Scripts to convert PATRIC GTO format to other formats.

PATRIC database (the Pathosystems Resource Integration Center) https://www.patricbrc.org/ stores genomes in the GTO format. The GTO format is contains nucleotide and amino-acid sequences and various annotation information.

The repository provides lightweight scripts for converting GTO format to:

• FNA (nucleotide contigs in fasta format)
• FNN (genes nucleotide sequences in fasta format)
• FAA (translated genes amino acid sequences in fasta format)
• GFF (gene annotations and nucleotide contigs in GFF3 format)

Scripts are written on Perl and Python. Located in the ./scripts folder.

The Perl scrips require JSON library. It could be installed with CPAN (The Comprehensive Perl Archive Network): https://metacpan.org/pod/JSON.

With cpanm:

cpanm JSON

With CPAN shell:

perl -MCPAN -e shell
install JSON

Converts GTO files to files with nucleotide contigs in fasta format.

Input: Directory with GTO files. Files should have ".gto" extension.

Output: Creates directory "fna" with ".fna" files. One FNA file per one GTO file. Names preserved the same as in GTO files.

usage: perl fna_from_gto.pl [directory with GTO files]

Converts GTO files to files with gene nucleotide sequences in fasta format.

Input: Directory with GTO files. Files should have ".gto" extension.

Output: Make ".fnn" files in the directory defined by "-o" flag. One FNN file per one GTO file. Names preserved the same as in GTO files.

usage: python3 fnn_from_gto.py [-h] [-g GTO] [-o OUTPUT]

Converts GTO files to FNN with nucleotide sequences for each gene

optional arguments:
  -h, --help            show this help message and exit
  -g GTO, --gto GTO     Directory with GTO files
  -o OUTPUT, --output OUTPUT
                        Output directory for FNN files
                        Default: "fnn" directory

Converts GTO files to files with amino acid sequences in fasta format.

Input: Directory with GTO files. Files should have ".gto" extension.

Output: Creates directory "faa" with ".faa" files. One FAA file per one GTO file. Names preserved the same as in GTO files.

usage: perl faa_from_gto.pl [directory with GTO files]

Converts GTO files to files with annotations in GFF format. Script adds ##FASTA section at the end of file that contains nucleotide contigs.

Input: Directory with GTO files. Files should have ".gto" extension.

Output: Creates directory "faa" with ".faa" files. One GFF file per one GTO file. Names are generated from genome ids recorded in GTO file.

Annotation records are often unsorted or sorted by position in reverse order. Two version of script:

• Script that sorts annotations in ascending order (Preferred):

usage: perl gff_from_gto_sorted.pl [directory with GTO files]

• Script that outputs annotations in the order how they are written in GTO file:

usage perl gff_from_gto_no_sotring.pl [directory with GTO files]