gb2fasta.pl

Perl script to convert GenBank records to FASTA format

The program reads a file with one or multiple genbank records and extract the senquences in FASTA format. The script can also retrieve some meta-data, such as voucher name and geographic location.

Just download the code

wget https://raw.githubusercontent.com/santiagosnchez/gb2fasta/master/gb2fasta.pl

Or install (UNIX systems)

git clone https://github.com/santiagosnchez/gb2fasta
cd gb2fasta
chmod +x gb2fasta.pl
sudo cp gb2fasta.pl /usr/local/bin

Running the code

Use the -h flag for more details:

perl gb2fasta.pl -h

Try:
perl gb2fasta.pl -gb <gb.file> -out <outfile.fasta> [options]
Options:
-geo    will include only records with a geographic location
-oc     will only include the country if the record has a geographic location
-nv     will exclude the voucher label