Commit 7ee04ac6 authored by Jorge Navarro Muñoz's avatar Jorge Navarro Muñoz
Browse files

Remove unused --skip_all parameter

parent 1415b5b2
# BiG-SCAPE installation
Although each library could be installed on its own, the use of a virtual
environment is highly recommended. Here is a quick guide of BiG-SCAPE
installation using Miniconda
* Install [Miniconda](https://conda.io/miniconda.html). This will install Python 2 as default for all new conda environments. You'll need to re-log for the changes to go into effect.
```
> wget https://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh
> chmod u+x Miniconda2-latest-Linux-x86_64.sh
> ./Miniconda2-latest-Linux-x86_64.sh
```
* Create new environmnent (you can choose Python 3 using ``python=3`` at the end of the next command):
```
> conda create --name bigscape
```
* Activate new environmnent
```
> source activate bigscape
```
* Install packages:
```
> conda install numpy scipy scikit-learn
> conda install -c bioconda hmmer biopython mafft fasttree
> conda install -c anaconda networkx
```
......@@ -1928,6 +1928,12 @@ def CMD_parser():
help="Input directory of gbk files, if left empty, all \
gbk files in current and lower directories will be used.")
parser.add_argument("--exclude_gbk_str", dest="exclude_gbk_str",
default="final", nargs="+",
help="If any string in this list occurs in the gbk \
filename, this file will not be used for the analysis.\
(default: final)")
parser.add_argument("-o", "--outputdir", dest="outputdir", default="",
required=True, help="Output directory, this will contain \
all output data files.")
......@@ -1980,7 +1986,13 @@ def CMD_parser():
help="Classes that should NOT be included in the \
classification. E.g. \"--banned_classes PKSI PKSOther\"")
parser.add_argument("--cutoffs", dest="cutoffs", nargs="+", default=[0.10,
0.15, 0.20, 0.25, 0.30, 0.35, 0.40, 0.45, 0.50, 0.55, 0.60,
0.65, 0.70, 0.75, 0.80], type=float, choices=[FloatRange(0.0,
1.0)], help="Generate networks using multiple raw distance \
cutoff values, example: --cutoffs 0.1, 0.25, 0.5, 1.0. Default: \
all values from 0.10 to 0.80 with 0.05 intervals.")
parser.add_argument("--clans", dest="clans",action="store_true",
default=False, help="BiG-SCAPE will perform a second \
layer of clustering and attempt to group families \
......@@ -2001,7 +2013,7 @@ def CMD_parser():
default=False, help="Toggle to also add BGCs with hybrid\
predicted products from the PKS/NRPS Hybrids and Others\
classes to each subclass (e.g. a 'terpene-nrps' BGC from\
Others would be added to the Terpene and NRPS classes")
Others would be added to the Terpene and NRPS classes)")
parser.add_argument("--mode", dest="mode", default="global", choices=["global",
"lcs", "auto"], help="Alignment mode for each pair of\
......@@ -2019,12 +2031,6 @@ def CMD_parser():
default=os.path.join(os.path.dirname(os.path.realpath(__file__)),"anchor_domains.txt"),
help="Provide a custom location for the anchor domains \
file, default is anchor_domains.txt.")
parser.add_argument("--exclude_gbk_str", dest="exclude_gbk_str",
default="final", nargs="+",
help="If any string in this list occurs in the gbk \
filename, this file will not be used for the analysis.\
(default: final)")
parser.add_argument("--force_hmmscan", dest="force_hmmscan", action="store_true",
default=False, help="Force domain prediction using \
......@@ -2034,14 +2040,7 @@ def CMD_parser():
default=False, help="Skip multiple alignment of domains'\
sequences. Use if alignments have been generated in a \
previous run.")
parser.add_argument("--skip_all", dest="skip_all", action="store_true",
default = False, help ="Only generate new network files.")
parser.add_argument("--cutoffs", dest="cutoffs", nargs="+", default=[0.10,
0.15, 0.20, 0.25, 0.30, 0.35, 0.40, 0.45, 0.50, 0.55, 0.60,
0.65, 0.70, 0.75, 0.80], type=float, choices=[FloatRange(0.0,
1.0)], help="Generate networks using multiple raw distance \
cutoff values, example: --cutoffs 0.1, 0.25, 0.5, 1.0. Default: \
all values from 0.10 to 0.80 with 0.05 intervals.")
parser.add_argument("--mibig", dest="use_relevant_mibig", action=
"store_true", default=False, help="Use included BGCs from MIBiG bundle\
(version 1.3). See https://mibig.secondarymetabolites.org/")
......@@ -2193,11 +2192,6 @@ if __name__=="__main__":
else:
run_mode_string += "_full"
if options.skip_all and options.skip_ma:
print("Overriding --skip_ma with --skip_all parameter")
options.skip_hmmscan = False
options.skip_ma = False
time1 = time.time()
start_time = time.localtime()
......
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