Provide utilities for genotype files

Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi

* gn3/db/genotypes.py: New module
* gn3/settings.py: Add new configuration variable
* qtlfilesexport.py: Test out new code

  Add a module containing functions dealing with the genotype files.
  Add a configuration variable to point to the location of the genotype files.

3 files changed, 76 insertions, 30 deletions

diff --git a/gn3/db/genotypes.py b/gn3/db/genotypes.py
new file mode 100644
index 0000000..610ddde
--- /dev/null
+++ b/gn3/db/genotypes.py
@@ -0,0 +1,69 @@
+"""Genotype utilities"""
+
+import os
+import gzip
+from gn3.settings import GENOTYPE_FILES
+
+def build_genotype_file(
+        geno_name: str, base_dir: str = GENOTYPE_FILES,
+        extension: str = "geno"):
+    """Build the absolute path for the genotype file."""
+    return "{}/{}.{}".format(os.path.abspath(base_dir), geno_name, extension)
+
+def load_genotype_samples(genotype_filename: str, file_type: str = "geno"):
+    """
+    Load sample of strains from genotype files.
+
+    DESCRIPTION:
+    Traits can contain a varied number of strains, some of which do not exist in
+    certain genotypes. In order to compute QTLs, GEMMAs, etc, we need to ensure
+    to pick only those strains that exist in the genotype under consideration
+    for the traits used in the computation.
+
+    This function loads a list of samples from the genotype files for use in
+    filtering out unusable strains.
+
+
+    PARAMETERS:
+    genotype_filename: The absolute path to the genotype file to load the
+        samples from.
+    file_type: The type of file. Currently supported values are 'geno' and
+        'plink'.
+    """
+    file_type_fns = {
+        "geno": __load_genotype_samples_from_geno,
+        "plink": __load_genotype_samples_from_plink
+    }
+    return file_type_fns[file_type](genotype_filename)
+
+def __load_genotype_samples_from_geno(genotype_filename: str):
+    """
+    Helper function for `load_genotype_samples` function.
+
+    Loads samples from '.geno' files.
+    """
+    gzipped_filename = "{}.gz".format(genotype_filename)
+    if os.path.isfile(gzipped_filename):
+        genofile = gzip.open(gzipped_filename)
+    else:
+        genofile = open(genotype_filename)
+
+    for row in genofile:
+        line = row.strip()
+        if (not line) or (line.startswith(("#", "@"))):
+            continue
+        break
+
+    headers = line.split("\t")
+    if headers[3] == "Mb":
+        return headers[4:]
+    return headers[3:]
+
+def __load_genotype_samples_from_plink(genotype_filename: str):
+    """
+    Helper function for `load_genotype_samples` function.
+
+    Loads samples from '.plink' files.
+    """
+    genofile = open(genotype_filename)
+    return [line.split(" ")[1] for line in genofile]
diff --git a/gn3/settings.py b/gn3/settings.py
index d137370..a08f846 100644
--- a/gn3/settings.py
+++ b/gn3/settings.py
@@ -27,3 +27,7 @@ BIWEIGHT_RSCRIPT = "~/genenetwork3/scripts/calculate_biweight.R"
 
 # qtlreaper command
 REAPER_COMMAND = "{}/bin/qtlreaper".format(os.environ.get("GUIX_ENVIRONMENT"))
+
+# genotype files
+GENOTYPE_FILES = os.environ.get(
+    "GENOTYPE_FILES", "{}/genotype_files/genotype".format(os.environ.get("HOME")))
diff --git a/qtlfilesexport.py b/qtlfilesexport.py
index adc5e77..1db4ab6 100644
--- a/qtlfilesexport.py
+++ b/qtlfilesexport.py
@@ -11,6 +11,7 @@ from gn3.computations.slink import slink
 from gn3.db_utils import database_connector
 from gn3.computations.heatmap import export_trait_data
 from gn3.db.traits import retrieve_trait_data, retrieve_trait_info
+from gn3.db.genotypes import build_genotype_file, load_genotype_samples
 from gn3.computations.qtlreaper import random_string, generate_traits_file
 from gn3.computations.heatmap import (
     cluster_traits,
@@ -41,36 +42,8 @@ def main():
         retrieve_trait_info(threshold, fullname, conn)
         for fullname in trait_fullnames()]
     traits_data_list = [retrieve_trait_data(t, conn) for t in traits]
-    # strains = list(set([k for td in traits_data_list for k in td["data"].keys()]))
-    strains = [# Use only the strains in the BXD.geno genotype file
-        "BXD1", "BXD2", "BXD5", "BXD6", "BXD8", "BXD9", "BXD11", "BXD12",
-        "BXD13", "BXD14", "BXD15", "BXD16", "BXD18", "BXD19", "BXD20", "BXD21",
-        "BXD22", "BXD23", "BXD24", "BXD24a", "BXD25", "BXD27", "BXD28", "BXD29",
-        "BXD30", "BXD31", "BXD32", "BXD33", "BXD34", "BXD35", "BXD36", "BXD37",
-        "BXD38", "BXD39", "BXD40", "BXD41", "BXD42", "BXD43", "BXD44", "BXD45",
-        "BXD48", "BXD48a", "BXD49", "BXD50", "BXD51", "BXD52", "BXD53", "BXD54",
-        "BXD55", "BXD56", "BXD59", "BXD60", "BXD61", "BXD62", "BXD63", "BXD64",
-        "BXD65", "BXD65a", "BXD65b", "BXD66", "BXD67", "BXD68", "BXD69",
-        "BXD70", "BXD71", "BXD72", "BXD73", "BXD73a", "BXD73b", "BXD74",
-        "BXD75", "BXD76", "BXD77", "BXD78", "BXD79", "BXD81", "BXD83", "BXD84",
-        "BXD85", "BXD86", "BXD87", "BXD88", "BXD89", "BXD90", "BXD91", "BXD93",
-        "BXD94", "BXD95", "BXD98", "BXD99", "BXD100", "BXD101", "BXD102",
-        "BXD104", "BXD105", "BXD106", "BXD107", "BXD108", "BXD109", "BXD110",
-        "BXD111", "BXD112", "BXD113", "BXD114", "BXD115", "BXD116", "BXD117",
-        "BXD119", "BXD120", "BXD121", "BXD122", "BXD123", "BXD124", "BXD125",
-        "BXD126", "BXD127", "BXD128", "BXD128a", "BXD130", "BXD131", "BXD132",
-        "BXD133", "BXD134", "BXD135", "BXD136", "BXD137", "BXD138", "BXD139",
-        "BXD141", "BXD142", "BXD144", "BXD145", "BXD146", "BXD147", "BXD148",
-        "BXD149", "BXD150", "BXD151", "BXD152", "BXD153", "BXD154", "BXD155",
-        "BXD156", "BXD157", "BXD160", "BXD161", "BXD162", "BXD165", "BXD168",
-        "BXD169", "BXD170", "BXD171", "BXD172", "BXD173", "BXD174", "BXD175",
-        "BXD176", "BXD177", "BXD178", "BXD180", "BXD181", "BXD183", "BXD184",
-        "BXD186", "BXD187", "BXD188", "BXD189", "BXD190", "BXD191", "BXD192",
-        "BXD193", "BXD194", "BXD195", "BXD196", "BXD197", "BXD198", "BXD199",
-        "BXD200", "BXD201", "BXD202", "BXD203", "BXD204", "BXD205", "BXD206",
-        "BXD207", "BXD208", "BXD209", "BXD210", "BXD211", "BXD212", "BXD213",
-        "BXD214", "BXD215", "BXD216", "BXD217", "BXD218", "BXD219", "BXD220"
-    ]
+    genotype_filename = build_genotype_file(traits[0]["riset"])
+    strains = load_genotype_samples(genotype_filename)
     exported_traits_data_list = [
         export_trait_data(td, strains) for td in traits_data_list]
     slinked = slink(cluster_traits(exported_traits_data_list))