# AUTOGENERATED! DO NOT EDIT! File to edit: nbs/Uniprot_integration.ipynb (unless otherwise specified).

__all__ = ['extract_note', 'extract_note_end', 'resolve_unclear_position', 'extract_positions', 'preprocess_uniprot',
           'uniprot_feature_dict']

# Cell
import re

import pandas as pd
import numpy as np

# Cell
def extract_note(string: str, splitted:bool = False):
    """
    Helper function to extract information about note of the protein from Uniprot using regular expression.

    Args:
        string (str): Uniprot annotation string.
        splitted (bool, optional): Flag to allow linebreaks. Default is 'False'.
    Returns:
        str: Extracted string of the uniprot note section.
    """
    if not splitted:
        regex = r"\/note=\"(?P<note>.+?)\""
    else:
        regex = r"\/note=\"(?P<note>.*)"
    result = re.findall(regex, string)
    return result

def extract_note_end(string: str, has_mark:bool = True):
    """
    Helper function to extract information about note of the protein from Uniprot using regular expression.

    Args:
        string (str): Uniprot annotation string.
        has_mark (bool, optional): Flag if end quotation marks are present. Default is 'False'.
    Returns:
        str: Extracted string of the uniprot note section.
    """
    if has_mark:
        regex = r"FT\s+(?P<note>.*)\""
    else:
        regex = r"FT\s+(?P<note>.*)"
    result = re.findall(regex, string)
    return result

# Cell
def resolve_unclear_position(value: str):
    """
    Replace unclear position of the start/end of the modification defined as '?' with -1 and if it's defined as '?N'
    or ">N" - by removing the '?'/'>'/'<' signs.

    Args:
        value (str): Unclear sequence position from uniprot.
    Returns:
        float: Resolved sequence position.
    """
    # if it's "1..?" or "?..345" for start or end -> remove -1 that we can filter later
    # if it's "31..?327" or "?31..327" -> remove the question mark
    # if it's "<1..106" or "22..>115" -> remove the "<" or ">" signs
    if value == '?':
        return -1
    value = value.replace('?', '').replace('>', '').replace('<', '')
    return float(value)

def extract_positions(posit_string: str):
    """
    Extract isoform_id(str) and start/end positions(float) of any feature key from the string.

    Args:
        posit_string (str): Uniprot position string.
    Returns:
        [str, float, float]: str: Uniprot isoform accession, float: start position, float: end position
    """
    isoform = ''
    start = end = np.nan
    if '..' in posit_string:
        start, end = posit_string.split('..')
    if ':' in posit_string:
        if isinstance(start, str):
            isoform, start = start.split(':')
        else:
            isoform, start = posit_string.split(':')
    # in the case when we have only one numeric value as a posit_string
    if isinstance(start, float):
        start = posit_string
    # change the type of start and end into int/float(np.nan)
    if isinstance(start, str):
        start = resolve_unclear_position(start)
    if isinstance(end, str):
        end = resolve_unclear_position(end)
    return isoform, start, end

# Cell
def preprocess_uniprot(path_to_file: str):
    """
    A complex complete function to preprocess Uniprot data from specifying the path to a flat text file
    to the returning a dataframe containing information about:
        - protein_id(str)
        - feature(category)
        - isoform_id(str)
        - start(float)
        - end(float)
        - note information(str)

    Args:
        path_to_file (str): Path to a .txt annotation file directly downloaded from uniprot.
    Returns:
        pd.DataFrame: Dataframe with formatted uniprot annotations for alphamap.

    """
    all_data = []
    with open(path_to_file) as f:

        is_splitted = False
        new_instance = False
        combined_note = []
        line_type = ''

        for line in f:

            if line.startswith(('AC', 'FT')):
                if is_splitted:
                    # in case when the note information is splitted into several lines
                    if line.rstrip().endswith('"'):
                        # if it's the final part of the note
                        combined_note.extend(extract_note_end(line))
                        all_data.append([protein_id, feature, isoform, start, end, " ".join(combined_note)])
                        is_splitted = False
                        new_instance = False
                    else:
                        # if it's the middle part of the note
                        combined_note.extend(extract_note_end(line, has_mark=False))
                elif line.startswith('AC'):
                    # contains the protein_id information
                    if line_type != 'AC':
                        # to prevent a situation when the protein has several AC lines with different names
                        # in this case we are taking the first name in the first line
                        protein_id = line.split()[1].replace(';', '')
                    line_type = 'AC'
                elif line.startswith('FT'):
                    line_type = 'FT'
                    # contains all modifications/preprocessing events/etc., their positions, notes
                    data = line.split()
                    if data[1].isupper() and not data[1].startswith('ECO'):
                            feature = data[1]
                            isoform, start, end = extract_positions(data[2])
                            new_instance = True
                    else:
                        if data[1].startswith('/note'):
                            note = extract_note(line)
                            if note:
                                # if note was created > it contains just one line and can be already added to the data
                                all_data.append([protein_id, feature, isoform, start, end, note[0]])
                                new_instance = False
                            else:
                                # if note is empty > it's splitted into several lines and we create combined_note
                                combined_note = extract_note(line, splitted=True)
                                is_splitted = True
                        else:
                            if new_instance:
                                # in case when we don't have any note but need to add other information about instance
                                all_data.append([protein_id, feature, isoform, start, end, ''])
                                new_instance = False

    # create a dataframe for preprocessed data
    uniprot_df = pd.DataFrame(all_data, columns=['protein_id', 'feature', 'isoform_id', 'start', 'end', 'note'])
    # change the dtypes of the columns
    uniprot_df.feature = uniprot_df.feature.astype('category')
    # to filter the instances that don't have a defined start/end position(start=-1 or end=-1)
    uniprot_df = uniprot_df[(uniprot_df.start != -1) & (uniprot_df.end != -1)].reset_index(drop=True)

    return uniprot_df

# Cell
uniprot_feature_dict = {
    'Chain': 'CHAIN',
    'Initiator methionine': 'INIT_MET',
    'Peptide': 'PEPTIDE',
    'Propeptide': 'PROPEP',
    'Signal peptide': 'SIGNAL',
    'Transit peptide': 'TRANSIT',
    'Cross-link': 'CROSSLNK',
    'Disulfide bond': 'DISULFID',
    'Glycosylation': 'CARBOHYD',
    'Lipidation': 'LIPID',
    'Modified residue': 'MOD_RES',
    'Coiled coil': 'COILED',
    'Compositional bias': 'COMPBIAS',
    'Domain': 'DOMAIN',
    'Motif': 'MOTIF',
    'Region': 'REGION',
    'Repeat': 'REPEAT',
    'Zinc finger': 'ZN_FING',
    'Intramembrane': 'INTRAMEM',
    'Topological domain': 'TOPO_DOM',
    'Transmembrane': 'TRANSMEM',
    'Beta strand': 'STRAND',
    'Helix': 'HELIX',
    'Turn': 'TURN',
    'Active site': 'ACT_SITE',
    'Binding site': 'BINDING',
    'Calcium binding': 'CA_BIND',
    'DNA binding': 'DNA_BIND',
    'Metal binding': 'METAL',
    'Nucleotide binding': 'NP_BIND',
    'Site': 'SITE',
    'Non-standard residue': 'NON_STD',
    'Non-adjacent residues': 'NON_CONS',
    'Non-terminal residue': 'NON_TER',
    'Natural variant': 'VARIANT',
    'Sequence conflict': 'CONFLICT',
    'Alternative sequence': 'VAR_SEQ',
    'Sequence uncertainty': 'UNSURE',
    'Secondary structure': 'STRUCTURE',
    'Mutagenesis': 'MUTAGEN'
}
# AUTOGENERATED! DO NOT EDIT! File to edit: nbs/Uniprot_integration.ipynb (unless otherwise specified).

__all__ = ['extract_note', 'extract_note_end', 'resolve_unclear_position', 'extract_positions', 'preprocess_uniprot',
           'uniprot_feature_dict']

# Cell
import re

import pandas as pd
import numpy as np

# Cell
def extract_note(string: str, splitted:bool = False):
    """
    Helper function to extract information about note of the protein from Uniprot using regular expression.

    Args:
        string (str): Uniprot annotation string.
        splitted (bool, optional): Flag to allow linebreaks. Default is 'False'.
    Returns:
        str: Extracted string of the uniprot note section.
    """
    if not splitted:
        regex = r"\/note=\"(?P<note>.+?)\""
    else:
        regex = r"\/note=\"(?P<note>.*)"
    result = re.findall(regex, string)
    return result

def extract_note_end(string: str, has_mark:bool = True):
    """
    Helper function to extract information about note of the protein from Uniprot using regular expression.

    Args:
        string (str): Uniprot annotation string.
        has_mark (bool, optional): Flag if end quotation marks are present. Default is 'False'.
    Returns:
        str: Extracted string of the uniprot note section.
    """
    if has_mark:
        regex = r"FT\s+(?P<note>.*)\""
    else:
        regex = r"FT\s+(?P<note>.*)"
    result = re.findall(regex, string)
    return result

# Cell
def resolve_unclear_position(value: str):
    """
    Replace unclear position of the start/end of the modification defined as '?' with -1 and if it's defined as '?N'
    or ">N" - by removing the '?'/'>'/'<' signs.

    Args:
        value (str): Unclear sequence position from uniprot.
    Returns:
        float: Resolved sequence position.
    """
    # if it's "1..?" or "?..345" for start or end -> remove -1 that we can filter later
    # if it's "31..?327" or "?31..327" -> remove the question mark
    # if it's "<1..106" or "22..>115" -> remove the "<" or ">" signs
    if value == '?':
        return -1
    value = value.replace('?', '').replace('>', '').replace('<', '')
    return float(value)

def extract_positions(posit_string: str):
    """
    Extract isoform_id(str) and start/end positions(float) of any feature key from the string.

    Args:
        posit_string (str): Uniprot position string.
    Returns:
        [str, float, float]: str: Uniprot isoform accession, float: start position, float: end position
    """
    isoform = ''
    start = end = np.nan
    if '..' in posit_string:
        start, end = posit_string.split('..')
    if ':' in posit_string:
        if isinstance(start, str):
            isoform, start = start.split(':')
        else:
            isoform, start = posit_string.split(':')
    # in the case when we have only one numeric value as a posit_string
    if isinstance(start, float):
        start = posit_string
    # change the type of start and end into int/float(np.nan)
    if isinstance(start, str):
        start = resolve_unclear_position(start)
    if isinstance(end, str):
        end = resolve_unclear_position(end)
    return isoform, start, end

# Cell
def preprocess_uniprot(path_to_file: str):
    """
    A complex complete function to preprocess Uniprot data from specifying the path to a flat text file
    to the returning a dataframe containing information about:
        - protein_id(str)
        - feature(category)
        - isoform_id(str)
        - start(float)
        - end(float)
        - note information(str)

    Args:
        path_to_file (str): Path to a .txt annotation file directly downloaded from uniprot.
    Returns:
        pd.DataFrame: Dataframe with formatted uniprot annotations for alphamap.

    """
    all_data = []
    with open(path_to_file) as f:

        is_splitted = False
        new_instance = False
        combined_note = []
        line_type = ''

        for line in f:

            if line.startswith(('AC', 'FT')):
                if is_splitted:
                    # in case when the note information is splitted into several lines
                    if line.rstrip().endswith('"'):
                        # if it's the final part of the note
                        combined_note.extend(extract_note_end(line))
                        all_data.append([protein_id, feature, isoform, start, end, " ".join(combined_note)])
                        is_splitted = False
                        new_instance = False
                    else:
                        # if it's the middle part of the note
                        combined_note.extend(extract_note_end(line, has_mark=False))
                elif line.startswith('AC'):
                    # contains the protein_id information
                    if line_type != 'AC':
                        # to prevent a situation when the protein has several AC lines with different names
                        # in this case we are taking the first name in the first line
                        protein_id = line.split()[1].replace(';', '')
                    line_type = 'AC'
                elif line.startswith('FT'):
                    line_type = 'FT'
                    # contains all modifications/preprocessing events/etc., their positions, notes
                    data = line.split()
                    if data[1].isupper() and not data[1].startswith('ECO'):
                            feature = data[1]
                            isoform, start, end = extract_positions(data[2])
                            new_instance = True
                    else:
                        if data[1].startswith('/note'):
                            note = extract_note(line)
                            if note:
                                # if note was created > it contains just one line and can be already added to the data
                                all_data.append([protein_id, feature, isoform, start, end, note[0]])
                                new_instance = False
                            else:
                                # if note is empty > it's splitted into several lines and we create combined_note
                                combined_note = extract_note(line, splitted=True)
                                is_splitted = True
                        else:
                            if new_instance:
                                # in case when we don't have any note but need to add other information about instance
                                all_data.append([protein_id, feature, isoform, start, end, ''])
                                new_instance = False

    # create a dataframe for preprocessed data
    uniprot_df = pd.DataFrame(all_data, columns=['protein_id', 'feature', 'isoform_id', 'start', 'end', 'note'])
    # change the dtypes of the columns
    uniprot_df.feature = uniprot_df.feature.astype('category')
    # to filter the instances that don't have a defined start/end position(start=-1 or end=-1)
    uniprot_df = uniprot_df[(uniprot_df.start != -1) & (uniprot_df.end != -1)].reset_index(drop=True)

    return uniprot_df

# Cell
uniprot_feature_dict = {
    'Chain': 'CHAIN',
    'Initiator methionine': 'INIT_MET',
    'Peptide': 'PEPTIDE',
    'Propeptide': 'PROPEP',
    'Signal peptide': 'SIGNAL',
    'Transit peptide': 'TRANSIT',
    'Cross-link': 'CROSSLNK',
    'Disulfide bond': 'DISULFID',
    'Glycosylation': 'CARBOHYD',
    'Lipidation': 'LIPID',
    'Modified residue': 'MOD_RES',
    'Coiled coil': 'COILED',
    'Compositional bias': 'COMPBIAS',
    'Domain': 'DOMAIN',
    'Motif': 'MOTIF',
    'Region': 'REGION',
    'Repeat': 'REPEAT',
    'Zinc finger': 'ZN_FING',
    'Intramembrane': 'INTRAMEM',
    'Topological domain': 'TOPO_DOM',
    'Transmembrane': 'TRANSMEM',
    'Beta strand': 'STRAND',
    'Helix': 'HELIX',
    'Turn': 'TURN',
    'Active site': 'ACT_SITE',
    'Binding site': 'BINDING',
    'Calcium binding': 'CA_BIND',
    'DNA binding': 'DNA_BIND',
    'Metal binding': 'METAL',
    'Nucleotide binding': 'NP_BIND',
    'Site': 'SITE',
    'Non-standard residue': 'NON_STD',
    'Non-adjacent residues': 'NON_CONS',
    'Non-terminal residue': 'NON_TER',
    'Natural variant': 'VARIANT',
    'Sequence conflict': 'CONFLICT',
    'Alternative sequence': 'VAR_SEQ',
    'Sequence uncertainty': 'UNSURE',
    'Secondary structure': 'STRUCTURE',
    'Mutagenesis': 'MUTAGEN'
}
# AUTOGENERATED! DO NOT EDIT! File to edit: nbs/Uniprot_integration.ipynb (unless otherwise specified). # Cell # Cell Helper function to extract information about note of the protein from Uniprot using regular expression.      Args:         string (str): Uniprot annotation string.         splitted (bool, optional): Flag to allow linebreaks. Default is 'False'.     Returns:         str: Extracted string of the uniprot note section. Helper function to extract information about note of the protein from Uniprot using regular expression.      Args:         string (str): Uniprot annotation string.         has_mark (bool, optional): Flag if end quotation marks are present. Default is 'False'.     Returns:         str: Extracted string of the uniprot note section. # Cell Replace unclear position of the start/end of the modification defined as '?' with -1 and if it's defined as '?N'     or ">N" - by removing the '?'/'>'/'<' signs.      Args:         value (str): Unclear sequence position from uniprot.     Returns:         float: Resolved sequence position. # if it's "1..?" or "?..345" for start or end -> remove -1 that we can filter later # if it's "31..?327" or "?31..327" -> remove the question mark # if it's "<1..106" or "22..>115" -> remove the "<" or ">" signs Extract isoform_id(str) and start/end positions(float) of any feature key from the string.      Args:         posit_string (str): Uniprot position string.     Returns:         [str, float, float]: str: Uniprot isoform accession, float: start position, float: end position # in the case when we have only one numeric value as a posit_string # change the type of start and end into int/float(np.nan) # Cell A complex complete function to preprocess Uniprot data from specifying the path to a flat text file     to the returning a dataframe containing information about:         - protein_id(str)         - feature(category)         - isoform_id(str)         - start(float)         - end(float)         - note information(str)      Args:         path_to_file (str): Path to a .txt annotation file directly downloaded from uniprot.     Returns:         pd.DataFrame: Dataframe with formatted uniprot annotations for alphamap. # in case when the note information is splitted into several lines # if it's the final part of the note # if it's the middle part of the note # contains the protein_id information # to prevent a situation when the protein has several AC lines with different names # in this case we are taking the first name in the first line # contains all modifications/preprocessing events/etc., their positions, notes # if note was created > it contains just one line and can be already added to the data # if note is empty > it's splitted into several lines and we create combined_note # in case when we don't have any note but need to add other information about instance # create a dataframe for preprocessed data # change the dtypes of the columns # to filter the instances that don't have a defined start/end position(start=-1 or end=-1) # Cell