Usage gdtools - barricklab/breseq GitHub Wiki
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.
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.
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.