snplib 1.0.7__py3-none-any.whl → 1.0.9__py3-none-any.whl

snplib/format/_plink.py

@@ -1,305 +1,291 @@
-#!/usr/bin/env python
-# coding: utf-8
-__author__ = "Igor Loschinin (igor.loschinin@gmail.com)"
-
-__all__ = [
-    "make_map", "make_ped", "make_fam", "make_lgen"
-]
-
-import re
-import pandas as pd
-
-
-def make_map(manifest: pd.DataFrame) -> pd.DataFrame:
-    """ PLINK text fileset variant information file
-    https://www.cog-genomics.org/plink/1.9/formats#map
-
-    A text file with no header line, and one line per variant with the following 3-4 fields:
-
-        1. Chromosome code. PLINK 1.9 also permits contig names here, but most
-            older programs do not.
-        2. Variant identifier
-        3. Position in morgans or centimorgans (optional; also safe to use
-            dummy value of '0')
-        4. Base-pair coordinate
-
-        All lines must have the same number of columns (so either no lines
-    contain the morgans/centimorgans column, or all of them do).
-
-    :param manifest: The file that is taken on the Illumina website with full
-    information about the chip
-    https://support.illumina.com/downloads/bovinesnp50-v3-0-product-files.html
-
-    :return: Return data in formate .map
-    """
-
-    fields = ['Chr', 'Name', 'MapInfo']
-
-    if all([
-        True
-        if item not in manifest.columns
-        else False
-        for item in fields
-    ]):
-        raise KeyError("Manifest has no data to build map format!")
-
-    # Rearrange the columns and replace the names of the sex and mitochondrial
-    # chromosomes
-    permute_cols = manifest[fields].\
-        sort_values(by='Name').\
-        replace({'X': 30, 'Y': 31, 'MT': 33}).\
-        dropna(axis=0)
-
-    # Insert distances in centimorganides
-    permute_cols.insert(2, 'morgans', [0] * len(manifest))
-
-    return permute_cols
-
-
-def make_ped(
-        data: pd.DataFrame,
-        sid_col: str,
-        snp_col: str,
-        fid_col: str = None,
-        father_col: str = None,
-        mother_col: str = None,
-        sex_col: str = None,
-) -> pd.DataFrame | None:
-    """ Original standard text format for sample pedigree information and
-    genotype calls. Normally must be accompanied by a .map file.
-    https://www.cog-genomics.org/plink/1.9/formats#ped
-
-        The PED file has 6 fixed columns at the beginning followed by the SNP
-    information. The columns should be separated by a whitespace or a tab. The
-    first six columns hold the following information:
-
-        1. Family ID (if unknown use the same id as for the sample id in
-            column two)
-        2. Sample ID
-        3. Paternal ID (if unknown use 0)
-        4. Maternal ID (if unknown use 0)
-        5. Sex (1=male; 2=female; 0=unknown)
-        6. Affection (0=unknown; 1=unaffected; 2=affected)
-        7. Genotypes (space or tab separated, 2 for each marker. 0/-9=missing)
-
-        Here is a brief example of a genotype PED file containing 5 samples
-    with 10 homozygous SNPs:
-        4304 4304 0 0 0 0 C C C C G G G G G G C C G G C C T T T T
-        6925 6925 0 0 0 0 C C C C T T G G A A C C G G C C T T T T
-        7319 7319 0 0 0 0 C C C C G G G G G G C C G G C C T T T T
-        6963 6963 0 0 0 0 A A C C T T G G A A C C G G C C T T T T
-        6968 6968 0 0 0 0 C C C C G G G G G G G G G G C C T T T T
-
-    :param data: Snp data that contain full or partial information on the
-        animal
-    :param sid_col: Sample ID. Column name in data
-    :param snp_col: Snp column name in data
-    :param fid_col: Family ID column name in data (if unknown use the same
-        id as for the sample id in column two)
-    :param father_col: Paternal ID column name in data (if unknown use 0)
-    :param mother_col: Maternal ID column name in data (if unknown use 0)
-    :param sex_col: Sex column name in data (if unknown use 0)
-    :return: Returns an array of data in ped format to work with the plink
-        program
-    """
-
-    _fields = ["fid", "sid", "father", "mother", "sex", "not_used", "snp"]
-    _f_dtype = dict(zip(_fields, (str for _ in range(len(_fields)))))
-
-    _ped = pd.DataFrame(columns=_fields)
-
-    if sid_col not in data.columns or snp_col not in data.columns:
-        raise KeyError(f"Data has not in name columns!")
-
-    # Checked Sample ID on underscope - '_'
-    _ped["sid"] = data[sid_col].astype(str)
-    if _ped["sid"].apply(_check_underscore).any():
-        raise Exception(
-            "Replace in 'Sample ID' columns '_' on another a simbols"
-        )
-
-    # Checked Family ID on underscope - '_'
-    if fid_col is not None:
-        if fid_col not in data.columns:
-            raise KeyError(f"Data has not in name columns {fid_col}!")
-
-        if (data[fid_col].dtype.hasobject and
-                data[fid_col].apply(_check_underscore).any()):
-            raise Exception(
-                "Replace in 'Family ID' columns '_' on another a simbols"
-            )
-
-        _ped["fid"] = data[fid_col]
-
-    else:
-        _ped["fid"] = data[sid_col].astype(str)
-
-    _ped["father"] = data[father_col] if father_col is not None else 0
-    _ped["mother"] = data[mother_col] if mother_col is not None else 0
-    _ped["sex"] = data[sex_col] if sex_col is not None else 0
-    _ped["not_used"] = 0
-    _ped["snp"] = data[snp_col]
-
-    return _ped[_fields].astype(_f_dtype)
-
-
-def make_fam(
-        data: pd.DataFrame,
-        sid_col: str,
-        fid_col: str = None,
-        father_col: str = None,
-        mother_col: str = None,
-        sex_col: str = None,
-        sex_val: int = 0,
-        pheno_col: str = None,
-        pheno_val: int = -9
-
-) -> pd.DataFrame | None:
-    """ PLINK sample information file
-    https://www.cog-genomics.org/plink/1.9/formats#fam
-
-        A text file with no header line, and one line per sample with the
-    following six fields:
-
-        1. Family ID ('FID')
-        2. Within-family ID ('IID'; cannot be '0')
-        3. Within-family ID of father ('0' if father isn't in dataset)
-        4. Within-family ID of mother ('0' if mother isn't in dataset)
-        5. Sex code ('1' = male, '2' = female, '0' = unknown)
-        6. Phenotype value ('1' = control, '2' = case, '-9'/'0'/non-numeric =
-            missing data if case/control)
-
-    :param data: Snp data that contain full or partial information on the
-        animal
-    :param fid_col: Family ID, default value "1". Must not contain
-        underline - "_"
-    :param sid_col: Within-family ID ('IID'; cannot be '0'). Must not contain
-        underline - "_"
-    :param father_col: Within-family ID of father ('0' if father isn't in
-        dataset)
-    :param mother_col: Within-family ID of mother ('0' if mother isn't in
-        dataset)
-    :param sex_col: Sex column name in data
-    :param sex_val: Sex code ('1' = male, '2' = female, '0' = unknown)
-    :param pheno_col: Pheno column name in data
-    :param pheno_val: Phenotype value ('1' = control, '2' = case,
-        '-9'/'0'/non-numeric = missing data if case/control)
-    :return: Return data in formate .fam
-    """
-
-    _fields = ['fid', 'sid', 'father', 'mother', 'sex', 'pheno']
-    _f_dtype = dict(zip(_fields, (str for _ in range(len(_fields)))))
-
-    _fam = pd.DataFrame(columns=_fields)
-
-    if sid_col not in data.columns:
-        raise KeyError(f"Data has not in name columns {sid_col}!")
-
-    # Checked Sample ID on underscope - '_'
-    _fam["sid"] = data[sid_col].astype(str)
-    if _fam["sid"].apply(_check_underscore).any():
-        raise Exception(
-            "Replace in 'Sample ID' columns '_' on another a simbols"
-        )
-
-    # Checked Family ID on underscope - '_'
-    if fid_col is not None:
-        if fid_col not in data.columns:
-            raise KeyError(f"Data has not in name columns {fid_col}!")
-
-        if (data[fid_col].dtype.hasobject and
-                data[fid_col].apply(_check_underscore).any()):
-            raise Exception(
-                "Replace in 'Family ID' columns '_' on another a simbols"
-            )
-
-        _fam["fid"] = data[fid_col]
-
-    else:
-        _fam["fid"] = 1
-
-    _fam["father"] = data[father_col] if father_col is not None else 0
-    _fam["mother"] = data[mother_col] if mother_col is not None else 0
-    _fam["sex"] = data[sex_col] if sex_col is not None else sex_val
-    _fam['pheno'] = data[pheno_col] if pheno_col is not None else pheno_val
-
-    return _fam[_fields].astype(_f_dtype)
-
-
-def make_lgen(
-        data: pd.DataFrame,
-        sid_col: str,
-        snp_name: str,
-        alleles: list[str],
-        fid_col: str = None
-) -> pd.DataFrame | None:
-    """ PLINK long-format genotype file
-    https://www.cog-genomics.org/plink/1.9/formats#lgen
-
-        A text file with no header line, and one line per genotype call (or
-    just not-homozygous-major calls if 'lgen-ref' was invoked) usually with
-    the following five fields:
-
-        1. Family ID
-        2. Within-family ID
-        3. Variant identifier
-        4. Allele call 1 ('0' for missing)
-        5. Allele call 2
-
-        There are several variations which are also handled by PLINK; see the
-    original discussion for details.
-
-    :param data: Data the after parsing FinalReport.txt
-    :param sid_col:
-    :param snp_name:
-    :param fid_col: Family ID, default value "1"
-    :param alleles:
-    :return: - Return data in formate .lgen
-    """
-    _fields = ['fid', 'sid', 'snp_name', 'allele1', 'allele2']
-    _f_dtype = dict(zip(_fields, (str for _ in range(len(_fields)))))
-
-    _lgen = pd.DataFrame(columns=_fields)
-
-    try:
-        # Checked Sample ID on underscope - '_'
-        _lgen["sid"] = data[sid_col].astype(str)
-        if _lgen["sid"].apply(_check_underscore).any():
-            raise Exception(
-                "Replace in 'Sample ID' columns '_' on another a simbols"
-            )
-
-        # Checked Family ID on underscope - '_'
-        if fid_col is not None:
-            if (data[fid_col].dtype.hasobject and
-                    data[fid_col].apply(_check_underscore).any()):
-                raise Exception(
-                    "Replace in 'Family ID' columns '_' on another a simbols"
-                )
-
-            _lgen["fid"] = data[fid_col]
-
-        else:
-            _lgen["fid"] = 1
-
-        _lgen["snp_name"] = data[snp_name]
-        _lgen[["allele1", "allele2"]] = data[alleles].replace({'-': 0})
-
-    except Exception as e:
-        raise e
-
-    return _lgen[_fields].astype(_f_dtype)
-
-
-def _check_underscore(value: str) -> bool:
-    """ Checking for underscore in a string
-
-    :param value: String for checked
-    :return: Return True if there is an underline in the string, False if not
-    """
-    _under_l = re.compile(r"_")
-
-    if _under_l.findall(value):
-        return True
-
-    return False
+#!/usr/bin/env python
+# coding: utf-8
+__author__ = "Igor Loschinin (igor.loschinin@gmail.com)"
+
+__all__ = [
+    "make_map", "make_ped", "make_fam", "make_lgen"
+]
+
+import re
+import pandas as pd
+
+
+def make_map(manifest: pd.DataFrame) -> pd.DataFrame:
+    """ PLINK text fileset variant information file
+    https://www.cog-genomics.org/plink/1.9/formats#map
+
+    A text file with no header line, and one line per variant with the
+    following 3-4 fields:
+
+        1. Chromosome code. PLINK 1.9 also permits contig names here, but most older programs do not.
+        2. Variant identifier.
+        3. Position in morgans or centimorgans (optional; also safe to use dummy value of '0').
+        4. Base-pair coordinate.
+
+    All lines must have the same number of columns (so either no lines contain
+    the morgans/centimorgans column, or all of them do).
+
+    :param manifest: The file that is taken on the Illumina website with full information about the chip https://support.illumina.com/downloads/bovinesnp50-v3-0-product-files.html.
+
+    :return: Return data in formate .map.
+    """
+
+    fields = ['Chr', 'Name', 'MapInfo']
+
+    if all([
+        True
+        if item not in manifest.columns
+        else False
+        for item in fields
+    ]):
+        raise KeyError("Manifest has no data to build map format!")
+
+    # Rearrange the columns and replace the names of the sex and mitochondrial
+    # chromosomes
+    permute_cols = manifest[fields].\
+        sort_values(by='Name').\
+        replace({'X': 30, 'Y': 31, 'MT': 33}).\
+        dropna(axis=0)
+
+    # Insert distances in centimorganides
+    permute_cols.insert(2, 'morgans', [0] * len(manifest))
+
+    return permute_cols
+
+
+def make_ped(
+        data: pd.DataFrame,
+        sid_col: str,
+        snp_col: str,
+        fid_col: str = None,
+        father_col: str = None,
+        mother_col: str = None,
+        sex_col: str = None,
+) -> pd.DataFrame | None:
+    """ Original standard text format for sample pedigree information and
+    genotype calls. Normally must be accompanied by a .map file.
+    https://www.cog-genomics.org/plink/1.9/formats#ped
+
+    The PED file has 6 fixed columns at the beginning followed by the SNP
+    information. The columns should be separated by a whitespace or a tab. The
+    first six columns hold the following information:
+
+        1. Family ID (if unknown use the same id as for the sample id in column two)
+        2. Sample ID
+        3. Paternal ID (if unknown use 0)
+        4. Maternal ID (if unknown use 0)
+        5. Sex (1=male; 2=female; 0=unknown)
+        6. Affection (0=unknown; 1=unaffected; 2=affected)
+        7. Genotypes (space or tab separated, 2 for each marker. 0/-9=missing)
+
+    Here is a brief example of a genotype PED file containing 5 samples
+    with 10 homozygous SNPs:
+
+    4304 4304 0 0 0 0 C C C C G G G G G G C C G G C C T T T T
+    6925 6925 0 0 0 0 C C C C T T G G A A C C G G C C T T T T
+    7319 7319 0 0 0 0 C C C C G G G G G G C C G G C C T T T T
+    6963 6963 0 0 0 0 A A C C T T G G A A C C G G C C T T T T
+    6968 6968 0 0 0 0 C C C C G G G G G G G G G G C C T T T T
+
+    :param data: Snp data that contain full or partial information on the animal.
+    :param sid_col: Sample ID. Column name in data.
+    :param snp_col: Snp column name in data.
+    :param fid_col: Family ID column name in data (if unknown use the same id as for the sample id in column two).
+    :param father_col: Paternal ID column name in data (if unknown use 0).
+    :param mother_col: Maternal ID column name in data (if unknown use 0).
+    :param sex_col: Sex column name in data (if unknown use 0).
+    :return: Returns an array of data in ped format to work with the plink program.
+    """
+
+    _fields = ["fid", "sid", "father", "mother", "sex", "not_used", "snp"]
+    _f_dtype = dict(zip(_fields, (str for _ in range(len(_fields)))))
+
+    _ped = pd.DataFrame(columns=_fields)
+
+    if sid_col not in data.columns or snp_col not in data.columns:
+        raise KeyError(f"Data has not in name columns!")
+
+    # Checked Sample ID on underscope - '_'
+    _ped["sid"] = data[sid_col].astype(str)
+    if _ped["sid"].apply(_check_underscore).any():
+        raise Exception(
+            "Replace in 'Sample ID' columns '_' on another a simbols"
+        )
+
+    # Checked Family ID on underscope - '_'
+    if fid_col is not None:
+        if fid_col not in data.columns:
+            raise KeyError(f"Data has not in name columns {fid_col}!")
+
+        if (data[fid_col].dtype.hasobject and
+                data[fid_col].apply(_check_underscore).any()):
+            raise Exception(
+                "Replace in 'Family ID' columns '_' on another a simbols"
+            )
+
+        _ped["fid"] = data[fid_col]
+
+    else:
+        _ped["fid"] = data[sid_col].astype(str)
+
+    _ped["father"] = data[father_col] if father_col is not None else 0
+    _ped["mother"] = data[mother_col] if mother_col is not None else 0
+    _ped["sex"] = data[sex_col] if sex_col is not None else 0
+    _ped["not_used"] = 0
+    _ped["snp"] = data[snp_col]
+
+    return _ped[_fields].astype(_f_dtype)
+
+
+def make_fam(
+        data: pd.DataFrame,
+        sid_col: str,
+        fid_col: str = None,
+        father_col: str = None,
+        mother_col: str = None,
+        sex_col: str = None,
+        sex_val: int = 0,
+        pheno_col: str = None,
+        pheno_val: int = -9
+) -> pd.DataFrame | None:
+    """ PLINK sample information file
+    https://www.cog-genomics.org/plink/1.9/formats#fam
+
+    A text file with no header line, and one line per sample with the following
+    six fields:
+
+        1. Family ID ('FID')
+        2. Within-family ID ('IID'; cannot be '0')
+        3. Within-family ID of father ('0' if father isn't in dataset)
+        4. Within-family ID of mother ('0' if mother isn't in dataset)
+        5. Sex code ('1' = male, '2' = female, '0' = unknown)
+        6. Phenotype value ('1' = control, '2' = case, '-9'/'0'/non-numeric = missing data if case/control)
+
+    :param data: Snp data that contain full or partial information on the animal
+    :param fid_col: Family ID, default value "1". Must not contain underline - "_"
+    :param sid_col: Within-family ID ('IID'; cannot be '0'). Must not contain underline - "_"
+    :param father_col: Within-family ID of father ('0' if father isn't in dataset)
+    :param mother_col: Within-family ID of mother ('0' if mother isn't in dataset)
+    :param sex_col: Sex column name in data
+    :param sex_val: Sex code ('1' = male, '2' = female, '0' = unknown)
+    :param pheno_col: Pheno column name in data
+    :param pheno_val: Phenotype value ('1' = control, '2' = case,'-9'/'0'/non-numeric = missing data if case/control)
+    :return: Return data in formate .fam
+    """
+
+    _fields = ['fid', 'sid', 'father', 'mother', 'sex', 'pheno']
+    _f_dtype = dict(zip(_fields, (str for _ in range(len(_fields)))))
+
+    _fam = pd.DataFrame(columns=_fields)
+
+    if sid_col not in data.columns:
+        raise KeyError(f"Data has not in name columns {sid_col}!")
+
+    # Checked Sample ID on underscope - '_'
+    _fam["sid"] = data[sid_col].astype(str)
+    if _fam["sid"].apply(_check_underscore).any():
+        raise Exception(
+            "Replace in 'Sample ID' columns '_' on another a simbols"
+        )
+
+    # Checked Family ID on underscope - '_'
+    if fid_col is not None:
+        if fid_col not in data.columns:
+            raise KeyError(f"Data has not in name columns {fid_col}!")
+
+        if (data[fid_col].dtype.hasobject and
+                data[fid_col].apply(_check_underscore).any()):
+            raise Exception(
+                "Replace in 'Family ID' columns '_' on another a simbols"
+            )
+
+        _fam["fid"] = data[fid_col]
+
+    else:
+        _fam["fid"] = 1
+
+    _fam["father"] = data[father_col] if father_col is not None else 0
+    _fam["mother"] = data[mother_col] if mother_col is not None else 0
+    _fam["sex"] = data[sex_col] if sex_col is not None else sex_val
+    _fam['pheno'] = data[pheno_col] if pheno_col is not None else pheno_val
+
+    return _fam[_fields].astype(_f_dtype)
+
+
+def make_lgen(
+        data: pd.DataFrame,
+        sid_col: str,
+        snp_name: str,
+        alleles: list[str],
+        fid_col: str = None
+) -> pd.DataFrame | None:
+    """ PLINK long-format genotype file
+    https://www.cog-genomics.org/plink/1.9/formats#lgen
+
+    A text file with no header line, and one line per genotype call (or
+    just not-homozygous-major calls if 'lgen-ref' was invoked) usually with
+    the following five fields:
+
+        1. Family ID
+        2. Within-family ID
+        3. Variant identifier
+        4. Allele call 1 ('0' for missing)
+        5. Allele call 2
+
+    There are several variations which are also handled by PLINK; see the
+    original discussion for details.
+
+    :param data: Data the after parsing FinalReport.txt
+    :param sid_col:
+    :param snp_name:
+    :param fid_col: Family ID, default value "1"
+    :param alleles:
+    :return: Return data in formate .lgen
+    """
+    _fields = ['fid', 'sid', 'snp_name', 'allele1', 'allele2']
+    _f_dtype = dict(zip(_fields, (str for _ in range(len(_fields)))))
+
+    _lgen = pd.DataFrame(columns=_fields)
+
+    try:
+        # Checked Sample ID on underscope - '_'
+        _lgen["sid"] = data[sid_col].astype(str)
+        if _lgen["sid"].apply(_check_underscore).any():
+            raise Exception(
+                "Replace in 'Sample ID' columns '_' on another a simbols"
+            )
+
+        # Checked Family ID on underscope - '_'
+        if fid_col is not None:
+            if (data[fid_col].dtype.hasobject and
+                    data[fid_col].apply(_check_underscore).any()):
+                raise Exception(
+                    "Replace in 'Family ID' columns '_' on another a simbols"
+                )
+
+            _lgen["fid"] = data[fid_col]
+
+        else:
+            _lgen["fid"] = 1
+
+        _lgen["snp_name"] = data[snp_name]
+        _lgen[["allele1", "allele2"]] = data[alleles].replace({'-': 0})
+
+    except Exception as e:
+        raise e
+
+    return _lgen[_fields].astype(_f_dtype)
+
+
+def _check_underscore(value: str) -> bool:
+    """ Checking for underscore in a string
+
+    :param value: String for checked
+    :return: Return True if there is an underline in the string, False if not.
+    """
+    _under_l = re.compile(r"_")
+
+    if _under_l.findall(value):
+        return True
+
+    return False