Cannot get BOA working - annotated_genes.py file is missing

[TimSkvortsov]

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.

[idoerg]

can you try cloning from here? https://github.com/nafizh/Boa Sorry for the mess. Iddo

…

On Thu, May 4, 2017 at 10:33 AM, Tim ***@***.***> wrote: Hi @idoerg <https://github.com/idoerg> and @mortonjt <https://github.com/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 <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. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#1>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AAD98ETnZPKwgNjWQ_7QPX_nf6Ae0yXSks5r2e-ygaJpZM4NQ17U> .

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