obisilva: converts silva database into an ecoPCR database¶
obisilva: converts and optionally download the Silva database
into an ecoPCR database. The formated database include the taxonomy as defined by the Silva authors.
Warning
Take care that the numeric taxids associated to the sequences are specific to this Silva database and not compatible with the NCBI taxids. The taxids present in a version of the Silva database (i.e ssu, lsu, parc, ref...) are are just valid for this version of the database and not compatible with the taxids used in another version.
obisilva specific options¶
-
-s,--ssu¶ - Specify that you are interested in the SSU database.
Example:
> obisilva --ssu --parc
This download and format into an ecoPCR database the latest version of the SSUParc database of Silva.
-
-l,--lsu¶ - Specify that you are interested in the LSU database.
Example:
> obisilva --ssu --parc
This download and format into an ecoPCR database the latest version of the LSUParc database of Silva.
-
-p,--parc¶ Specify that you are interested in the Parc (complete) version of the Silva database.
-
-r,--ref¶ Specify that you are interested in the Reference (cleaned to keep only high quality sequences) version of the Silva database.
-
-n,--nr¶ Specify that you are interested in the Non redundant version of the Silva database. just a version of the to closely related sequence is kept in this version of the database
Warning
Non redundant version of Silva exists only for the SSU sequences in its Reference and Truncated version
-
-t,--trunc¶ Specify that you are interested in the Truncated (limited to the rDNA element without flanked regions) version of the Silva database.
-
--local=<DIRNAME>¶ - Specify you have already downloaded a copy of the Silva database located at the following URL http://www.arb-**Silva**.de/no_cache/download/archive/current/Exports/
Example:
> obisilva --ssu --parc --local=**Silva**DirThis format the SSUParc version of the Silva database pre-downloaded in the **Silva**Dir directory.