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

Usage:

gdtools ANNOTATE -r reference.gbk [--html -o output.html] input1.gd input2.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.

-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 mutation table. DEFAULT: “annotated.gd” or “annotated.html”.

--html

Output an HTML table instead of a GenomeDiff file.

input1.gd input2.gd ...

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

Command: APPLY

Usage:

gdtools APPLY -r reference.gbk -f GFF3 [-o output.html] 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 mutation table. DEFAULT: “output.*”

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

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

input.gd

Input GenomeDiff file. REQUIRED

Command: SUBTRACT

Usage:

gdtools SUBTRACT [-o output.gd] input.gd subtract1.gd [subtract2.gd ...]

Creates a new GenomeDiff file of mutations from the input file that are present after removing mutations present in any of the subtracted GenomeDiff files.

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

Output GenomeDiff file. DEFAULT: “output.gd”.

input.gd

Input GenomeDiff file.

subtract.gd [subtract2.gd ...]

GenomeDiff files to subtract from input file.

Command: INTERSECT

Usage:

gdtools INTERSECT [-o output.gd] input1.gd input2.gd ...

Creates a new GenomeDiff file with mutations that are present in ALL input GenomeDiff files.

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

Output GenomeDiff file. DEFAULT: “output.gd”.

input1.gd input2.gd ...

Input GenomeDiff files.