From e841dd524ee33386a47abb694dea90363de144b8 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Fri, 28 Jan 2022 22:31:01 +0000
Subject: Add in-progress gen_ind_genofiles.py

gen_ind_genofiles.py is a command line script to generate genotype files for groups of
individuals/samples, taking a source .geno or .json file and a target 'dummy' .geno file as input
---
 wqflask/maintenance/gen_ind_genofiles.py | 120 +++++++++++++++++++++++++++++++
 1 file changed, 120 insertions(+)
 create mode 100644 wqflask/maintenance/gen_ind_genofiles.py

(limited to 'wqflask')

diff --git a/wqflask/maintenance/gen_ind_genofiles.py b/wqflask/maintenance/gen_ind_genofiles.py
new file mode 100644
index 00000000..546bc60d
--- /dev/null
+++ b/wqflask/maintenance/gen_ind_genofiles.py
@@ -0,0 +1,120 @@
+# Example command: env GN2_PROFILE=/usr/local/guix-profiles/gn-latest-20220122 TMPDIR=/export/local/home/zas1024/gn2-zach/tmp WEBSERVER_MODE=DEBUG LOG_LEVEL=DEBUG SERVER_PORT=5002 GENENETWORK_FILES=/export/local/home/zas1024/gn2-zach/genotype_files SQL_URI=mysql://webqtlout:webqtlout@localhost/db_webqtl ./bin/genenetwork2 ./etc/default_settings.py -c ./maintenance/gen_ind_genofiles.py
+
+import sys
+
+import MySQLdb
+
+#from flask import Blueprint
+
+from wqflask import app
+
+from gn3.db.datasets import retrieve_group_samples
+
+#gen_geno = Blueprint('gen_geno', __name__)
+
+def db_conn():
+    return MySQLdb.Connect(db=app.config.get("DB_NAME"),
+                           user=app.config.get("DB_USER"),
+                           passwd=app.config.get("DB_PASS"),
+                           host=app.config.get("DB_HOST"))
+
+def main(args):
+
+    # The file of the "main" .geno file for the group in question
+    # For example: BXD.geno or BXD.6.geno if converting to BXD individual genofiles
+    strain_genofile = args[1] 
+
+    # Get genotypes from the source strain genofile
+    strain_genotypes(strain_genofile)
+
+    # The target individuals/samples group(s) we're generating the .geno files for
+    # This can be passed as either a specific .geno file, or as a JSON file
+    # containing a set of .geno files (and their corresponding file names and sample lists)
+    if ".json" in args[2]:
+        target_groups = json.load(args[2])['genofile']
+    else:
+        target_groups = [args[2]]
+
+def group_samples(target_group):
+    """
+    Get the group samples from its "dummy" .geno file (which still contains the sample list)
+    """
+
+    # Allow for inputting the target group as either the group name or .geno file
+    file_location = app.config.get("GENENETWORK_FILES") + "/genotype/" + target_group\
+    if ".geno" not in target_group:
+        file_location += ".geno"
+
+    sample_list = []
+    with open(file_location, "r") as target_geno:
+        for i, line in enumerate(target_geno):
+            # Skip header lines
+            if line[0] in ["#", "@"] or not len(line):
+                continue
+    
+            line_items = line.split("\t")
+            sample_list = [item for item in line_items if item not in ["Chr", "Locus", "Mb", "cM"]]
+            break
+
+    return sample_list
+
+def strain_genotypes(strain_genofile: str) -> List:
+    """
+    Read genotypes from source strain .geno file
+
+    :param strain_genofile: string of genofile filename
+    :return: a list of dictionaries representing each marker's genotypes
+
+    Example output: [
+        {
+            'Chr': '1',
+            'Locus': 'marker1',
+            'Mb': '10.0',
+            'cM': '8.0',
+            'genotypes': [('BXD1', 'B'), ('BXD2', 'D'), ('BXD3', 'H'), ...]
+        },
+        ...
+    ]
+    """
+
+    file_location = app.config.get("GENENETWORK_FILES") + "/genotype/" + strain_genofile
+
+    geno_start_col = None
+    header_columns = []
+    sample_list = []
+    marker_genotypes = []
+    with open(file_location, "r") as source_geno:
+        for i, line in enumerate(source_geno):
+            # Skip header lines
+            if line[0] in ["#", "@"] or not len(line):
+                continue
+
+            line_items = line.split("\t")
+
+            if "Chr" in line_items: # Header row
+                # Get the first column index containing genotypes
+                header_columns = line_items
+                for j, item in enumerate(line_items):
+                    if item not in ["Chr", "Locus", "Mb", "cM"]:
+                        geno_start_col = j
+                        break
+
+                sample_list = line_items[geno_start_col:]
+                if not geno_start_col:
+                    print("Check .geno file - expected columns not found")
+                    sys.exit()
+            else: # Marker rows
+                this_marker = {
+                    'Chr': line_items[header_columns.index("Chr")],
+                    'Locus': line_items[header_columns.index("Locus")],
+                    'Mb': line_items[header_columns.index("Mb")],
+                    'cM': line_items[header_columns.index("cM")],
+                    'genotypes': zip(sample_list, line_items[geno_start_col:])
+                }
+                marker_genotypes.append(this_marker)
+
+    return marker_genotypes
+            
+if __name__ == "__main__":
+    print("command line arguments:\n\t%s" % sys.argv)
+    main(sys.argv)
-- 
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