Usage gdtools

Performs various functions on GenomeDiff format 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.

gtools ANNOTATE (or gtools COMPARE)

Usage:

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

Annotate a file with information about mutations (what genes they affect, amino acid substitutions, etc.) Default output is to another , but an HTML table can be produced with a table of mutations in a single file or to compare the mutations present in several 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 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 file(s). This option may be entered multiple times to compare across files. REQUIRED

Warning

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

gdtools APPLY

Usage:

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

Apply the mutations described in the input 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

input.gd

Input file. REQUIRED

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

Output file containing the mutated reference genome. DEFAULT: "output.*"

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

Output format. Possible values: GENBANK, FASTA, or GFF3.