#!/usr/bin/env python
"""PdbVariants Module"""
import re
import requests
from typing import Optional
from biobb_common.generic.biobb_object import BiobbObject
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 <https://mdb-login.bsc.es/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.
* **sandbox_path** (*str*) - ("./") [WF property] Parent path to the sandbox directory.
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 = "https://mdb-login.bsc.es/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=True).json()
if not unfiltered_dic:
fu.log("No mutation found", self.out_log, self.global_log)
return 1
mapdic = requests.get(url_mapPDBRes, verify=True).json()
mutations = []
uniprot_var_list = get_variants(uniprot_id, url, self.out_log, self.global_log)
for var in uniprot_var_list:
match = pattern.match(var)
if match:
uni_mut = match.groupdict()
else:
continue
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,
)
if not self.output_mutations_list_txt:
raise ValueError("Output mutations list file path is not specified.")
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: Optional[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(**dict(locals())).launch()
pdb_variants.__doc__ = PdbVariants.__doc__
main = PdbVariants.get_main(pdb_variants, "Wrapper for the UNIPROT (http://www.uniprot.org/) mirror of the MMB group REST API (https://mdb-login.bsc.es/api/) for creating a list of all the variants mapped to a PDB code from the corresponding UNIPROT entries.")
if __name__ == "__main__":
main()