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comparison blast.py @ 5:b3a3ba0c1d47

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Uploaded v0.0.15 which updates the BLAST database definitions. Fixes a MetadataElement bug and includes more of the optional BLAST database files (contribution from Nicola Soranzo).
author peterjc
date Wed, 20 Mar 2013 10:39:27 -0400
parents f9a7783ed7b6
children a44a7a5456e1
comparison
equal deleted inserted replaced
4:f9a7783ed7b6 5:b3a3ba0c1d47
4 4
5 from galaxy.datatypes.data import get_file_peek 5 from galaxy.datatypes.data import get_file_peek
6 from galaxy.datatypes.data import Text, Data 6 from galaxy.datatypes.data import Text, Data
7 from galaxy.datatypes.xml import GenericXml 7 from galaxy.datatypes.xml import GenericXml
8 from galaxy.datatypes.metadata import MetadataElement 8 from galaxy.datatypes.metadata import MetadataElement
9
9 10
10 class BlastXml( GenericXml ): 11 class BlastXml( GenericXml ):
11 """NCBI Blast XML Output data""" 12 """NCBI Blast XML Output data"""
12 file_ext = "blastxml" 13 file_ext = "blastxml"
13 14
172 173
173 class BlastNucDb( _BlastDb, Data ): 174 class BlastNucDb( _BlastDb, Data ):
174 """Class for nucleotide BLAST database files.""" 175 """Class for nucleotide BLAST database files."""
175 file_ext = 'blastdbn' 176 file_ext = 'blastdbn'
176 composite_type ='basic' 177 composite_type ='basic'
177 MetadataElement( readonly=True, optional=True, visible=False, no_value=0 ) 178
178 179 def __init__(self, **kwd):
179 def __init__(self,**kwd):
180 Data.__init__(self, **kwd) 180 Data.__init__(self, **kwd)
181 self.add_composite_file('blastdb.nhr') 181 self.add_composite_file('blastdb.nhr', is_binary=True) # sequence headers
182 self.add_composite_file('blastdb.nin') 182 self.add_composite_file('blastdb.nin', is_binary=True) # index file
183 self.add_composite_file('blastdb.nsq') 183 self.add_composite_file('blastdb.nsq', is_binary=True) # nucleotide sequences
184 self.add_composite_file('blastdb.nhd', optional=True) 184 self.add_composite_file('blastdb.nal', is_binary=False, optional=True) # alias ( -gi_mask option of makeblastdb)
185 self.add_composite_file('blastdb.nsi', optional=True) 185 self.add_composite_file('blastdb.nhd', is_binary=True, optional=True) # sorted sequence hash values ( -hash_index option of makeblastdb)
186 self.add_composite_file('blastdb.nhi', optional=True) 186 self.add_composite_file('blastdb.nhi', is_binary=True, optional=True) # index of sequence hash values ( -hash_index option of makeblastdb)
187 self.add_composite_file('blastdb.nog', optional=True) 187 self.add_composite_file('blastdb.nnd', is_binary=True, optional=True) # sorted GI values ( -parse_seqids option of makeblastdb and gi present in the description lines)
188 self.add_composite_file('blastdb.nsd', optional=True) 188 self.add_composite_file('blastdb.nni', is_binary=True, optional=True) # index of GI values ( -parse_seqids option of makeblastdb and gi present in the description lines)
189 self.add_composite_file('blastdb.nog', is_binary=True, optional=True) # OID->GI lookup file ( -hash_index or -parse_seqids option of makeblastdb)
190 self.add_composite_file('blastdb.nsd', is_binary=True, optional=True) # sorted sequence accession values ( -hash_index or -parse_seqids option of makeblastdb)
191 self.add_composite_file('blastdb.nsi', is_binary=True, optional=True) # index of sequence accession values ( -hash_index or -parse_seqids option of makeblastdb)
192 # self.add_composite_file('blastdb.naa', is_binary=True, optional=True) # index of a WriteDB column for e.g. mask data
193 # self.add_composite_file('blastdb.nab', is_binary=True, optional=True) # data of a WriteDB column
194 # self.add_composite_file('blastdb.nac', is_binary=True, optional=True) # multiple byte order for a WriteDB column
195 # The last 3 lines should be repeated for each WriteDB column, with filename extensions like ('.nba', '.nbb', '.nbc'), ('.nca', '.ncb', '.ncc'), etc.
189 196
190 def display_data(self, trans, data, preview=False, filename=None, 197 def display_data(self, trans, data, preview=False, filename=None,
191 to_ext=None, size=None, offset=None, **kwd): 198 to_ext=None, size=None, offset=None, **kwd):
192 """Apparently an old display method, but still gets called. 199 """Apparently an old display method, but still gets called.
193 200
194 This allows us to format the data shown in the central pane via the "eye" icon. 201 This allows us to format the data shown in the central pane via the "eye" icon.
195 """ 202 """
196 return "This is a BLAST nucleotide database." 203 return "This is a BLAST nucleotide database."
204
197 205
198 class BlastProtDb( _BlastDb, Data ): 206 class BlastProtDb( _BlastDb, Data ):
199 """Class for protein BLAST database files.""" 207 """Class for protein BLAST database files."""
200 file_ext = 'blastdbp' 208 file_ext = 'blastdbp'
201 composite_type ='basic' 209 composite_type ='basic'
202 MetadataElement( readonly=True, optional=True, visible=False, no_value=0 ) 210
203 211 def __init__(self, **kwd):
204 def __init__(self,**kwd):
205 Data.__init__(self, **kwd) 212 Data.__init__(self, **kwd)
206 self.add_composite_file('blastdb.phr') 213 # Component file comments are as in BlastNucDb except where noted
207 self.add_composite_file('blastdb.pin') 214 self.add_composite_file('blastdb.phr', is_binary=True)
208 self.add_composite_file('blastdb.psq') 215 self.add_composite_file('blastdb.pin', is_binary=True)
209 self.add_composite_file('blastdb.pnd', optional=True) 216 self.add_composite_file('blastdb.psq', is_binary=True) # protein sequences
210 self.add_composite_file('blastdb.pni', optional=True) 217 self.add_composite_file('blastdb.phd', is_binary=True, optional=True)
211 self.add_composite_file('blastdb.psd', optional=True) 218 self.add_composite_file('blastdb.phi', is_binary=True, optional=True)
212 self.add_composite_file('blastdb.psi', optional=True) 219 self.add_composite_file('blastdb.pnd', is_binary=True, optional=True)
213 self.add_composite_file('blastdb.psq', optional=True) 220 self.add_composite_file('blastdb.pni', is_binary=True, optional=True)
214 self.add_composite_file('blastdb.phd', optional=True) 221 self.add_composite_file('blastdb.pog', is_binary=True, optional=True)
215 self.add_composite_file('blastdb.phi', optional=True) 222 self.add_composite_file('blastdb.psd', is_binary=True, optional=True)
216 self.add_composite_file('blastdb.pog', optional=True) 223 self.add_composite_file('blastdb.psi', is_binary=True, optional=True)
224 # self.add_composite_file('blastdb.paa', is_binary=True, optional=True)
225 # self.add_composite_file('blastdb.pab', is_binary=True, optional=True)
226 # self.add_composite_file('blastdb.pac', is_binary=True, optional=True)
227 # The last 3 lines should be repeated for each WriteDB column, with filename extensions like ('.pba', '.pbb', '.pbc'), ('.pca', '.pcb', '.pcc'), etc.
217 228
218 def display_data(self, trans, data, preview=False, filename=None, 229 def display_data(self, trans, data, preview=False, filename=None,
219 to_ext=None, size=None, offset=None, **kwd): 230 to_ext=None, size=None, offset=None, **kwd):
220 """Apparently an old display method, but still gets called. 231 """Apparently an old display method, but still gets called.
221 232