gdtools Utility Program

Performs various functions on GenomeDiff formatted files. Options depend on the COMMAND supplied. Only a small subset of these commands are described below. For a full list of gdtools subcommands run it from the command line with no options:

gdtools

Command: ANNOTATE (or COMPARE)

Usage:

gdtools ANNOTATE [-o annotated.html] -r reference.gbk input.1.gd [input.2.gd ... ]

Annotate a GenomeDiff file with information about mutations (what genes they affect, amino acid substitutions, etc.) Default output is to another GenomeDiff, but an HTML table can be produced with a table of mutations in a single GenomeDiff file or to compare the mutations present in several GenomeDiff files. This subcommand can be called as ANNOTATE or COMPARE. Both have the same effect.

-r <file_path>, --reference=<file_path>

Reference sequence files (Genbank, GFF, or FASTA). This option may be entered multiple times. REQUIRED

-o <file_path>, --output=<file_path>

File name for the output|Genome Diff| or HTML. DEFAULT: “annotated.gd” or “annotated.html”.

-f <format>,--format <format>

Type of output file to generate. See options below (DEFAULT=HTML)

Format

Description

HTML

Descriptive table viewable in a web browser

GD

GenomeDiff with added annotation of mutations

TSV

Tab-separated values file suitable for input into R or Excel

PHYLIP

Alignment file suitable for input into PHYLIP

JSON

JavaScript object notation file suitable for parsing

input1.gd input2.gd …

Input GenomeDiff file(s). This option may be entered multiple times to compare across files. REQUIRED

Warning

Some advanced GenomeDiff attributes for mutations, such as within and before, are ignored when generating compare tables.

Command: APPLY

Usage:

gdtools APPLY [ -o output.gff3 -f GFF3 ] -r reference.gbk input.gd

Apply the mutations described in the input GenomeDiff to the reference sequence(s).

-r <file_path>, --reference=<file_path>

Reference sequence files (Genbank, GFF, or FASTA). This option may be entered multiple times. REQUIRED

-o <file_path>, --output=<file_path>

Output file containing the muta. DEFAULT: “output.*”

-f <output_format>, --format=<output_format>

Output format. Possible values are “fasta” or “gff3”.

input.gd

Input GenomeDiff file. REQUIRED