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and indeed the self table was changed, but the sample name also appears as layer or sample_id in other tables of the PROFILE.db , but they aren't modified, e.g., all the mean_coverage_* tables. Because of this, when trying to run anvi-merge, it complains:
Config Error: The incoming layer orders data for std_coverage include layer names that do not
match the ones in the database :/ Here they are: 'glu2'
(glu2 is the old sample name).
No idea if there is some new command to do this that I'm not aware...
Hey @xvazquezc, renaming sample names once the single or merged profiles are generated is an absolute pain. We don't have a script for that, unfortunately. But there is a way to do it using SQLite via the command line. You can dump the entire content of the db file as flat text, literally search/replace the sample name, and generate a new db from the SQL file. Please let me know if you end up going this direction and it works.
Since the contigs-db files don't care about sample names, this change should not effect anything else downstream and work smoothly in theory.
Short description of the problem
I was trying to rename a
PROFILE.db
based on #946, i.e.:and indeed the
self
table was changed, but the sample name also appears aslayer
orsample_id
in other tables of thePROFILE.db
, but they aren't modified, e.g., all themean_coverage_*
tables. Because of this, when trying to runanvi-merge
, it complains:(glu2 is the old sample name).
No idea if there is some new command to do this that I'm not aware...
anvi'o version
8-dev up to date
System info
Ubuntu 22.04, up to date.
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