scout-browser 4.96.0__py3-none-any.whl → 4.98.0__py3-none-any.whl

scout/parse/peddy.py

@@ -1,149 +0,0 @@
-from scout.utils.convert import convert_number, make_bool
-
-
-def parse_peddy_ped(lines):
-    """Parse a peddy.ped file
-
-    Args:
-        lines(iterable(str))
-
-    Returns:
-        peddy_ped(list(dict))
-    """
-    peddy_ped = []
-    header = []
-    for i, line in enumerate(lines):
-        line = line.rstrip()
-        if i == 0:
-            # Header line
-            header = line.lstrip("#").split("\t")
-        else:
-            ind_info = dict(zip(header, line.split("\t")))
-
-            # PC1/PC2/PC3/PC4: the first 4 values after this sample was
-            # projected onto the thousand genomes principle components.
-            ind_info["PC1"] = convert_number(ind_info["PC1"])
-            ind_info["PC2"] = convert_number(ind_info["PC2"])
-            ind_info["PC3"] = convert_number(ind_info["PC3"])
-            # ancestry-prediction one of AFR AMR EAS EUR SAS UNKNOWN
-
-            ind_info["het_call_rate"] = convert_number(ind_info["het_call_rate"])
-
-            # idr_baf: inter-decile range (90th percentile - 10th percentile)
-            # of b-allele frequency. We make a distribution of all sites of
-            # alts / (ref + alts) and then report the difference between the
-            # 90th and the 10th percentile.
-            # Large values indicated likely sample contamination.
-            ind_info["het_idr_baf"] = convert_number(ind_info["het_idr_baf"])
-
-            ind_info["het_mean_depth"] = convert_number(ind_info["het_mean_depth"])
-
-            peddy_ped.append(ind_info)
-    return peddy_ped
-
-
-def parse_peddy_ped_check(lines):
-    """Parse a .ped_check.csv file
-
-    Args:
-        lines(iterable(str))
-
-    Returns:
-        ped_check(list(dict))
-    """
-    ped_check = []
-    header = []
-    for i, line in enumerate(lines):
-        line = line.rstrip()
-        if i == 0:
-            # Header line
-            header = line.lstrip("#").split(",")
-        else:
-            pair_info = dict(zip(header, line.split(",")))
-
-            # the number of sites at which sample_a was heterozygous
-            pair_info["hets_a"] = convert_number(pair_info["hets_a"])
-
-            # the number of sites at which sample_b was heterozygous
-            pair_info["hets_b"] = convert_number(pair_info["hets_b"])
-
-            # the number of sites at which the 2 samples shared no alleles
-            # (should approach 0 for parent-child pairs).
-            pair_info["ibs0"] = convert_number(pair_info["ibs0"])
-
-            # the number of sites and which the 2 samples where both
-            # hom-ref, both het, or both hom-alt.
-            pair_info["ibs2"] = convert_number(pair_info["ibs2"])
-
-            # the number of sites that was used to predict the relatedness.
-            pair_info["n"] = convert_number(pair_info["n"])
-
-            # the relatedness reported in the ped file.
-            pair_info["rel"] = convert_number(pair_info["rel"])
-
-            # the relatedness reported in the ped file.
-            pair_info["pedigree_relatedness"] = convert_number(pair_info["pedigree_relatedness"])
-
-            # difference between the preceding 2 colummns.
-            pair_info["rel_difference"] = convert_number(pair_info["rel_difference"])
-
-            # the number of sites at which both samples were hets.
-            pair_info["shared_hets"] = convert_number(pair_info["shared_hets"])
-
-            # boolean indicating that this pair is a parent-child pair
-            # according to the ped file.
-            pair_info["pedigree_parents"] = make_bool(pair_info.get("pedigree_parents"))
-
-            # boolean indicating that this pair is expected to be a parent-child
-            # pair according to the ibs0 (< 0.012) calculated from the genotypes.
-            pair_info["predicted_parents"] = make_bool(pair_info.get("predicted_parents"))
-
-            # boolean indicating that the preceding 2 columns do not match
-            pair_info["parent_error"] = make_bool(pair_info.get("parent_error"))
-
-            #  boolean indicating that rel > 0.75 and ibs0 < 0.012
-            pair_info["sample_duplication_error"] = make_bool(
-                pair_info.get("sample_duplication_error")
-            )
-
-            ped_check.append(pair_info)
-
-    return ped_check
-
-
-def parse_peddy_sex_check(lines):
-    """Parse a .ped_check.csv file
-
-    Args:
-        lines(iterable(str))
-
-    Returns:
-        sex_check(list(dict))
-    """
-    sex_check = []
-    header = []
-    for i, line in enumerate(lines):
-        line = line.rstrip()
-        if i == 0:
-            # Header line
-            header = line.lstrip("#").split(",")
-        else:
-            ind_info = dict(zip(header, line.split(",")))
-
-            # boolean indicating wether there is a mismatch between X
-            # genotypes and ped sex.
-            ind_info["error"] = make_bool(ind_info.get("error"))
-
-            # number of homozygous-alternate calls
-            ind_info["hom_alt_count"] = convert_number(ind_info["hom_alt_count"])
-            # number of homozygous-reference calls
-            ind_info["hom_ref_count"] = convert_number(ind_info["hom_ref_count"])
-            # number of heterozygote calls
-            ind_info["het_count"] = convert_number(ind_info["het_count"])
-
-            # ratio of het_count / hom_alt_count. Low for males, high for females
-            ind_info["het_ratio"] = convert_number(ind_info["het_ratio"])
-
-            sex_check.append(ind_info)
-
-    return sex_check

scout/utils/sort.py

@@ -1,21 +0,0 @@
-from scout.constants import FILE_TYPE_MAP
-
-
-def get_load_priority(category: str = None, variant_type: str = None, file_type: str = None) -> int:
-    """
-    Returns most urgent, highest load priority (numerically the lowest prio number) for the given variables
-    from a FILE_TYPE_MAP dict of dicts. Helper useful in a sort function.
-    """
-    ordered_file_type_map = sorted(FILE_TYPE_MAP.items(), key=lambda ftm: ftm[1]["load_priority"])
-
-    for ftm in ordered_file_type_map:
-        if file_type and file_type != ftm[0]:
-            continue
-
-        if category and category != ftm[1]["category"]:
-            continue
-
-        if variant_type and variant_type != ftm[1]["variant_type"]:
-            continue
-
-        return ftm[1]["load_priority"]