GenomeDiff Utility Program

Performs various functions on genomediff formatted files. Options depend on the COMMAND supplied.

Command: VALIDATE

Usage:

genomediff VALIDATE [-o output.gb] input.gd

Checks the syntax of a GenomeDiff file and outputs a clean version. Entries are re-numbered consecutively and unused evidence and validation entries are removed form the output GenomeDiff.

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

Output file path. DEFAULT: input.validated.gd

<input.gd>
Input GenomeDiff file. Only one is allowed. REQUIRED

Command: HTML

Usage:

genomediff HTML -r reference.gbk [-o output.html] input.gd

Create an HTML table of mutations in a GenomeDiff file.

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

GenBank files for reference sequences. This option may be entered multiple times. REQUIRED

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

Output HTML file containing the mutation table. DEFAULT: “input.html”.

<input.gd>
Input GenomeDiff file. Only one is allowed. REQUIRED

Command: COMPARE

Usage:

genomediff COMPARE -r reference.gbk [-o output.html] input1.gd [input2.gd ...]

Create an HTML table comparing mutations from different samples.

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

GenBank files for reference sequences. This option may be entered multiple times. REQUIRED

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

Output HTML file containing the comparison table. DEFAULT: “compare.html”.

<input1.gd [input2.gd ...]>
Input GenomeDiff files, one for each sample. REQUIRED

Command: SUBTRACT

Usage:

genomediff SUBTRACT -o output.gd -1 input1.gd [input2.gd ...]

Create a GenomeDiff containing only mutations that are in GenomeDiff #1 but not in GenomeDiff #2.

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

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

-1 <file_path>, -input1=<file_path>

Input GenomeDiff file #1. REQUIRED

-2 <file_path>, -input2=<file_path>

Input GenomeDiff file #2. REQUIRED

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