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Addition Description
Using BLAST indexed databases would allow faster searching as well as parallelization (e.g., see use of blastn in q2-feature-classifier, also used in q2-quality-control and some other plugins). This would be in addition to the current use of FASTA (in which case the indexed db is built on the fly).
Current Behavior
No blastdb formats are supported.
Proposed Behavior
Create a new type (proposed name: BLASTDB)
Create a new format (proposed: BLASTDBv5Format). There are versioned formats (v4 is deprecated, v5 is current for some time). 3. Create transformers (to/from FASTAformat(s)) (EDIT: these should probably be actions, not transformers, and could be placed in q2-feature-classifier re: Wrap makeblastdb to generate indexed blast database q2-feature-classifier#158)
One problem is that the format specification does not appear to be described anywhere that I can find. So I am not sure that we can write a detailed format validator. However, format validation could use blastdbcmd (ships with blast+) to get db info, like:
blastdbcmd -db -info
Questions
Do we need separate types for protein vs. nucleotide dbs? The format would be the same but linked to different types.
Is blastdbcmd sufficient for validation?
Is this even a type that we want in q2-types? A few plugins would wind up using this (q2-feature-classifier, q2-moshpit, external plugins?) so I personally feel certain enough to open the issue here first.
The text was updated successfully, but these errors were encountered:
Addition Description
Using BLAST indexed databases would allow faster searching as well as parallelization (e.g., see use of blastn in q2-feature-classifier, also used in q2-quality-control and some other plugins). This would be in addition to the current use of FASTA (in which case the indexed db is built on the fly).
Current Behavior
No blastdb formats are supported.
Proposed Behavior
BLASTDB
)BLASTDBv5Format
). There are versioned formats (v4 is deprecated, v5 is current for some time).3. Create transformers (to/from FASTAformat(s))(EDIT: these should probably be actions, not transformers, and could be placed in q2-feature-classifier re: Wrap makeblastdb to generate indexed blast database q2-feature-classifier#158)One problem is that the format specification does not appear to be described anywhere that I can find. So I am not sure that we can write a detailed format validator. However, format validation could use
blastdbcmd
(ships withblast+
) to get db info, like:blastdbcmd -db -info
Questions
blastdbcmd
sufficient for validation?The text was updated successfully, but these errors were encountered: