Merge remote-tracking branch 'origin/testing' into feature/add_rqtl_pairscan

1 files changed, 249 insertions, 0 deletions

diff --git a/wqflask/maintenance/gen_ind_genofiles.py b/wqflask/maintenance/gen_ind_genofiles.py
new file mode 100644
index 00000000..8b958efa
--- /dev/null
+++ b/wqflask/maintenance/gen_ind_genofiles.py
@@ -0,0 +1,249 @@
+#!/usr/bin/env python3
+"""A script that generates the genotype files for groups of individuals, using an existing strain genotype file as a basis
+
+Example commands:
+python3 gen_ind_genofiles.py
+        /home/zas1024/gn2-zach/genotype_files/genotype/
+        /home/zas1024/gn2-zach/new_geno/
+        BXD-Micturition.geno
+        BXD.json
+python3 gen_ind_genofiles.py
+        /home/zas1024/gn2-zach/genotype_files/genotype
+        /home/zas1024/gn2-zach/new_geno/
+        BXD-Micturition.geno
+        BXD.2.geno BXD.4.geno BXD.5.geno
+
+"""
+
+import json
+import os
+import sys
+from typing import List
+
+import MySQLdb
+
+def conn():
+    return MySQLdb.Connect(db=os.environ.get("DB_NAME"),
+                           user=os.environ.get("DB_USER"),
+                           passwd=os.environ.get("DB_PASS"),
+                           host=os.environ.get("DB_HOST"))
+
+def main(args):
+
+    # Directory in which .geno files are located
+    geno_dir = args[1]
+
+    # Directory in which to output new files
+    out_dir = args[2]
+
+    # The individuals group that we want to generate a .geno file for
+    target_file = geno_dir + args[3]
+
+    # The source group(s) we're generating the .geno files from
+    # This can be passed as either a specific .geno file (or set of files as multiple arguments),
+    # or as a JSON file containing a set of .geno files (and their corresponding file names and sample lists)
+    geno_json = {}
+    source_files = []
+    if ".json" in args[4]:
+        geno_json = json.load(open(geno_dir + args[4], "r"))
+        par_f1s = {
+            "mat": geno_json['mat'],
+            "pat": geno_json['pat'],
+            "f1s": geno_json['f1s']
+        }
+
+        # List of file titles and locations from JSON
+        source_files = [{'title': genofile['title'], 'location': geno_dir + genofile['location']} for genofile in geno_json['genofile']]
+    else:
+        par_f1s = {}
+        # List of files directly taken from command line arguments, with titles just set to the filename
+        for group in args[4:]:
+            file_name = geno_dir + group + ".geno" if ".geno" not in group else group
+            source_files.append({'title': file_name[:-5], 'location': file_name})
+
+    if len(source_files) > 1:
+        # Generate a JSON file pointing to the new target genotype files, in situations where there are multiple source .geno files
+        target_json_loc = out_dir + ".".join(args[3].split(".")[:-1]) + ".json"
+        target_json = {'genofile': []}
+
+    # Generate the output .geno files
+    for source_file in source_files:
+        filename, samples = generate_new_genofile(source_file['location'], target_file, par_f1s, out_dir)
+
+        target_json['genofile'].append({
+            'location': filename.split("/")[-1],
+            'title': source_file['title'],
+            'sample_list': samples
+        })
+
+    json.dump(target_json, open(target_json_loc, "w"))
+
+def get_strain_for_sample(sample):
+    query = (
+        "SELECT CaseAttributeXRefNew.Value "
+        "FROM CaseAttributeXRefNew, Strain "
+        "WHERE CaseAttributeXRefNew.CaseAttributeId=11 "
+        "AND CaseAttributeXRefNew.StrainId = Strain.Id "
+        "AND Strain.Name = %(name)s" )
+
+    with conn().cursor() as cursor:
+        cursor.execute(query, {"name": sample.strip()})
+        return cursor.fetchone()[0]
+
+def generate_new_genofile(source_genofile, target_genofile, par_f1s, out_dir):
+    source_samples = group_samples(source_genofile)
+    source_genotypes = strain_genotypes(source_genofile)
+    target_samples = group_samples(target_genofile)
+    strain_pos_map = map_strain_pos_to_target_group(source_samples, target_samples, par_f1s)
+
+    if len(source_genofile.split("/")[-1].split(".")) > 2:
+        # The number in the source genofile; for example 4 in BXD.4.geno
+        source_num = source_genofile.split("/")[-1].split(".")[-2]
+        target_filename = ".".join(target_genofile.split("/")[-1].split(".")[:-1]) + "." + source_num + ".geno"
+    else:
+        target_filename = ".".join(target_genofile.split("/")[-1].split(".")[:-1]) + ".geno"
+
+    file_location = out_dir + target_filename
+
+    with open(file_location, "w") as fh:
+        for metadata in ["name", "type", "mat", "pat", "het", "unk"]:
+            fh.write("@" + metadata + ":" + source_genotypes[metadata] + "\n")
+
+        header_line = ["Chr", "Locus", "cM", "Mb"] + target_samples
+        fh.write("\t".join(header_line))
+
+        for marker in source_genotypes['markers']:
+            line_items = [
+                marker['Chr'],
+                marker['Locus'],
+                marker['cM'],
+                marker['Mb']
+            ]
+
+            for pos in strain_pos_map:
+                if isinstance(pos, int):
+                    line_items.append(marker['genotypes'][pos])
+                else:
+                    if pos in ["mat", "pat"]:
+                        line_items.append(source_genotypes[pos])
+                    elif pos == "f1s":
+                        line_items.append("H")
+                    else:
+                        line_items.append("U")
+
+            fh.write("\t".join(line_items) + "\n")
+
+    return file_location, target_samples
+
+def map_strain_pos_to_target_group(source_samples, target_samples, par_f1s):
+    """
+    Retrieve corresponding strain position for each sample in the target group
+
+    This is so the genotypes from the base genofile can be mapped to the samples in the target group
+
+    For example:
+    Base strains: BXD1, BXD2, BXD3
+    Target samples: BXD1_1, BXD1_2, BXD2_1, BXD3_1, BXD3_2, BXD3_3
+    Returns: [0, 0, 1, 2, 2, 2]
+    """
+    pos_map = []
+    for sample in target_samples:
+        sample_strain = get_strain_for_sample(sample)
+        if sample_strain in source_samples:
+            pos_map.append(source_samples.index(sample_strain))
+        else:
+            val = "U"
+            for key in par_f1s.keys():
+                if sample_strain in par_f1s[key]:
+                    val = key
+            pos_map.append(val)
+
+    return pos_map
+
+def group_samples(target_file: str) -> List:
+    """
+    Get the group samples from its "dummy" .geno file (which still contains the sample list)
+    """
+
+    sample_list = []
+    with open(target_file, "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'), ...]
+        },
+        ...
+    ]
+    """
+
+    geno_dict = {}
+
+    geno_start_col = None
+    header_columns = []
+    sample_list = []
+    markers = []
+    with open(strain_genofile, "r") as source_geno:
+        for i, line in enumerate(source_geno):
+            if line[0] == "@":
+                metadata_type = line[1:].split(":")[0]
+                if metadata_type in ['name', 'type', 'mat', 'pat', 'het', 'unk']:
+                    geno_dict[metadata_type] = line.split(":")[1].strip()
+
+                continue
+
+            # Skip other header lines
+            if line[0] == "#" 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': [item.strip() for item in line_items][geno_start_col:]
+                }
+
+                markers.append(this_marker)
+
+    geno_dict['markers'] = markers
+
+    return geno_dict
+            
+if __name__ == "__main__":
+    main(sys.argv)
+