anvi-script-augustus-output-to-external-gene-calls

Authors
Requires
Provides
Usage
Command line interface

Command line usage
Parameters and their descriptions

Additional Resources

Takes in gene calls by AUGUSTUS v3.3.3, generates an anvi'o external gene calls file. It may work well with other versions of AUGUSTUS, too. It is just no one has tested the script with different versions of the program.

🔙 To the main page of anvi’o programs and artifacts.

Authors

A. Murat Eren (Meren)

Requires

augustus-gene-calls

Provides

external-gene-calls

Usage

This program converts a gene call file from AUGUSTUS (as an augustus-gene-calls artifact) to an anvi’o external-gene-calls artifact.

This essentially just reformats the data in the augustus-gene-calls artifact (for example, removing the UTR information) so that it can be read by other anvi’o programs.

A run of this program will look something like this:

anvi-script-augustus-output-to-external-gene-calls -i augustus-gene-calls -o external-gene-calls

Here is an example of what the resulting external-gene-calls file will look like (from the gff file used as an example on the augustus-gene-calls page):

gene_callers_id    contig       start    stop    direction    partial    call_type    source      version    aa_sequence
0                  unnamed-1    56       1252    f            0          1            AUGUSTUS    v3.3.3     MSEGNAAGEPSTPGGPRPLLTGARGLIGRRPAPPLTPGRLPSIRSRDLTLGGVKKKTFTPNIISRKIKEEPKEEVTVKKEKRERDRDRQREGHGRGRGRPEVIQSHSIFEQGPAEMMKKKGNWDKTVDVSDMGPSHIINIKKEKRETDEETKQILRMLEKDDFLDDPGLRNDTRNMPVQLPLAHSGWLFKEENDEPDVKPWLAGPKEEDMEVDIPAVKVKEEPRDEEEEAKMKAPPKAARKTPGLPKDVSVAELLRELSLTKEEELLFLQLPDTLPGQPPTQDIKPIKTEVQGEDGQVVLIKQEKDREAKLAENACTLADLTEGQVGKLLIRKSGRVQLLLGKVTLDVTMGTACSFLQELVSVGLGDSRTGEMTVLGHVKHKLVCSPDFESLLDHKHR

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-script-augustus-output-to-external-gene-calls.

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

anvi-script-augustus-output-to-external-gene-calls [-h] -i INPUT_FILE [-o FILE_PATH] [--just-do-it]

Parameters and their descriptions

options

-i, --input-file INPUT_FILE required: Gene calls file from AUGUSTUS (that ends with .gff). Please note that the script is only tested with AUGUSTUS v3.3.3 output (although it may still work with other versions of the program).
-o, --output-file FILE_PATH: File path to store results.
--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.