#!/usr/bin/env python
"""PdbVariants Module"""
import re
import argparse
import requests
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.tools.file_utils import launchlogger
from biobb_io.api.common import check_mandatory_property, check_output_path, get_uniprot, get_variants
[docs]class PdbVariants(BiobbObject):
"""
| biobb_io PdbVariants
| This class creates a text file containing a list of all the variants mapped to a PDB code from the corresponding UNIPROT entries.
| Wrapper for the `UNIPROT <http://www.uniprot.org/>`_ mirror of the `MMB group REST API <http://mmb.irbbarcelona.org/api/>`_ for creating a list of all the variants mapped to a PDB code from the corresponding UNIPROT entries.
Args:
output_mutations_list_txt (str): Path to the TXT file containing an ASCII comma separated values of the mutations. File type: output. `Sample file <https://github.com/bioexcel/biobb_io/raw/master/biobb_io/test/reference/api/output_pdb_variants.txt>`_. Accepted formats: txt (edam:format_2330).
properties (dic - Python dictionary object containing the tool parameters, not input/output files):
* **pdb_code** (*str*) - (None) RSCB PDB four letter code.
* **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.
* **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.
Examples:
This is a use example of how to use the PdbVariants module from Python
from biobb_io.api.pdb_variants import pdb_variants
prop = {
'pdb_code': '2VGB'
}
pdb_variants(output_mutations_list_txt='/path/to/newMutationsList.txt',
properties=prop)
Info:
* wrapped_software:
* name: UNIPROT
* license: Creative Commons
* ontology:
* name: EDAM
* schema: http://edamontology.org/EDAM.owl
"""
def __init__(self, output_mutations_list_txt,
properties=None, **kwargs) -> None:
properties = properties or {}
# Call parent class constructor
super().__init__(properties)
self.locals_var_dict = locals().copy()
# Input/Output files
self.io_dict = {
"out": {"output_mutations_list_txt": output_mutations_list_txt}
}
# Properties specific for BB
self.pdb_code = properties.get('pdb_code', None)
self.properties = properties
# Check the properties
self.check_properties(properties)
self.check_arguments()
[docs] def check_data_params(self, out_log, err_log):
""" Checks all the input/output paths and parameters """
self.output_mutations_list_txt = check_output_path(self.io_dict["out"]["output_mutations_list_txt"], "output_mutations_list_txt", False, out_log, self.__class__.__name__)
[docs] @launchlogger
def launch(self) -> int:
"""Execute the :class:`PdbVariants <api.pdb_variants.PdbVariants>` api.pdb_variants.PdbVariants 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
check_mandatory_property(self.pdb_code, 'pdb_code', self.out_log, self.__class__.__name__)
self.pdb_code = self.pdb_code.strip().lower()
url = 'http://mmb.irbbarcelona.org/api'
uniprot_id = get_uniprot(self.pdb_code, url, self.out_log, self.global_log)
url_mapPDBRes = (url+"/uniprot/"+uniprot_id+"/mapPDBRes?pdbId="+self.pdb_code)
pattern = re.compile((r"p.(?P<wt>[a-zA-Z]{3})(?P<resnum>\d+)(?P<mt>[a-zA-Z]{3})"))
fu.log('Fetching variants for uniprot_id: %s and pdb_code: %s' % (uniprot_id, self.pdb_code), self.out_log, self.global_log)
unfiltered_dic = requests.get(url_mapPDBRes, verify=False).json()
if not unfiltered_dic:
fu.log("No mutation found", self.out_log, self.global_log)
return None
mapdic = requests.get(url_mapPDBRes, verify=False).json()
mutations = []
uniprot_var_list = get_variants(uniprot_id, url, self.out_log, self.global_log)
for var in uniprot_var_list:
uni_mut = pattern.match(var).groupdict()
for k in mapdic.keys():
for fragment in mapdic[k]:
if int(fragment['unp_start']) <= int(uni_mut['resnum']) <= int(fragment['unp_end']):
resnum = int(uni_mut['resnum']) + int(fragment['pdb_start']) - int(fragment['unp_start'])
mutations.append(k[-1]+'.'+uni_mut['wt']+str(resnum)+uni_mut['mt'])
fu.log('Found %d mutations mapped to PDB: %s' % (len(mutations), self.pdb_code), self.out_log, self.global_log)
fu.log('Writting mutations to: %s' % self.output_mutations_list_txt, self.out_log, self.global_log)
with open(self.output_mutations_list_txt, 'w') as mut_file:
mutations.sort()
mut_file.write(",".join(mutations))
self.check_arguments(output_files_created=True, raise_exception=False)
return 0
[docs]def pdb_variants(output_mutations_list_txt: str, properties: dict = None, **kwargs) -> int:
"""Execute the :class:`PdbVariants <api.pdb_variants.PdbVariants>` class and
execute the :meth:`launch() <api.pdb_variants.PdbVariants.launch>` method."""
return PdbVariants(output_mutations_list_txt=output_mutations_list_txt,
properties=properties, **kwargs).launch()
[docs]def main():
"""Command line execution of this building block. Please check the command line documentation."""
parser = argparse.ArgumentParser(description="Wrapper for the UNIPROT (http://www.uniprot.org/) mirror of the MMB group REST API (http://mmb.irbbarcelona.org/api/) for creating a list of all the variants mapped to a PDB code from the corresponding UNIPROT entries.", 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
required_args = parser.add_argument_group('required arguments')
required_args.add_argument('-o', '--output_mutations_list_txt', required=True, help="Path to the TXT file containing an ASCII comma separated values of the mutations. Accepted formats: txt.")
args = parser.parse_args()
config = args.config if args.config else None
properties = settings.ConfReader(config=config).get_prop_dic()
# Specific call of each building block
pdb_variants(output_mutations_list_txt=args.output_mutations_list_txt,
properties=properties)
if __name__ == '__main__':
main()