anvi-delete-misc-data
Table of Contents
Remove stuff from 'additional data' or 'order' tables for either items or layers in either pan or profile databases. OR, remove stuff from the 'additional data' tables for nucleotides or amino acids in contigs databases.
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Authors
Requires
Can use
pan-db 
misc-data-items 
misc-data-layers misc-data-layer-orders misc-data-nucleotides misc-data-amino-acids
Provides
This program does not seem to provide any artifacts. Such programs usually print out some information for you to see or alter some anvi’o artifacts without producing any immediate outputs.
Usage
After you’ve added misc-data of some kind (misc-data-items, misc-data-layers, misc-data-layer-orders, misc-data-nucleotides, or misc-data-amino-acids) using anvi-import-misc-data, you can delete that data and remove it from the interactive interface using this program.
This program will release your data into the ether, never to be seen again. If you would like to first export it into a text file (so that it can be seen again), you can do so with anvi-export-misc-data.
This program only works on data that is listed as an available key (most often because it was previously imported by the user). To view available keys, call either
anvi-delete-misc-data -p profile-db \ --target-data-table items|layers|layer_orders \ --list-available-keys
or
anvi-delete-misc-data -c contigs-db \ --target-data-table nucleotides|amino_acids \ --list-available-keys
where you choose the appropriate option for the taget-data-table.
If your misc-data is associated with a specific data group, you can provide that data group to this program with the -D flag. For example, to delete the homogeneity data that anvi-pan-genome or anvi-compute-gene-cluster-homogeneity stored in a pan-db:
anvi-delete-misc-data -p pan-db \ --target-data-table items \ -D homogeneity \ --keys-to-remove functional_homogeneity_index,geometric_homogeneity_index,combined_homogeneity_index
For a list of common data groups created by anvi’o programs, see misc-data-items.
Data types you can delete
From a pan-db or profile-db: items, layers, layer orders
From a pan-db or profile-db, you can delete
- items data (misc-data-items)
anvi-delete-misc-data -p profile-db \ --target-data-table items \ --keys-to-remove key_1
- layers data (misc-data-layers)
anvi-delete-misc-data -p pan-db \ --target-data-table layers \ --keys-to-remove key_2,key_3
- layer orders data (misc-data-layer-orders)
anvi-delete-misc-data -p profile-db \ --target-data-table layer_orders \ --keys-to-remove key_4
From a contigs-db: nucleotide and amino acid data
From a contigs-db, you can delete
- nucleotide data (misc-data-nucleotides)
anvi-delete-misc-data -c contigs-db \ --target-data-table nucleotides \ --keys-to-remove key_1
- amino acid data (misc-data-amino-acids)
anvi-delete-misc-data -c contigs-db \ --target-data-table amino_acids \ --keys-to-remove key_2
Edit this file to update this information.
Command line interface
The following is the list of parameters and their descriptions in the latest version of anvi-delete-misc-data.
The code that generates this web page ensures that this information is the latest available in 9-dev (eunice). Which means, in some cases the information in this section (generated automatically) might be more comprehensive or up-to-date compared to the descriptions above (written by humans).
Command line usage
Parameters and their descriptions
-p, --pan-or-profile-dbPAN_OR_PROFILE_DB- An anvi'o pan-db or profile-db (and even genes-db or pan-graph-db in appropriate contexts).
-c, --contigs-dbCONTIGS_DB- Anvi'o contigs database generated by 'anvi-gen-contigs-database'
-t, --target-data-tableNAMErequired- The target table is the table you are interested in accessing. Currently it can be 'items','layers', or 'layer_orders'. Please see most up-to-date online documentation for more information.
--keys-to-removeKEYS_TO_REMOVE- A comma-separated list of data keys to remove from the database. If you do not use this parameter, anvi'o will simply remove everything from the target data table immediately. Please note that you should not use this parameter together with `--groups-to-remove` in a single command.
--groups-to-removeGROUPS_TO_REMOVE- A comma-separated list of data groups to remove from the database. If you do not use this parameter, anvi'o will simply remove everything from the target data table immediately. Please note that you should not use this parameter together with `--keys-to-remove` in a single command.
--list-available-keys- Using this flag will list available data keys in the target data table and quit without doing anything else.
--just-do-it- Don't bother me with questions or warnings, just do it.
Additional Resources
Are you aware of resources that may help users better understand the utility of this program? Please feel free to edit this file on GitHub. If you are not sure how to do that, find the __resources__ tag in this file to see an example.