piotrsenkow / genbank-converter

A way to convert your genbank file to an *.rnt or *.ptt file

Genbank Converter

A way to convert your genbank file to a *.fna, *.rnt, or *.ptt file formats.

• Scrapes your genbank file of protein / RNA records.
• Creates a 9 column tab delimited file ready for Rockhopper.
• Convert your genbank to a FASTA-like file format (*.fna).
• Perfect for Rockhopper inputs

Installation

This program requires Python3 to run.

Open the folder and install the dependencies.

$ cd ($PATH TO FOLDER WHERE YOU DOWNLOADED) 
$ pip install -r requirements.txt

Running The Program

There are a few flags to keep in mind before running the program from console .

• -i or --input (Specify the name of your genbank file that you would like to convert. Remember to include file extension.)
• -o or --output (Specify the name of the file that you would like to be created. Omit the file extension.)
• -t or --type (Specify "rnt" or "ptt" for the type of genbank conversion that you would like to happen.)

Genbank(.gb) to FASTA Format DNA (.fna)

$ cd ($PATH TO FOLDER WHERE YOU DOWNLOADED)
$ python genbank_converter.py -i Mycoplasma_genitalium.gb -o Mycoplasma_SEQ -t fna

Genbank(.gb) to NCBI Protein Table (.ptt)

$ cd ($PATH TO FOLDER WHERE YOU DOWNLOADED)
$ python genbank_converter.py -i Mycoplasma_genitalium.gb -o Mycoplasma_Proteins -t ptt

Genbank(.gb) to NCBI RNA Table (.rnt)

$ cd ($PATH TO FOLDER WHERE YOU DOWNLOADED)
$ python genbank_converter.py -i Mycoplasma_genitalium.gb -o Mycoplasma_RNAS -t rtt