Source code for pypath.inputs.instruct

#!/usr/bin/env python
# -*- coding: utf-8 -*-

#
#  This file is part of the `pypath` python module
#
#  Copyright 2014-2023
#  EMBL, EMBL-EBI, Uniklinik RWTH Aachen, Heidelberg University
#
#  Authors: see the file `README.rst`
#  Contact: Dénes Türei (turei.denes@gmail.com)
#
#  Distributed under the GPLv3 License.
#  See accompanying file LICENSE.txt or copy at
#      https://www.gnu.org/licenses/gpl-3.0.html
#
#  Website: https://pypath.omnipathdb.org/
#

import re

import pypath.resources.urls as urls
import pypath.share.curl as curl




def get_instruct():
    """
    Instruct contains residue numbers in UniProt sequences, it means
    no further calculations of offsets in chains of PDB structures needed.
    Chains are not given, only a set of PDB structures supporting the
    domain-domain // protein-protein interaction.
    """

    non_digit = re.compile(r'[^\d.-]+')
    c = curl.Curl(urls.urls['instruct_human']['url'], silent = False)
    data = c.result

    if data is None:
        return None

    data = data.replace('\r', '').split('\n')
    del data[0]
    instruct = []

    for l in data:
        l = l.split('\t')

        if len(l) > 12:
            domain1 = l[6]
            domain2 = l[7]
            pdb = l[12].split(';')
            uniprot1 = l[0]
            uniprot2 = l[1]
            seq1 = [[non_digit.sub('', n) for n in s.split(',')]
                    for s in l[10].split(';')]
            seq2 = [[non_digit.sub('', n) for n in s.split(',')]
                    for s in l[11].split(';')]
            instruct.append({
                uniprot1: {
                    'pfam': domain1,
                    'chain': None,
                    'seq': seq1
                },
                uniprot2: {
                    'pfam': domain2,
                    'chain': None,
                    'seq': seq2
                },
                'uniprots': [uniprot1, uniprot2],
                'source': 'Instruct',
                'pdb': pdb,
                'references': l[13].split(';')
            })

    return instruct





def get_instruct_offsets():
    """
    These offsets should be understood as from UniProt to PDB.
    """

    non_digit = re.compile(r'[^\d.-]+')
    c = curl.Curl(urls.urls['instruct_offsets']['url'], silent = False)
    data = c.result

    if data is None:
        return None

    data = data.replace('\r', '').split('\n')
    del data[0]
    offsets = {}

    for l in data:
        l = l.split('\t')

        if len(l) > 2:
            pdb = l[0].lower()
            uniprot = l[1]

            try:
                offset = int(non_digit.sub('', l[2]))
                offsets[(pdb, uniprot)] = offset

            except:
                sys.stdout.write('Error processing line:\n')
                sys.stdout.write(l[2])
                sys.stdout.write('\n')
                sys.stdout.flush()

    return offsets