idoerg/boa

boa's Issues

Cannot get BOA working - annotated_genes.py file is missing

Hi @idoerg and @mortonjt , I was trying to use your program to find some bacteriocins in newly annotated genomes, but I cannot get BOA working.

I downloaded the latest version of BOA and set up all dependencies.
Then I tried to follow the instructions in the readme file:

Getting Started

First set PATH=$PATH:Bacfinder/src:Bacfinder/scripts

Before running the pipeline, two databases must be setup, the annotated genes database, and the intergenes database. This is assuming that you already have a set of genbank files and fasta genomes contained within a root directory.

To create the annotated genes database, execute the following command:

python annotated_genes.py --root-dir=< root directory of genbank files > 
                          --output-file=< output file of annotated regions >

To create the intergenes database, execute the following command:

python intergene.py --root-dir=<root directory genbank files> 
                    --output-file=< output file of intergenic regions >

It looks like that Bacfinder was renamed as BOA at one stage, so I just set my PATH accordingly.
But I wasn't able to create the database with annotated genes, as annotated_genes.py is missing. I went through the history of commits, and found that it had been removed without any comment in the commit b86e85b. I downloaded the removed file (annotated_genes.py) and tried to use it to generate a file with annotated genes, but it didn't work. The next step (python intergene.py) worked though, a file containing intergenic regions from my genbank file was generated. Anyway, I am stuck at the very beginning and cannot figure out what to do to get BOA working.

I don't know, am I doing something wrong? I would really appreciate your help.

Thank you in advance.