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comparison blast.py @ 9:2bda64d39931 draft

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Uploaded v0.0.19, adds blastdbp and pssm-asn1 datatypes.
author peterjc
date Wed, 26 Nov 2014 06:55:48 -0500
parents de11e1a921c4
children 5482a8cd0f36
comparison
equal deleted inserted replaced
8:de11e1a921c4 9:2bda64d39931
1 """ 1 """
2 BlastXml class 2 BlastXml class
3 """ 3 """
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, GenericAsn1
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 from time import sleep 10 from time import sleep
11 import os 11 import os
178 to_ext, size, offset, **kwd) 178 to_ext, size, offset, **kwd)
179 if self.file_ext == "blastdbn": 179 if self.file_ext == "blastdbn":
180 title = "This is a nucleotide BLAST database" 180 title = "This is a nucleotide BLAST database"
181 elif self.file_ext =="blastdbp": 181 elif self.file_ext =="blastdbp":
182 title = "This is a protein BLAST database" 182 title = "This is a protein BLAST database"
183 elif self.file_ext =="blastdbd":
184 title = "This is a domain BLAST database"
183 else: 185 else:
184 #Error? 186 #Error?
185 title = "This is a BLAST database." 187 title = "This is a BLAST database."
186 msg = "" 188 msg = ""
187 try: 189 try:
188 #Try to use any text recorded in the dummy index file: 190 #Try to use any text recorded in the dummy index file:
189 handle = open(data.file_name, "rU") 191 handle = open(data.file_name, "rU")
257 self.add_composite_file('blastdb.psi', is_binary=True, optional=True) 259 self.add_composite_file('blastdb.psi', is_binary=True, optional=True)
258 # self.add_composite_file('blastdb.paa', is_binary=True, optional=True) 260 # self.add_composite_file('blastdb.paa', is_binary=True, optional=True)
259 # self.add_composite_file('blastdb.pab', is_binary=True, optional=True) 261 # self.add_composite_file('blastdb.pab', is_binary=True, optional=True)
260 # self.add_composite_file('blastdb.pac', is_binary=True, optional=True) 262 # self.add_composite_file('blastdb.pac', is_binary=True, optional=True)
261 # The last 3 lines should be repeated for each WriteDB column, with filename extensions like ('.pba', '.pbb', '.pbc'), ('.pca', '.pcb', '.pcc'), etc. 263 # The last 3 lines should be repeated for each WriteDB column, with filename extensions like ('.pba', '.pbb', '.pbc'), ('.pca', '.pcb', '.pcc'), etc.
264
265
266 class BlastDomainDb( _BlastDb, Data ):
267 """Class for domain BLAST database files."""
268 file_ext = 'blastdbd'
269 allow_datatype_change = False
270 composite_type = 'basic'
271
272 def __init__(self, **kwd):
273 Data.__init__(self, **kwd)
274 self.add_composite_file('blastdb.phr', is_binary=True)
275 self.add_composite_file('blastdb.pin', is_binary=True)
276 self.add_composite_file('blastdb.psq', is_binary=True)
277 self.add_composite_file('blastdb.freq', is_binary=True, optional=True)
278 self.add_composite_file('blastdb.loo', is_binary=True, optional=True)
279 self.add_composite_file('blastdb.psd', is_binary=True, optional=True)
280 self.add_composite_file('blastdb.psi', is_binary=True, optional=True)
281 self.add_composite_file('blastdb.rps', is_binary=True, optional=True)
282 self.add_composite_file('blastdb.aux', is_binary=True, optional=True)