From 3e51fb24fd34bab2164a5f4056bc78d21827ca29 Mon Sep 17 00:00:00 2001
From: Frederick Muriuki Muriithi
Date: Wed, 3 Jan 2024 16:53:40 +0300
Subject: Use generic parser. Remove obsoleted functions.

---
 r_qtl/r_qtl2.py | 72 ---------------------------------------------------------
 1 file changed, 72 deletions(-)

(limited to 'r_qtl')

diff --git a/r_qtl/r_qtl2.py b/r_qtl/r_qtl2.py
index 4dac24b..da7db22 100644
--- a/r_qtl/r_qtl2.py
+++ b/r_qtl/r_qtl2.py
@@ -134,78 +134,6 @@ def make_process_data_geno(cdata) -> tuple[
             for items in zip(ids, vals[1:]))
     return (__non_transposed__, __transposed__)
 
-def genotype_data(zfile: ZipFile, cdata: dict) -> Iterator[dict]:
-    """Load the genotype file, making use of the control data."""
-    def replace_genotype_codes(val):
-        return cdata["genotypes"].get(val, val)
-
-    def replace_na_strings(val):
-        nastrings = cdata.get("na.strings")
-        if bool(nastrings):
-            return (None if val in nastrings else val)
-        return val
-
-    if not cdata.get("geno_transposed", False):
-        for line in with_non_transposed(
-                zfile,
-                "geno",
-                cdata,
-                lambda row: {
-                    key: thread_op(value, replace_genotype_codes, replace_na_strings)
-                    for key,value in row.items()
-                }):
-            yield line
-        return None
-
-    def __merge__(key, samples, line):
-        marker = line[0]
-        return tuple(
-            dict(zip(
-                [key, marker],
-                (thread_op(item, replace_genotype_codes, replace_na_strings)
-                 for item in items)))
-            for items in zip(samples, line[1:]))
-
-    for row in with_transposed(zfile, "geno", cdata, __merge__):
-        yield row
-
-def map_data(zfile: ZipFile, map_type: str, cdata: dict) -> Iterator[dict]:
-    """Read gmap files to get the genome mapping data"""
-    assert map_type in ("genetic-map", "physical-map"), "Invalid map type"
-    map_file_key = {
-        "genetic-map": "gmap",
-        "physical-map": "pmap"
-    }[map_type]
-    transposed_dict = {
-        "genetic-map": "gmap_transposed",
-        "physical-map": "pmap_transposed"
-    }
-    if not cdata.get(transposed_dict[map_type], False):
-        for row in with_non_transposed(zfile, map_file_key, cdata):
-            yield row
-        return None
-
-    def __merge__(key, samples, line):
-        marker = line[0]
-        return tuple(dict(zip([key, marker], items))
-                     for items in zip(samples, line[1:]))
-
-    for row in with_transposed(zfile, map_file_key, cdata, __merge__):
-        yield row
-
-def phenotype_data(zfile: ZipFile, cdata: dict) -> Iterator[dict]:
-    """Load phenotype file data."""
-    if not cdata.get("pheno_transposed", False):
-        for row in with_non_transposed(zfile, "pheno", cdata, lambda val: val):
-            yield row
-        return
-
-    def __merge__(id_key, ids, vals):
-        return tuple(dict(zip([id_key, vals[0]], items))
-                     for items in zip(ids, vals[1:]))
-    for row in with_transposed(zfile, "pheno", cdata, __merge__):
-        yield row
-
 def __default_process_value_transposed__(
         id_key: str,
         ids: tuple[str, ...],
-- 
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