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Input: BiG-SCAPE now accepts antiSMASH 5 files. Parameters: updated parameters authored by Jorge Navarro Muñoz's avatar Jorge Navarro Muñoz
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parameters.md
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......@@ -16,6 +16,7 @@ Type `-h` or `--help` to display all current available options
By default, BiG-SCAPE runs will have a name such as `YYYY-MM-DD_HH-MM-SS_[extra]` where the extra string is `hybrids` (if activated) and the mode (i.e. `glocal`). With the `--label` option, it is possible to add an extra string to the run name. This will be reflected in the dropdown menu in the visualization page.
## Input folder
```
......@@ -24,21 +25,34 @@ By default, BiG-SCAPE runs will have a name such as `YYYY-MM-DD_HH-MM-SS_[extra]
Specify a path with the starting point to look for `.gbk` files. If empty, the search will start where the BiG-SCAPE files are located. The search is recursive. See more information [here](input)
## Exclude string
## Output folder
```
--exclude_gbk_str EXCLUDE_GBK_STR
-o OUTPUTDIR, --outputdir OUTPUTDIR
```
If any string in this list occurs in the filename, this file will not be used for the analysis. (default: 'final')
Output directory, this will contain all output data files. See its structure and more details about each type of result [here](output)
## Output folder
## Include string
```
-o OUTPUTDIR, --outputdir OUTPUTDIR
--include_gbk_str INCLUDE_GBK_STR
```
Output directory, this will contain all output data files. See its structure and more details about each type of result [here](output)
If any string in this list occurs in the filename, this file will be included in the analysis. (default: `cluster, region`)
## Exclude string
```
--exclude_gbk_str EXCLUDE_GBK_STR
```
If any string in this list occurs in the filename, this file will not be used for the analysis. (default: `final`)
## Pfam database
......@@ -48,6 +62,7 @@ Output directory, this will contain all output data files. See its structure and
Location of Pfam files. Default is same location of BiG-SCAPE. See how to prepare these files in the [installation instructions](installation)
## Cores
```
......@@ -56,6 +71,7 @@ Location of Pfam files. Default is same location of BiG-SCAPE. See how to prepar
BiG-SCAPE will try to paralellize some steps in the analysis like domain prediction and distance calculation. Use this option to set the number of cores the script may use. If not specified, BiG-SCAPE will use all available cores.
## Verbose
```
......@@ -68,6 +84,7 @@ Prints more detailed information of each step in the analysis. Toggle to activat
$> python bigscape.py <options> --verbose > run.log &
```
## Include singletons
```
......@@ -76,6 +93,7 @@ $> python bigscape.py <options> --verbose > run.log &
Toggle to activate. This will include BGCs that don't have a distance lower than the cutoff distance specified.
## Domain overlap
```
......@@ -84,6 +102,7 @@ Toggle to activate. This will include BGCs that don't have a distance lower than
Specify at which overlap percentage domains are considered to overlap. Domain with the best score is kept (default=0.1). See also [domain prediction](domain prediction).
## Minimum size
```
......@@ -92,6 +111,7 @@ Specify at which overlap percentage domains are considered to overlap. Domain wi
Provide the minimum size of a BGC to be included in the analysis. Default is 0 base pairs. This includes the sum of all loci in a multi-record GenBank file.
## Mix
```
......@@ -100,6 +120,7 @@ Provide the minimum size of a BGC to be included in the analysis. Default is 0 b
By default, BiG-SCAPE separates the analysis according to the BGC product and will create network directories for each class (see [BiG-SCAPE classes](BiG-SCAPE classes)). Toggle to include an analysis mixing all classes. As BiG-SCAPE needs to calculate an all-vs-all distance network, this might use a lot of memory.
## No classify
```
......@@ -108,6 +129,7 @@ By default, BiG-SCAPE separates the analysis according to the BGC product and wi
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
```
......@@ -116,6 +138,7 @@ By default, BiG-SCAPE classifies the output files analysis based on the BGC prod
BiG-SCAPE Classes that should NOT be included in the classification. E.g. "`--banned_classes PKSI PKSOther`". Strings in lowercase are also allowed.
## Cutoffs
```
......@@ -124,6 +147,7 @@ BiG-SCAPE Classes that should NOT be included in the classification. E.g. "`--ba
Generate networks using multiple raw distance cutoff values, example: `--cutoffs 0.1, 0.25, 0.5, 1.0`. Default: `c=0.3`. For every cutoff value, a different network file will be generated. Regarding the interactive visualization, only the highest cutoff will be shown. Automatic clustering of Gene Cluster Families will be done using each cutoff.
## Clans
```
......@@ -140,6 +164,7 @@ Cutoff Parameters for which clustering families into clans will be performed in
Learn more about [GCFs and GCCs](GCFs and GCCs).
## Hybrids
```
......@@ -148,6 +173,7 @@ Learn more about [GCFs and GCCs](GCFs and GCCs).
By default, BGCs with hybrid predicted products from the PKS/NRPS Hybrids and Others classes will be included into each subclass (e.g. a `terpene-nrps` BGC that will usually be classified in Others would be added to both the Terpene and NRPS classes). This means that the same cluster may appear in different classes. Toggle to deactivate
## Alignment Mode
```
......@@ -155,7 +181,8 @@ By default, BGCs with hybrid predicted products from the PKS/NRPS Hybrids and Ot
```
Alignment mode used when comparing each pair of gene clusters. `global`: the whole list of domains of each BGC are compared; `glocal` (default): Longest Common Subcluster mode. In it, the subset of the domains used to calculate distance is redefined by finding the longest slice of common domain content per gene in both BGCs, then expands each slice. `auto`: use glocal mode when at least one of the BGCs in each pair has the `contig_edge` annotation from antiSMASH v4+, otherwise use global mode on that pair. Learn more about the alignment modes [here](alignment)
## Anchorfile
```
......@@ -163,7 +190,8 @@ Alignment mode used when comparing each pair of gene clusters. `global`: the who
```
Point to a custom anchor file. Default is `anchor_domains.txt`, included in with the repository. Learn more about the anchor file [here](anchor file).
## Force hmmscan
```
......@@ -171,7 +199,8 @@ Point to a custom anchor file. Default is `anchor_domains.txt`, included in with
```
Force domain prediction using `hmmscan` even if BiG-SCAPE finds processed domtable files (e.g. to use a new version of the Pfam database).
## Skip alignment
```
......@@ -180,13 +209,14 @@ Force domain prediction using `hmmscan` even if BiG-SCAPE finds processed domtab
Skip multiple alignment of domains' sequences. Use if alignments have been generated in a previous run. Domain sequence alignment will also be skipped if BiG-SCAPE reutilizes an output directory and no new BGCs are found within the input folder
## MIBiG
```
--mibig
--mibig, --mibig13
```
Use included BGCs from the [MIBiG database](https://mibig.secondarymetabolites.org/). Currently, version 1.3 of the database is included in the BiG-SCAPE project (about 1,400 BGCs) as a compressed file, which will be unzipped the first time the `--mibig` option is used. (Note that this set is different from the bundle found in the downloads section of the MIBiG site; these GenBank files have been processed by antiSMASH to annotate the BGC type and correspond to the files found in each entries' pages)
Use included BGCs from the [MIBiG database](https://mibig.secondarymetabolites.org/). Currently, versions 1.4 (`--mibig`) and 1.3 (`--mibig13`) of the database are included in the BiG-SCAPE project as a compressed file, which will be unzipped the first time the `--mibig` or `--mibig13` option are used. (Note that this set is different from the bundle found in the downloads section of the MIBiG site; these GenBank files have been processed by antiSMASH to annotate the BGC type; they correspond to the files found in each entries' pages)
## Query BGC mode
......