anvi-script-augustus-output-to-external-gene-calls
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.
🔙 To the main page of anvi’o programs and artifacts.
Authors
Can consume
Can provide
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.