biobb-io 4.0.0__tar.gz → 4.1.1__tar.gz

{biobb_io-4.0.0 → biobb_io-4.1.1}/PKG-INFO

@@ -1,28 +1,31 @@
 Metadata-Version: 2.1
 Name: biobb_io
-Version: 4.0.0
+Version: 4.1.1
 Summary: Biobb_io is the Biobb module collection to fetch data to be consumed by the rest of the Biobb building blocks.
 Home-page: https://github.com/bioexcel/biobb_io
 Author: Biobb developers
 Author-email: pau.andrio@bsc.es
-Project-URL: Documentation, http://biobb_io.readthedocs.io/en/latest/
+Project-URL: Documentation, http://biobb-io.readthedocs.io/en/latest/
 Project-URL: Bioexcel, https://bioexcel.eu/
 Keywords: Bioinformatics Workflows BioExcel Compatibility
 Classifier: Development Status :: 3 - Alpha
-Classifier: Programming Language :: Python :: 3.7
+Classifier: Programming Language :: Python :: 3.8
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
 Classifier: License :: OSI Approved :: Apache Software License
 Classifier: Operating System :: MacOS :: MacOS X
 Classifier: Operating System :: POSIX
-Requires-Python: >=3.7,<3.10
+Requires-Python: >=3.8
 Description-Content-Type: text/markdown
 License-File: LICENSE
+Requires-Dist: biobb_common==4.1.0
 
 [![](https://img.shields.io/github/v/tag/bioexcel/biobb_io?label=Version)](https://GitHub.com/bioexcel/biobb_io/tags/)
 [![](https://img.shields.io/pypi/v/biobb-io.svg?label=Pypi)](https://pypi.python.org/pypi/biobb-io/)
 [![](https://img.shields.io/conda/vn/bioconda/biobb_io?label=Conda)](https://anaconda.org/bioconda/biobb_io)
 [![](https://img.shields.io/conda/dn/bioconda/biobb_io?label=Conda%20Downloads)](https://anaconda.org/bioconda/biobb_io)
 [![](https://img.shields.io/badge/Docker-Quay.io-blue)](https://quay.io/repository/biocontainers/biobb_io?tab=tags)
-[![](https://img.shields.io/badge/Singularity-GalaxyProject-blue)](https://depot.galaxyproject.org/singularity/biobb_io:4.0.0--pyhdfd78af_0)
+[![](https://img.shields.io/badge/Singularity-GalaxyProject-blue)](https://depot.galaxyproject.org/singularity/biobb_io:4.1.1--pyhdfd78af_0)
 
 [![](https://img.shields.io/badge/OS-Unix%20%7C%20MacOS-blue)](https://github.com/bioexcel/biobb_io)
 [![](https://img.shields.io/pypi/pyversions/biobb-io.svg?label=Python%20Versions)](https://pypi.org/project/biobb-io/)
@@ -41,6 +44,13 @@ License-File: LICENSE
 [![](https://img.shields.io/github/last-commit/bioexcel/biobb_io?label=Last%20Commit)](https://github.com/bioexcel/biobb_io/commits/master)
 [![](https://img.shields.io/github/issues/bioexcel/biobb_io.svg?color=brightgreen&label=Issues)](https://GitHub.com/bioexcel/biobb_io/issues/)
 
+[![fair-software.eu](https://img.shields.io/badge/fair--software.eu-%E2%97%8F%20%20%E2%97%8F%20%20%E2%97%8F%20%20%E2%97%8F%20%20%E2%97%8F-green)](https://fair-software.eu)
+[![](https://www.bestpractices.dev/projects/8847/badge)](https://www.bestpractices.dev/projects/8847)
+
+[](https://bestpractices.coreinfrastructure.org/projects/8847/badge)
+
+[//]: # (The previous line invisible link is for compatibility with the howfairis script https://github.com/fair-software/howfairis-github-action/tree/main wich uses the old bestpractices URL)
+
 # biobb_io
 
 ### Introduction
@@ -50,10 +60,10 @@ Biobb (BioExcel building blocks) packages are Python building blocks that
 create new layer of compatibility and interoperability over popular
 bioinformatics tools.
 The latest documentation of this package can be found in our readthedocs site:
-[latest API documentation](http://biobb_io.readthedocs.io/en/latest/).
+[latest API documentation](http://biobb-io.readthedocs.io/en/latest/).
 
 ### Version
-v4.0.0 2023.1
+v4.1.1 2024.1
 
 ### Installation
 Using PIP:
@@ -62,7 +72,7 @@ Using PIP:
 
 * Installation:
 
-        pip install "biobb_io==4.0.0"
+        pip install "biobb_io==4.1.1"
         
 * Usage: [Python API documentation](https://biobb-io.readthedocs.io/en/latest/modules.html)
 
@@ -70,7 +80,7 @@ Using ANACONDA:
 * Installation:
 
 
-        conda install -c bioconda "biobb_io==4.0.0"
+        conda install -c bioconda "biobb_io==4.1.1"
 
 
 * Usage: With conda installation BioBBs can be used with the [Python API documentation](https://biobb-io.readthedocs.io/en/latest/modules.html) and the [Command Line documentation](https://biobb-io.readthedocs.io/en/latest/command_line.html)
@@ -79,12 +89,12 @@ Using DOCKER:
 * Installation:
 
 
-        docker pull quay.io/biocontainers/biobb_io:4.0.0--pyhdfd78af_0
+        docker pull quay.io/biocontainers/biobb_io:4.1.1--pyhdfd78af_0
 
 * Usage:
 
 
-        docker run quay.io/biocontainers/biobb_io:4.0.0--pyhdfd78af_0 <command>
+        docker run quay.io/biocontainers/biobb_io:4.1.1--pyhdfd78af_0 <command>
 
 
 The command list and specification can be found at the [Command Line documentation](https://biobb-io.readthedocs.io/en/latest/command_line.html).
@@ -96,7 +106,7 @@ Using SINGULARITY:
 * Installation:
 
 
-        singularity pull --name biobb_io.sif https://depot.galaxyproject.org/singularity/biobb_io:4.0.0--pyhdfd78af_0
+        singularity pull --name biobb_io.sif https://depot.galaxyproject.org/singularity/biobb_io:4.1.1--pyhdfd78af_0
 
 
 * Usage:
@@ -111,8 +121,8 @@ The command list and specification can be found at the [Command Line documentati
 ### Copyright & Licensing
 This software has been developed in the [MMB group](http://mmb.irbbarcelona.org) at the [BSC](http://www.bsc.es/) & [IRB](https://www.irbbarcelona.org/) for the [European BioExcel](http://bioexcel.eu/), funded by the European Commission (EU H2020 [823830](http://cordis.europa.eu/projects/823830), EU H2020 [675728](http://cordis.europa.eu/projects/675728)).
 
-* (c) 2015-2023 [Barcelona Supercomputing Center](https://www.bsc.es/)
-* (c) 2015-2023 [Institute for Research in Biomedicine](https://www.irbbarcelona.org/)
+* (c) 2015-2024 [Barcelona Supercomputing Center](https://www.bsc.es/)
+* (c) 2015-2024 [Institute for Research in Biomedicine](https://www.irbbarcelona.org/)
 
 Licensed under the
 [Apache License 2.0](https://www.apache.org/licenses/LICENSE-2.0), see the file LICENSE for details.

{biobb_io-4.0.0 → biobb_io-4.1.1}/README.md

@@ -3,7 +3,7 @@
 [![](https://img.shields.io/conda/vn/bioconda/biobb_io?label=Conda)](https://anaconda.org/bioconda/biobb_io)
 [![](https://img.shields.io/conda/dn/bioconda/biobb_io?label=Conda%20Downloads)](https://anaconda.org/bioconda/biobb_io)
 [![](https://img.shields.io/badge/Docker-Quay.io-blue)](https://quay.io/repository/biocontainers/biobb_io?tab=tags)
-[![](https://img.shields.io/badge/Singularity-GalaxyProject-blue)](https://depot.galaxyproject.org/singularity/biobb_io:4.0.0--pyhdfd78af_0)
+[![](https://img.shields.io/badge/Singularity-GalaxyProject-blue)](https://depot.galaxyproject.org/singularity/biobb_io:4.1.1--pyhdfd78af_0)
 
 [![](https://img.shields.io/badge/OS-Unix%20%7C%20MacOS-blue)](https://github.com/bioexcel/biobb_io)
 [![](https://img.shields.io/pypi/pyversions/biobb-io.svg?label=Python%20Versions)](https://pypi.org/project/biobb-io/)
@@ -22,6 +22,13 @@
 [![](https://img.shields.io/github/last-commit/bioexcel/biobb_io?label=Last%20Commit)](https://github.com/bioexcel/biobb_io/commits/master)
 [![](https://img.shields.io/github/issues/bioexcel/biobb_io.svg?color=brightgreen&label=Issues)](https://GitHub.com/bioexcel/biobb_io/issues/)
 
+[![fair-software.eu](https://img.shields.io/badge/fair--software.eu-%E2%97%8F%20%20%E2%97%8F%20%20%E2%97%8F%20%20%E2%97%8F%20%20%E2%97%8F-green)](https://fair-software.eu)
+[![](https://www.bestpractices.dev/projects/8847/badge)](https://www.bestpractices.dev/projects/8847)
+
+[](https://bestpractices.coreinfrastructure.org/projects/8847/badge)
+
+[//]: # (The previous line invisible link is for compatibility with the howfairis script https://github.com/fair-software/howfairis-github-action/tree/main wich uses the old bestpractices URL)
+
 # biobb_io
 
 ### Introduction
@@ -31,10 +38,10 @@ Biobb (BioExcel building blocks) packages are Python building blocks that
 create new layer of compatibility and interoperability over popular
 bioinformatics tools.
 The latest documentation of this package can be found in our readthedocs site:
-[latest API documentation](http://biobb_io.readthedocs.io/en/latest/).
+[latest API documentation](http://biobb-io.readthedocs.io/en/latest/).
 
 ### Version
-v4.0.0 2023.1
+v4.1.1 2024.1
 
 ### Installation
 Using PIP:
@@ -43,7 +50,7 @@ Using PIP:
 
 * Installation:
 
-        pip install "biobb_io==4.0.0"
+        pip install "biobb_io==4.1.1"
         
 * Usage: [Python API documentation](https://biobb-io.readthedocs.io/en/latest/modules.html)
 
@@ -51,7 +58,7 @@ Using ANACONDA:
 * Installation:
 
 
-        conda install -c bioconda "biobb_io==4.0.0"
+        conda install -c bioconda "biobb_io==4.1.1"
 
 
 * Usage: With conda installation BioBBs can be used with the [Python API documentation](https://biobb-io.readthedocs.io/en/latest/modules.html) and the [Command Line documentation](https://biobb-io.readthedocs.io/en/latest/command_line.html)
@@ -60,12 +67,12 @@ Using DOCKER:
 * Installation:
 
 
-        docker pull quay.io/biocontainers/biobb_io:4.0.0--pyhdfd78af_0
+        docker pull quay.io/biocontainers/biobb_io:4.1.1--pyhdfd78af_0
 
 * Usage:
 
 
-        docker run quay.io/biocontainers/biobb_io:4.0.0--pyhdfd78af_0 <command>
+        docker run quay.io/biocontainers/biobb_io:4.1.1--pyhdfd78af_0 <command>
 
 
 The command list and specification can be found at the [Command Line documentation](https://biobb-io.readthedocs.io/en/latest/command_line.html).
@@ -77,7 +84,7 @@ Using SINGULARITY:
 * Installation:
 
 
-        singularity pull --name biobb_io.sif https://depot.galaxyproject.org/singularity/biobb_io:4.0.0--pyhdfd78af_0
+        singularity pull --name biobb_io.sif https://depot.galaxyproject.org/singularity/biobb_io:4.1.1--pyhdfd78af_0
 
 
 * Usage:
@@ -92,8 +99,8 @@ The command list and specification can be found at the [Command Line documentati
 ### Copyright & Licensing
 This software has been developed in the [MMB group](http://mmb.irbbarcelona.org) at the [BSC](http://www.bsc.es/) & [IRB](https://www.irbbarcelona.org/) for the [European BioExcel](http://bioexcel.eu/), funded by the European Commission (EU H2020 [823830](http://cordis.europa.eu/projects/823830), EU H2020 [675728](http://cordis.europa.eu/projects/675728)).
 
-* (c) 2015-2023 [Barcelona Supercomputing Center](https://www.bsc.es/)
-* (c) 2015-2023 [Institute for Research in Biomedicine](https://www.irbbarcelona.org/)
+* (c) 2015-2024 [Barcelona Supercomputing Center](https://www.bsc.es/)
+* (c) 2015-2024 [Institute for Research in Biomedicine](https://www.irbbarcelona.org/)
 
 Licensed under the
 [Apache License 2.0](https://www.apache.org/licenses/LICENSE-2.0), see the file LICENSE for details.

{biobb_io-4.0.0 → biobb_io-4.1.1}/biobb_io/__init__.py

@@ -1,3 +1,3 @@
 name = "biobb_io"
 __all__ = ["api"]
-__version__ = "4.0.0"
+__version__ = "4.1.1"

{biobb_io-4.0.0 → biobb_io-4.1.1}/biobb_io/api/__init__.py

@@ -1,2 +1,2 @@
 name = "api"
-__all__ = ["drugbank", "ligand", "pdb", "alphafold", "pdb_cluster_zip", "pdb_variants", "memprotmd_sim_list", "memprotmd_sim_search", "memprotmd_sim", "api_binding_site","canonical_fasta", "mmcif", "ideal_sdf", "structure_info"]
+__all__ = ["drugbank", "ligand", "pdb", "alphafold", "pdb_cluster_zip", "pdb_variants", "memprotmd_sim_list", "memprotmd_sim_search", "memprotmd_sim", "api_binding_site", "canonical_fasta", "mmcif", "ideal_sdf", "structure_info"]

{biobb_io-4.0.0 → biobb_io-4.1.1}/biobb_io/api/alphafold.py

@@ -3,10 +3,9 @@
 """Module containing the AlphaFold class and the command line interface."""
 import argparse
 from biobb_common.generic.biobb_object import BiobbObject
-from biobb_common.configuration import  settings
-from biobb_common.tools import file_utils as fu
+from biobb_common.configuration import settings
 from biobb_common.tools.file_utils import launchlogger
-from biobb_io.api.common import *
+from biobb_io.api.common import check_output_path, check_mandatory_property, check_uniprot_code, download_af, write_pdb
 
 
 class AlphaFold(BiobbObject):
@@ -26,10 +25,10 @@ class AlphaFold(BiobbObject):
         This is a use example of how to use the building block from Python::
 
             from biobb_io.api.alphafold import alphafold
-            prop = { 
+            prop = {
                 'uniprot_code': 'P00489'
             }
-            alphafold(output_pdb_path='/path/to/newStructure.pdb', 
+            alphafold(output_pdb_path='/path/to/newStructure.pdb',
                 properties=prop)
 
     Info:
@@ -42,8 +41,8 @@ class AlphaFold(BiobbObject):
 
     """
 
-    def __init__(self, output_pdb_path, 
-                properties=None, **kwargs) -> None:
+    def __init__(self, output_pdb_path,
+                 properties=None, **kwargs) -> None:
         properties = properties or {}
 
         # Call parent class constructor
@@ -51,8 +50,8 @@ class AlphaFold(BiobbObject):
         self.locals_var_dict = locals().copy()
 
         # Input/Output files
-        self.io_dict = { 
-            "out": { "output_pdb_path": output_pdb_path } 
+        self.io_dict = {
+            "out": {"output_pdb_path": output_pdb_path}
         }
 
         # Properties specific for BB
@@ -70,13 +69,13 @@ class AlphaFold(BiobbObject):
     @launchlogger
     def launch(self) -> int:
         """Execute the :class:`AlphaFold <api.alphafold.AlphaFold>` api.alphafold.AlphaFold object."""
-        
+
         # check input/output paths and parameters
         self.check_data_params(self.out_log, self.err_log)
 
         # Setup Biobb
-        if self.check_restart(): return 0
-        #self.stage_files()
+        if self.check_restart():
+            return 0
 
         check_mandatory_property(self.uniprot_code, 'uniprot_code', self.out_log, self.__class__.__name__)
 
@@ -92,12 +91,14 @@ class AlphaFold(BiobbObject):
 
         return 0
 
+
 def alphafold(output_pdb_path: str, properties: dict = None, **kwargs) -> int:
     """Execute the :class:`AlphaFold <api.alphafold.AlphaFold>` class and
     execute the :meth:`launch() <api.alphafold.AlphaFold.launch>` method."""
 
     return AlphaFold(output_pdb_path=output_pdb_path,
-                properties=properties, **kwargs).launch()
+                     properties=properties, **kwargs).launch()
+
 
 def main():
     """Command line execution of this building block. Please check the command line documentation."""
@@ -113,8 +114,9 @@ def main():
     properties = settings.ConfReader(config=config).get_prop_dic()
 
     # Specific call of each building block
-    alphafold(output_pdb_path=args.output_pdb_path, 
-        properties=properties)
+    alphafold(output_pdb_path=args.output_pdb_path,
+              properties=properties)
+
 
 if __name__ == '__main__':
     main()

{biobb_io-4.0.0 → biobb_io-4.1.1}/biobb_io/api/api_binding_site.py

@@ -2,11 +2,12 @@
 
 """Module containing the ApiBindingSite class and the command line interface."""
 import argparse
+import json
 from biobb_common.generic.biobb_object import BiobbObject
-from biobb_common.configuration import  settings
+from biobb_common.configuration import settings
 from biobb_common.tools import file_utils as fu
 from biobb_common.tools.file_utils import launchlogger
-from biobb_io.api.common import *
+from biobb_io.api.common import check_output_path, check_mandatory_property, download_binding_site, write_json
 
 
 class ApiBindingSite(BiobbObject):
@@ -26,10 +27,10 @@ class ApiBindingSite(BiobbObject):
         This is a use example of how to use the building block from Python::
 
             from biobb_io.api.api_binding_site import api_binding_site
-            prop = { 
-                'pdb_code': '4i23' 
+            prop = {
+                'pdb_code': '4i23'
             }
-            api_binding_site(output_json_path='/path/to/newBindingSites.json', 
+            api_binding_site(output_json_path='/path/to/newBindingSites.json',
                     properties=prop)
 
     Info:
@@ -42,8 +43,8 @@ class ApiBindingSite(BiobbObject):
 
     """
 
-    def __init__(self, output_json_path, 
-                properties=None, **kwargs) -> None:
+    def __init__(self, output_json_path,
+                 properties=None, **kwargs) -> None:
         properties = properties or {}
 
         # Call parent class constructor
@@ -51,8 +52,8 @@ class ApiBindingSite(BiobbObject):
         self.locals_var_dict = locals().copy()
 
         # Input/Output files
-        self.io_dict = { 
-            "out": { "output_json_path": output_json_path } 
+        self.io_dict = {
+            "out": {"output_json_path": output_json_path}
         }
 
         # Properties specific for BB
@@ -62,7 +63,7 @@ class ApiBindingSite(BiobbObject):
         # Check the properties
         self.check_properties(properties)
         self.check_arguments()
-        
+
     def check_data_params(self, out_log, err_log):
         """ Checks all the input/output paths and parameters """
         self.output_json_path = check_output_path(self.io_dict["out"]["output_json_path"], "output_json_path", False, out_log, self.__class__.__name__)
@@ -75,8 +76,9 @@ class ApiBindingSite(BiobbObject):
         self.check_data_params(self.out_log, self.err_log)
 
         # Setup Biobb
-        if self.check_restart(): return 0
-        #self.stage_files()
+        if self.check_restart():
+            return 0
+        # self.stage_files()
 
         check_mandatory_property(self.pdb_code, 'pdb_code', self.out_log, self.__class__.__name__)
 
@@ -96,19 +98,21 @@ class ApiBindingSite(BiobbObject):
 
         return 0
 
+
 def api_binding_site(output_json_path: str, properties: dict = None, **kwargs) -> int:
     """Execute the :class:`ApiBindingSite <api.api_binding_site.ApiBindingSite>` class and
     execute the :meth:`launch() <api.api_binding_site.ApiBindingSite.launch>` method."""
 
     return ApiBindingSite(output_json_path=output_json_path,
-                    properties=properties, **kwargs).launch()
+                          properties=properties, **kwargs).launch()
+
 
 def main():
     """Command line execution of this building block. Please check the command line documentation."""
     parser = argparse.ArgumentParser(description="This class is a wrapper for the PDBe REST API Binding Sites endpoint", formatter_class=lambda prog: argparse.RawTextHelpFormatter(prog, width=99999))
     parser.add_argument('-c', '--config', required=False, help="This file can be a YAML file, JSON file or JSON string")
 
-    #Specific args of each building block
+    # Specific args of each building block
     required_args = parser.add_argument_group('required arguments')
     required_args.add_argument('-o', '--output_json_path', required=True, help="Path to the JSON file with the binding sites for the requested structure. Accepted formats: json.")
 
@@ -116,9 +120,10 @@ def main():
     config = args.config if args.config else None
     properties = settings.ConfReader(config=config).get_prop_dic()
 
-    #Specific call of each building block
-    api_binding_site(output_json_path=args.output_json_path, 
-            properties=properties)
+    # Specific call of each building block
+    api_binding_site(output_json_path=args.output_json_path,
+                     properties=properties)
+
 
 if __name__ == '__main__':
     main()

{biobb_io-4.0.0 → biobb_io-4.1.1}/biobb_io/api/canonical_fasta.py

@@ -3,10 +3,9 @@
 """Module containing the CanonicalFasta class and the command line interface."""
 import argparse
 from biobb_common.generic.biobb_object import BiobbObject
-from biobb_common.configuration import  settings
-from biobb_common.tools import file_utils as fu
+from biobb_common.configuration import settings
 from biobb_common.tools.file_utils import launchlogger
-from biobb_io.api.common import *
+from biobb_io.api.common import check_output_path, check_mandatory_property, download_fasta, write_fasta
 
 
 class CanonicalFasta(BiobbObject):
@@ -27,11 +26,11 @@ class CanonicalFasta(BiobbObject):
         This is a use example of how to use the building block from Python::
 
             from biobb_io.api.canonical_fasta import canonical_fasta
-            prop = { 
+            prop = {
                 'pdb_code': '4i23',
                 'api_id': 'pdb'
             }
-            canonical_fasta(output_fasta_path='/path/to/newFasta.fasta', 
+            canonical_fasta(output_fasta_path='/path/to/newFasta.fasta',
                     properties=prop)
 
     Info:
@@ -44,8 +43,8 @@ class CanonicalFasta(BiobbObject):
 
     """
 
-    def __init__(self, output_fasta_path, 
-                properties=None, **kwargs) -> None:
+    def __init__(self, output_fasta_path,
+                 properties=None, **kwargs) -> None:
         properties = properties or {}
 
         # Call parent class constructor
@@ -53,8 +52,8 @@ class CanonicalFasta(BiobbObject):
         self.locals_var_dict = locals().copy()
 
         # Input/Output files
-        self.io_dict = { 
-            "out": { "output_fasta_path": output_fasta_path } 
+        self.io_dict = {
+            "out": {"output_fasta_path": output_fasta_path}
         }
 
         # Properties specific for BB
@@ -65,7 +64,7 @@ class CanonicalFasta(BiobbObject):
         # Check the properties
         self.check_properties(properties)
         self.check_arguments()
-        
+
     def check_data_params(self, out_log, err_log):
         """ Checks all the input/output paths and parameters """
         self.output_fasta_path = check_output_path(self.io_dict["out"]["output_fasta_path"], "output_fasta_path", False, out_log, self.__class__.__name__)
@@ -78,8 +77,8 @@ class CanonicalFasta(BiobbObject):
         self.check_data_params(self.out_log, self.err_log)
 
         # Setup Biobb
-        if self.check_restart(): return 0
-        #self.stage_files()
+        if self.check_restart():
+            return 0
 
         check_mandatory_property(self.pdb_code, 'pdb_code', self.out_log, self.__class__.__name__)
 
@@ -93,19 +92,21 @@ class CanonicalFasta(BiobbObject):
 
         return 0
 
+
 def canonical_fasta(output_fasta_path: str, properties: dict = None, **kwargs) -> int:
     """Execute the :class:`CanonicalFasta <api.canonical_fasta.CanonicalFasta>` class and
     execute the :meth:`launch() <api.canonical_fasta.CanonicalFasta.launch>` method."""
 
     return CanonicalFasta(output_fasta_path=output_fasta_path,
-                    properties=properties, **kwargs).launch()
+                          properties=properties, **kwargs).launch()
+
 
 def main():
     """Command line execution of this building block. Please check the command line documentation."""
     parser = argparse.ArgumentParser(description="This class is a wrapper for downloading a FASTA structure from the Protein Data Bank.", formatter_class=lambda prog: argparse.RawTextHelpFormatter(prog, width=99999))
     parser.add_argument('-c', '--config', required=False, help="This file can be a YAML file, JSON file or JSON string")
 
-    #Specific args of each building block
+    # Specific args of each building block
     required_args = parser.add_argument_group('required arguments')
     required_args.add_argument('-o', '--output_fasta_path', required=True, help="Path to the canonical FASTA file. Accepted formats: fasta.")
 
@@ -113,9 +114,10 @@ def main():
     config = args.config if args.config else None
     properties = settings.ConfReader(config=config).get_prop_dic()
 
-    #Specific call of each building block
-    canonical_fasta(output_fasta_path=args.output_fasta_path, 
-            properties=properties)
+    # Specific call of each building block
+    canonical_fasta(output_fasta_path=args.output_fasta_path,
+                    properties=properties)
+
 
 if __name__ == '__main__':
     main()