Coverage for biobb_io/api/pdb_variants.py: 81%
72 statements
« prev ^ index » next coverage.py v7.6.10, created at 2025-01-21 16:46 +0000
1#!/usr/bin/env python
3"""PdbVariants Module"""
5import argparse
6import re
7from typing import Optional
9import requests
10from biobb_common.configuration import settings
11from biobb_common.generic.biobb_object import BiobbObject
12from biobb_common.tools import file_utils as fu
13from biobb_common.tools.file_utils import launchlogger
15from biobb_io.api.common import (
16 check_mandatory_property,
17 check_output_path,
18 get_uniprot,
19 get_variants,
20)
23class PdbVariants(BiobbObject):
24 """
25 | biobb_io PdbVariants
26 | This class creates a text file containing a list of all the variants mapped to a PDB code from the corresponding UNIPROT entries.
27 | 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.
29 Args:
30 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).
31 properties (dic - Python dictionary object containing the tool parameters, not input/output files):
32 * **pdb_code** (*str*) - (None) RSCB PDB four letter code.
33 * **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.
34 * **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.
35 * **sandbox_path** (*str*) - ("./") [WF property] Parent path to the sandbox directory.
37 Examples:
38 This is a use example of how to use the PdbVariants module from Python
40 from biobb_io.api.pdb_variants import pdb_variants
41 prop = {
42 'pdb_code': '2VGB'
43 }
44 pdb_variants(output_mutations_list_txt='/path/to/newMutationslist.txt',
45 properties=prop)
47 Info:
48 * wrapped_software:
49 * name: UNIPROT
50 * license: Creative Commons
51 * ontology:
52 * name: EDAM
53 * schema: http://edamontology.org/EDAM.owl
55 """
57 def __init__(self, output_mutations_list_txt, properties=None, **kwargs) -> None:
58 properties = properties or {}
60 # Call parent class constructor
61 super().__init__(properties)
62 self.locals_var_dict = locals().copy()
64 # Input/Output files
65 self.io_dict = {"out": {"output_mutations_list_txt": output_mutations_list_txt}}
67 # Properties specific for BB
68 self.pdb_code = properties.get("pdb_code", None)
69 self.properties = properties
71 # Check the properties
72 self.check_properties(properties)
73 self.check_arguments()
75 def check_data_params(self, out_log, err_log):
76 """Checks all the input/output paths and parameters"""
77 self.output_mutations_list_txt = check_output_path(
78 self.io_dict["out"]["output_mutations_list_txt"],
79 "output_mutations_list_txt",
80 False,
81 out_log,
82 self.__class__.__name__,
83 )
85 @launchlogger
86 def launch(self) -> int:
87 """Execute the :class:`PdbVariants <api.pdb_variants.PdbVariants>` api.pdb_variants.PdbVariants object."""
89 # check input/output paths and parameters
90 self.check_data_params(self.out_log, self.err_log)
92 # Setup Biobb
93 if self.check_restart():
94 return 0
96 check_mandatory_property(
97 self.pdb_code, "pdb_code", self.out_log, self.__class__.__name__
98 )
100 self.pdb_code = self.pdb_code.strip().lower()
102 url = "http://mmb.irbbarcelona.org/api"
103 uniprot_id = get_uniprot(self.pdb_code, url, self.out_log, self.global_log)
104 url_mapPDBRes = (
105 url + "/uniprot/" + uniprot_id + "/mapPDBRes?pdbId=" + self.pdb_code
106 )
107 pattern = re.compile(
108 (r"p.(?P<wt>[a-zA-Z]{3})(?P<resnum>\d+)(?P<mt>[a-zA-Z]{3})")
109 )
111 fu.log(
112 "Fetching variants for uniprot_id: %s and pdb_code: %s"
113 % (uniprot_id, self.pdb_code),
114 self.out_log,
115 self.global_log,
116 )
117 unfiltered_dic = requests.get(url_mapPDBRes, verify=True).json()
118 if not unfiltered_dic:
119 fu.log("No mutation found", self.out_log, self.global_log)
120 return 1
122 mapdic = requests.get(url_mapPDBRes, verify=True).json()
123 mutations = []
124 uniprot_var_list = get_variants(uniprot_id, url, self.out_log, self.global_log)
125 for var in uniprot_var_list:
126 match = pattern.match(var)
127 if match:
128 uni_mut = match.groupdict()
129 else:
130 continue
131 for k in mapdic.keys():
132 for fragment in mapdic[k]:
133 if (
134 int(fragment["unp_start"]) <= int(uni_mut["resnum"]) <= int(fragment["unp_end"])
135 ):
136 resnum = (
137 int(uni_mut["resnum"]) + int(fragment["pdb_start"]) - int(fragment["unp_start"])
138 )
139 mutations.append(
140 k[-1] + "." + uni_mut["wt"] + str(resnum) + uni_mut["mt"]
141 )
143 fu.log(
144 "Found %d mutations mapped to PDB: %s" % (len(mutations), self.pdb_code),
145 self.out_log,
146 self.global_log,
147 )
148 fu.log(
149 "Writting mutations to: %s" % self.output_mutations_list_txt,
150 self.out_log,
151 self.global_log,
152 )
154 if not self.output_mutations_list_txt:
155 raise ValueError("Output mutations list file path is not specified.")
157 with open(self.output_mutations_list_txt, "w") as mut_file:
158 mutations.sort()
159 mut_file.write(",".join(mutations))
161 self.check_arguments(output_files_created=True, raise_exception=False)
163 return 0
166def pdb_variants(
167 output_mutations_list_txt: str, properties: Optional[dict] = None, **kwargs
168) -> int:
169 """Execute the :class:`PdbVariants <api.pdb_variants.PdbVariants>` class and
170 execute the :meth:`launch() <api.pdb_variants.PdbVariants.launch>` method."""
172 return PdbVariants(
173 output_mutations_list_txt=output_mutations_list_txt,
174 properties=properties,
175 **kwargs,
176 ).launch()
179def main():
180 """Command line execution of this building block. Please check the command line documentation."""
181 parser = argparse.ArgumentParser(
182 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.",
183 formatter_class=lambda prog: argparse.RawTextHelpFormatter(prog, width=99999),
184 )
185 parser.add_argument(
186 "-c",
187 "--config",
188 required=False,
189 help="This file can be a YAML file, JSON file or JSON string",
190 )
192 # Specific args of each building block
193 required_args = parser.add_argument_group("required arguments")
194 required_args.add_argument(
195 "-o",
196 "--output_mutations_list_txt",
197 required=True,
198 help="Path to the TXT file containing an ASCII comma separated values of the mutations. Accepted formats: txt.",
199 )
201 args = parser.parse_args()
202 config = args.config if args.config else None
203 properties = settings.ConfReader(config=config).get_prop_dic()
205 # Specific call of each building block
206 pdb_variants(
207 output_mutations_list_txt=args.output_mutations_list_txt, properties=properties
208 )
211if __name__ == "__main__":
212 main()