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parameters · Changes

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Update parameters authored May 11, 2018 by Jorge Navarro Muñoz's avatar Jorge Navarro Muñoz
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parameters.md
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......@@ -6,7 +6,7 @@ Type `python bigscape.py -h` to display a list of all available parameters. See
## help
Type `-h` or `--help` to display all available options
Type `-h` or `--help` to display all current available options
## Label
......@@ -106,7 +106,7 @@ By default, BiG-SCAPE separates the analysis according to the BGC product and wi
--no_classify
```
By default, BiG-SCAPE classifies the output files analysis based on the BGC product. Toggle to deactivate (note that if the `--mix` parameter is not activated, BiG-SCAPE will not create any network file but all intermetiate files will be processed)
By default, BiG-SCAPE classifies the output files analysis based on the BGC product. Toggle to deactivate (note that if the `--mix` parameter is not activated, BiG-SCAPE will not create any network file but all intermetiate files will be processed)
## Filter classes
......@@ -127,16 +127,16 @@ Generate networks using multiple raw distance cutoff values, example: `--cutoffs
## Clans
```
--clans
--clans-off
```
If activated, BiG-SCAPE will perform a second layer of clustering and attempt to group GCFs assigned from clustering
By default BiG-SCAPE will perform a second layer of clustering and attempt to group GCFs. Toggle to disactivate
```
--clan_cutoff {0.0-1.0}
--clan_cutoff {0.0-1.0} {0.0-1.0}
```
Cutoff Parameters for which clustering families into clans will be performed in raw distance. First value is the GCF cutoff value used in clan clustering (default: 0.5). If this GCF cutoff value is not included within `--cutoffs`, it will be added automatically. Second value is the GCC cutoff value for clustering families into clans (default: 0.8). Average linkage for BGCs in a family is used for distances between families, so, every pair of GCFs linked with an average distance of GCC cutoff value or less will be taken into account. Example: `--clan_cutoff 0.5 0.8`)
Cutoff Parameters for which clustering families into clans will be performed in raw distance. First value is the GCF cutoff value used in clan clustering (default: 0.3). If this GCF cutoff value is not included within `--cutoffs`, it will be added automatically. Second value is the GCC cutoff value for clustering families into clans (default: 0.7). Example: `--clan_cutoff 0.5 0.8`)
Learn more about [GCFs and GCCs](GCFs and GCCs).
......
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