Mercurial > repos > devteam > blast_datatypes
changeset 7:a44a7a5456e1 draft
Uploaded v0.0.16a, Nucleotide database definition aware of MegaBLAST index superheader
| author | peterjc |
|---|---|
| date | Mon, 05 Aug 2013 11:09:32 -0400 |
| parents | 8615fd8abc04 |
| children | 7ceb2ae30ff4 |
| files | README.rst blast.py |
| diffstat | 2 files changed, 5 insertions(+), 1 deletions(-) [+] |
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--- a/README.rst Mon Jul 29 12:55:49 2013 -0400 +++ b/README.rst Mon Aug 05 11:09:32 2013 -0400 @@ -33,6 +33,7 @@ BLAST database files (contribution from Nicola Soranzo) v0.0.16 - Adopt standard MIT License. - Development moved to GitHub, https://github.com/peterjc/galaxy_blast + - Nucleotide database definition aware of MegaBLAST index superheader ======= ======================================================================
--- a/blast.py Mon Jul 29 12:55:49 2013 -0400 +++ b/blast.py Mon Aug 05 11:09:32 2013 -0400 @@ -189,10 +189,13 @@ self.add_composite_file('blastdb.nog', is_binary=True, optional=True) # OID->GI lookup file ( -hash_index or -parse_seqids option of makeblastdb) self.add_composite_file('blastdb.nsd', is_binary=True, optional=True) # sorted sequence accession values ( -hash_index or -parse_seqids option of makeblastdb) self.add_composite_file('blastdb.nsi', is_binary=True, optional=True) # index of sequence accession values ( -hash_index or -parse_seqids option of makeblastdb) +# self.add_composite_file('blastdb.00.idx', is_binary=True, optional=True) # first volume of the MegaBLAST index generated by makembindex +# The previous line should be repeated for each index volume, with filename extensions like '.01.idx', '.02.idx', etc. + self.add_composite_file('blastdb.shd', is_binary=True, optional=True) # MegaBLAST index superheader (-old_style_index false option of makembindex) # self.add_composite_file('blastdb.naa', is_binary=True, optional=True) # index of a WriteDB column for e.g. mask data # self.add_composite_file('blastdb.nab', is_binary=True, optional=True) # data of a WriteDB column # self.add_composite_file('blastdb.nac', is_binary=True, optional=True) # multiple byte order for a WriteDB column -# The last 3 lines should be repeated for each WriteDB column, with filename extensions like ('.nba', '.nbb', '.nbc'), ('.nca', '.ncb', '.ncc'), etc. +# The previous 3 lines should be repeated for each WriteDB column, with filename extensions like ('.nba', '.nbb', '.nbc'), ('.nca', '.ncb', '.ncc'), etc. def display_data(self, trans, data, preview=False, filename=None, to_ext=None, size=None, offset=None, **kwd):