There Are Others: Exploring The Remaining GRIEVOUS Commands - jvtalwar/GRIEVOUS GitHub Wiki

There are a few other GRIEVOUS commands available that we did not touch on during the walkthrough. If you find GRIEVOUS' help for these commands (e.g., grievous records --help) and their descriptions on the Usage and Tutorial page insufficient to your comprehension, here I will aim to elucidate and elaborate more on their usage and purpose.

Project Management:

grievous records:

Lost track of which datasets have been grievous realigned with a particular GRIEVOUS database? The grievous records command directly addresses this potential problem, providing you with comprehensive records of the paths of all datasets that have been grievous realigned with a particular GRIEVOUS database.

grievous records --database DATABASE_ALIAS [--chr N N+1 --out FILE_OUTPUT_PATH]
  • --database, -d takes in a user-specified string corresponding to an already created GRIEVOUS database. For example, in our tutorial we defined our database during grievous realign as Tutorial_Sarcoidosis, which if desired (i.e., this is the database for which you would like to access GRIEVOUS' records) can be passed in here with --database Tutorial_Sarcoidosis.
    • Similar to grievous realign, if only one GRIEVOUS database exists and you fail to provide a --database DATABASE_ALIAS, GRIEVOUS will report records from your only existing GRIEVOUS database. In all other instances, the user is required to provide a --database DATABASE_ALIAS.
  • --chr, -c is an optional parameter to subset the record report to only specific desired chromosomes. It is passed in with any desired chromosomes in a space-delimited manner. Chromosomes should be passed in to --chr, -c in the GRIEVOUS standard for chromosomes: {1-22, X, Y, MT}.
  • --out, -o is an optional flag that will write the specified records (as defined by you with the --database and --chr flags) to an output file at FILE_OUTPUT_PATH (replace this with a defined valid path...), as opposed to the console/terminal.

In the context of our tutorial, the following might serve as an example:

#Obtain our tutorial database records for certain prime numbered chromosomes and write them to a file:
grievous records -d Tutorial_Sarcoidosis --chr 3 5 7 11 13 17 19 --out ~/GRIEVOUS_Tutorial/Tutorial_Prime_Chromosome_Records.txt

grievous list_dbs:

If you ever forget the names of your grievous databases or the genome assemblies they use, you can use grievous list_dbs to clear up any confusion. For example, after our tutorial, we observe the following after entering grievous list_dbs into the terminal:

grievous list_dbs

Current grievous database aliases:
-------------------------------------
Tutorial_Sarcoidosis --> Assembly: hg_imaginary

grievous delete_database:

Complete with your project and looking to simplify your GRIEVOUS library (i.e., collection of databases which you have defined)? You can use grievous delete_database to delete a specified GRIEVOUS database. Proceed with extreme caution!!! This is a permanent operation, and your database will not be able to be recovered. If there is any doubt as to whether you might require GRIEVOUS realignment of future datasets with GRIEVOUS standardized datasets in your current project, do not delete your database. If you do so, you will need to perform GRIEVOUS realignment and merging for all datasets with a new database, including for datasets that had already undergone this process.

grievous delete_database --database DATABASE_ALIAS
  • --database, -d takes in a user-specified string corresponding to an already created GRIEVOUS database. Unlike other GRIEVOUS commands, the user must explicitly provide the alias for the desired database to delete.

And Then There Was One:

grievous general:

Freed from the shackles of data quality by GRIEVOUS and don't know what to with all your unexpected free time? Perhaps, you might enjoy consulting with grievous general. It won't fill up all the hours of time you saved by using GRIEVOUS, but I hope you get at least a fraction of the enjoyment out of it as I had making it.