Mercurial > repos > iracooke > protk

comparison lib/galaxy/datatypes/proteomics.py @ 2:418f42b34049 draft

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Reuploading
author iracooke
date Mon, 23 Jul 2012 00:20:58 -0400
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1:deaedec14cc8 2:418f42b34049
1 """
2 Proteomics format classes
3 """
4 import logging
5 import re
6 from galaxy.datatypes.data import *
7 from galaxy.datatypes.xml import *
8 from galaxy.datatypes.sniff import *
9 from galaxy.datatypes.binary import *
10
11 log = logging.getLogger(__name__)
12
13
14 class Xls( Binary ):
15 """Class describing a binary excel spreadsheet file"""
16 file_ext = "xls"
17
18 def set_peek( self, dataset, is_multi_byte=False ):
19 if not dataset.dataset.purged:
20 dataset.peek = "Excel Spreadsheet file"
21 dataset.blurb = data.nice_size( dataset.get_size() )
22 else:
23 dataset.peek = 'file does not exist'
24 dataset.blurb = 'file purged from disk'
25 def display_peek( self, dataset ):
26 try:
27 return dataset.peek
28 except:
29 return "Binary xls file (%s)" % ( data.nice_size( dataset.get_size() ) )
30
31 class PepXml(GenericXml):
32 """pepXML data"""
33 file_ext = "pepxml"
34
35 def set_peek( self, dataset, is_multi_byte=False ):
36 """Set the peek and blurb text"""
37 if not dataset.dataset.purged:
38 dataset.peek = data.get_file_peek( dataset.file_name, is_multi_byte=is_multi_byte )
39 dataset.blurb = 'pepXML data'
40 else:
41 dataset.peek = 'file does not exist'
42 dataset.blurb = 'file purged from disk'
43 def sniff( self, filename ):
44 """
45 Determines whether the file is pepXML
46 """
47 #TODO - Use a context manager on Python 2.5+ to close handle
48 handle = open(filename)
49 xmlns_re = re.compile(".*pepXML\"")
50 for i in range(3):
51 line = handle.readline()
52 if xmlns_re.match(line.strip()):
53 handle.close()
54 return True
55
56 handle.close()
57 return False
58
59 class MzML( GenericXml ):
60 """mzML data"""
61 file_ext = "mzml"
62
63 def set_peek( self, dataset, is_multi_byte=False ):
64 """Set the peek and blurb text"""
65 if not dataset.dataset.purged:
66 dataset.peek = data.get_file_peek( dataset.file_name, is_multi_byte=is_multi_byte )
67 dataset.blurb = 'mzML Mass Spectrometry data'
68 else:
69 dataset.peek = 'file does not exist'
70 dataset.blurb = 'file purged from disk'
71
72 def sniff( self, filename ):
73 handle = open(filename)
74 xmlns_re = re.compile("^<mzML")
75 for i in range(3):
76 line = handle.readline()
77 if xmlns_re.match(line.strip()):
78 handle.close()
79 return True
80
81 handle.close()
82 return False
83
84
85 class ProtXML( Text ):
86 """protXML data"""
87 file_ext = "protxml"
88
89 def set_peek( self, dataset, is_multi_byte=False ):
90 """Set the peek and blurb text"""
91 if not dataset.dataset.purged:
92 dataset.peek = data.get_file_peek( dataset.file_name, is_multi_byte=is_multi_byte )
93 dataset.blurb = 'prot XML Search Results'
94 else:
95 dataset.peek = 'file does not exist'
96 dataset.blurb = 'file purged from disk'
97 def sniff( self, filename ):
98 protxml_header = [ '<?xml version="1.0" encoding="ISO-8859-1"?>',
99 'xmlns="http://regis-web.systemsbiology.net/protXML"' ]
100
101 for i, line in enumerate( file( filename ) ):
102 if i >= len( pepxml_header ):
103 return True
104 line = line.rstrip( '\n\r' )
105 if protxml_header[ i ] not in line:
106 return False
107
108
109
110 class MzXML( Text ):
111 """mzXML data"""
112 file_ext = "mzXML"
113
114 def set_peek( self, dataset, is_multi_byte=False ):
115 """Set the peek and blurb text"""
116 if not dataset.dataset.purged:
117 dataset.peek = data.get_file_peek( dataset.file_name, is_multi_byte=is_multi_byte )
118 dataset.blurb = 'mzXML Mass Spectrometry data'
119 else:
120 dataset.peek = 'file does not exist'
121 dataset.blurb = 'file purged from disk'
122 def sniff( self, filename ):
123 mzxml_header = [ '<?xml version="1.0" encoding="ISO-8859-1"?>',
124 '<mzXML xmlns="http://sashimi.sourceforge.net/schema_revision/mzXML_2.1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://sashimi.sourceforge.net/schema_revision/mzXML_2.1 http://sashimi.sourceforge.net/schema_revision/mzXML_2.1/mzXML_idx_2.1.xsd">' ]
125 for i, line in enumerate( file( filename ) ):
126 if i >= len( mzxml_header ):
127 return True
128 line = line.rstrip( '\n\r' )
129 if line != mzxml_header[ i ]:
130 return False
131
132 class Mgf( Text ):
133 """Mascot Generic Format data"""
134 file_ext = "mgf"
135
136 def set_peek( self, dataset, is_multi_byte=False ):
137 """Set the peek and blurb text"""
138 if not dataset.dataset.purged:
139 dataset.peek = data.get_file_peek( dataset.file_name, is_multi_byte=is_multi_byte )
140 dataset.blurb = 'mgf Mascot Generic Format'
141 else:
142 dataset.peek = 'file does not exist'
143 dataset.blurb = 'file purged from disk'
144
145
146 def sniff( self, filename ):
147 mgf_begin_ions = "BEGIN IONS"
148 max_lines=100
149
150 for i, line in enumerate( file( filename ) ):
151 line = line.rstrip( '\n\r' )
152 if line==mgf_begin_ions:
153 return True
154 if i>max_lines:
155 return False
156
157
158 class MascotDat( Text ):
159 """Mascot search results """
160 file_ext = "mascotdat"
161
162 def set_peek( self, dataset, is_multi_byte=False ):
163 """Set the peek and blurb text"""
164 if not dataset.dataset.purged:
165 dataset.peek = data.get_file_peek( dataset.file_name, is_multi_byte=is_multi_byte )
166 dataset.blurb = 'mascotdat Mascot Search Results'
167 else:
168 dataset.peek = 'file does not exist'
169 dataset.blurb = 'file purged from disk'
170
171
172 def sniff( self, filename ):
173 mime_version = "MIME-Version: 1.0 (Generated by Mascot version 1.0)"
174 max_lines=10
175
176 for i, line in enumerate( file( filename ) ):
177 line = line.rstrip( '\n\r' )
178 if line==mime_version:
179 return True
180 if i>max_lines:
181 return False
182
183
184 class RAW( Binary ):
185 """Class describing a Thermo Finnigan binary RAW file"""
186 file_ext = "raw"
187 def sniff( self, filename ):
188 # Thermo Finnigan RAW format is proprietary and hence not well documented.
189 # Files start with 2 bytes that seem to differ followed by F\0i\0n\0n\0i\0g\0a\0n
190 # This combination represents 17 bytes, but to play safe we read 20 bytes from
191 # the start of the file.
192 try:
193 header = open( filename ).read(20)
194 hexheader = binascii.b2a_hex( header )
195 finnigan = binascii.hexlify( 'F\0i\0n\0n\0i\0g\0a\0n' )
196 if hexheader.find(finnigan) != -1:
197 return True
198 return False
199 except:
200 return False
201 def set_peek( self, dataset, is_multi_byte=False ):
202 if not dataset.dataset.purged:
203 dataset.peek = "Thermo Finnigan RAW file"
204 dataset.blurb = data.nice_size( dataset.get_size() )
205 else:
206 dataset.peek = 'file does not exist'
207 dataset.blurb = 'file purged from disk'
208 def display_peek( self, dataset ):
209 try:
210 return dataset.peek
211 except:
212 return "Thermo Finnigan RAW file (%s)" % ( data.nice_size( dataset.get_size() ) )
213
214
215 class Msp(Text):
216 """ Output of NIST MS Search Program chemdata.nist.gov/mass-spc/ftp/mass-spc/PepLib.pdf """
217 file_ext = "msp"
218
219 @staticmethod
220 def next_line_starts_with(contents, prefix):
221 next_line = contents.readline()
222 return next_line != None and next_line.startswith(prefix)
223
224 def sniff(self, filename):
225 """ Determines whether the file is a NIST MSP output file.
226
227 >>> fname = get_test_fname('test.msp')
228 >>> Msp().sniff(fname)
229 True
230 >>> fname = get_test_fname('test.mzXML')
231 >>> Msp().sniff(fname)
232 False
233 """
234 with open(filename, 'r') as contents:
235 return Msp.next_line_starts_with(contents, "Name:") and Msp.next_line_starts_with(contents, "MW:")
236
237 class Ms2(Text):
238 file_ext = "ms2"
239
240 def sniff(self, filename):
241 """ Determines whether the file is a valid ms2 file.
242
243 >>> fname = get_test_fname('test.msp')
244 >>> Ms2().sniff(fname)
245 False
246 >>> fname = get_test_fname('test.ms2')
247 >>> Ms2().sniff(fname)
248 True
249 """
250
251 with open(filename, 'r') as contents:
252 header_lines = []
253 while True:
254 line = contents.readline()
255 if line == None or len(line) == 0:
256 pass
257 elif line.startswith('H\t'):
258 header_lines.append(line)
259 else:
260 break
261 for header_field in ['CreationDate', 'Extractor', 'ExtractorVersion', 'ExtractorOptions']:
262 found_header = False
263 for header_line in header_lines:
264 if header_line.startswith('H\t%s' % (header_field)):
265 found_header = True
266 break
267 if not found_header:
268 return False
269
270 return True
271
272 # unsniffable binary format, should do something about this
273 class XHunterAslFormat(Binary):
274 """ Annotated Spectra in the HLF format http://www.thegpm.org/HUNTER/format_2006_09_15.html """
275 file_ext = "hlf"