Mercurial > repos > devteam > blast_datatypes

comparison blast.py @ 6:a04cf51612f1 draft

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Uploaded v0.0.16, MIT License, development moved to GitHub, nucleotide database definition aware of MegaBLAST index superheader
author peterjc
date Mon, 23 Sep 2013 09:56:10 -0400
parents b3a3ba0c1d47
children de11e1a921c4
comparison
equal deleted inserted replaced
5:b3a3ba0c1d47 6:a04cf51612f1
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) 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.nni', is_binary=True, optional=True) # index of GI values ( -parse_seqids option of makeblastdb and gi present in the description lines) 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) 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) 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) 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.00.idx', is_binary=True, optional=True) # first volume of the MegaBLAST index generated by makembindex
193 # The previous line should be repeated for each index volume, with filename extensions like '.01.idx', '.02.idx', etc.
194 self.add_composite_file('blastdb.shd', is_binary=True, optional=True) # MegaBLAST index superheader (-old_style_index false option of makembindex)
192 # self.add_composite_file('blastdb.naa', is_binary=True, optional=True) # index of a WriteDB column for e.g. mask data 195 # 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 196 # 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 197 # 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. 198 # The previous 3 lines should be repeated for each WriteDB column, with filename extensions like ('.nba', '.nbb', '.nbc'), ('.nca', '.ncb', '.ncc'), etc.
196 199
197 def display_data(self, trans, data, preview=False, filename=None, 200 def display_data(self, trans, data, preview=False, filename=None,
198 to_ext=None, size=None, offset=None, **kwd): 201 to_ext=None, size=None, offset=None, **kwd):
199 """Apparently an old display method, but still gets called. 202 """Apparently an old display method, but still gets called.
200 203