 with open(filename, 'r') as contents:
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207 return Msp.next_line_starts_with(contents, "Name:") and Msp.next_line_starts_with(contents, "MW:")
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208
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209 class Ms2(Text):
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210 file_ext = "ms2"
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211
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212 def sniff(self, filename):
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213 """ Determines whether the file is a valid ms2 file.
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214
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215 >>> fname = get_test_fname('test.msp')
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216 >>> Ms2().sniff(fname)
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217 False
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218 >>> fname = get_test_fname('test.ms2')
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219 >>> Ms2().sniff(fname)
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220 True
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221 """
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222
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223 with open(filename, 'r') as contents:
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224 header_lines = []
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225 while True:
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226 line = contents.readline()
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227 if line == None or len(line) == 0:
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228 pass
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229 elif line.startswith('H\t'):
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230 header_lines.append(line)
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231 else:
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232 break
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233 for header_field in ['CreationDate', 'Extractor', 'ExtractorVersion', 'ExtractorOptions']:
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234 found_header = False
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235 for header_line in header_lines:
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236 if header_line.startswith('H\t%s' % (header_field)):
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237 found_header = True
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238 break
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239 if not found_header:
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240 return False
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241
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242 return True
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243
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244 # unsniffable binary format, should do something about this
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245 class XHunterAslFormat(Binary):
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246 """ Annotated Spectra in the HLF format http://www.thegpm.org/HUNTER/format_2006_09_15.html """
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247 file_ext = "hlf"
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248
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249
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250 if hasattr(Binary, 'register_unsniffable_binary_ext'):
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251 Binary.register_unsniffable_binary_ext('hlf')
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