Export
Description
Export a pangraph to a chosen file format(s)
Options
| Name | Type | Short Flag | Long Flag | Description |
|---|---|---|---|---|
| Edge minimum length | Integer | ell | edge-minimum-length | blocks below this length cutoff will be ignored for edges in graph |
| Edge maximum length | Integer | elu | edge-maximum-length | blocks above this length cutoff will be ignored for edges in graph |
| Edge minimum depth | Integer | edl | edge-minimum-depth | blocks below this depth cutoff will be ignored for edges in graph |
| Edge maximum depth | Integer | edu | edge-maximum-depth | blocks above this depth cutoff will be ignored for edges in graph |
| Minimum length | Integer | ll | minimum-length | blocks below this length cutoff will be ignored for export |
| Maximum length | Integer | lu | maximum-length | blocks above this length cutoff will be ignored for export |
| Minimum depth | Integer | dl | minimum-depth | blocks below this depth cutoff will be ignored for export |
| Maximum depth | Integer | du | maximum-depth | blocks above this depth cutoff will be ignored for export |
| No duplications | Boolean | nd | no-duplications | do not export any block that contains at least one strain repeated more than once |
| Output directory | String | o | output-directory | path to directory where output will be stored (default: export) |
| Prefix | String | p | prefix | basename of exported files (default: pangraph) |
| GFA | Boolean | ng | no-export-gfa | toggles whether pangraph is exported as GFA. |
| PanX | Boolean | pX | export-panX | toggles whether pangraph is exported to panX visualization compatible format. (requires fasttree) |
Arguments
Zero or one pangraph file which must be formatted as a JSON. If no file path is given, reads from stdin. In either case, the stream can be optionally gzipped.
Output
Outputs the constructed pangraph to the selected formats at the user-supplied paths.