Curating output episode

[Czirion]

1) Explore anvi-script-reformat-fasta to see if it gives the solution required here. If it does, maybe this episode is not necessary and the anvio script can be briefly explain at the end of the annotation episode.

2) Put uppercase in the title

3) Explain the problems of the files and the solution that is given.

4) I suggest taking the strain name from the DEFINITION line, instead of the accession from the LOCUS line to do the change. Explain what the script is doing and put the comments inside the script in english. Prokka has problems with the LOCUS line when the name of the contigs are long (such as the ones resulting from SPAdes), with the assemblies used in the lesson we do not have this problem but we should add a box explaining this very likely problem.

[Czirion]

Make box with Anvi-script-reformat-fasta Make the script with comments and maybe put it in the bash lesson and only use it here

[Czirion]

The correct_gbk.sh script and the anvi-script-reformat-fasta box are now in the Annotation episode.