Microbial 'omics


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anvi-script-augustus-output-to-external-gene-calls [program]

Table of Contents

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.

See program help menu or go back to the main page of anvi’o programs and artifacts.

Can provide

external-gene-calls

Can consume

augustus-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.

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.