Analyze Schema

At this point we assume that Taranis is successful installed in your system. If you need to install it, please check the installation chapter.

To analyse a schema, you need to enter 2 mandatory parameters:

• inputdir
• outputdir

And one optional parameter:

• alt

The inputdir parameter will indicate the directory where the fasta files belongs to the schema are located. Note that the script will consider all valid fasta files in the “inputdir”, only fasta files that belongs to the schema must be in the folder directory.

The outputdir parameter will be used to store all the information that Taranis generate. The output folder will be created by the script. In case that the folder exists, it will prompt to the user to decide if folder is deleted or script execution is cancelled.

The alt parameter will be used to decide if an alternative start codon “GTG” is allowed when allele is translated to protein. If the parameter is not set, in the command line, then only “ATG” is allowed, by typing “-alt” when executing the alternative start codon, it will be translated as start codon.

The command syntax for analysing the schema is:

taranis.py evaluate_schema –inputdir <your_schema_folder> -outputdir <folder_where_output> [-alt]

Your command should be similar to the follow:

taranis.py evaluate_schema –inputdir /home/listeria_schema –outputdir /home/schema_result

While script is executing the progress bar will show you the percentage executed and the remaining time. Once the script ends check the output folder to see the results.