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# 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 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)
if ".json" in args[4]:
source_files = [geno_dir + genofile['location'] for genofile in json.load(args[4])['genofile']]
else:
source_files = [geno_dir + group + ".geno" if ".geno" not in group else group for group in args[4:]]
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 + 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, target_file)
target_json['genofile'].append({
'location': filename.split("/")[-1],
'title': filename.split("/")[-1],
'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 CaseAttributeXRef.New.StrainId = Strain.Id "
"AND Strain.Name = %(name)s" )
with conn.cursor() as cursor:
return cursor.execute(query, {"name": name}).fetchone()[0]
def generate_new_genofiles(source_genofile, target_genofile):
base_samples = group_samples(source_genofile)
base_genotypes = strain_genotypes(source_genofile)
target_samples = group_samples(target_genofile)
strain_pos_map = map_strain_pos_to_target_group(base_samples, target_samples)
def map_strain_pos_to_target_group(base_samples, target_samples):
"""
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)
pos_map.append(base_samples.index(sample_strain))
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 = []
marker_genotypes = []
with open(file_location, "r") as source_geno:
for i, line in enumerate(source_geno):
if line[0] == "@":
if "@type" in line:
geno_dict['type'] = line.split(":")[1]
if "@mat" in line:
geno_dict['mat'] = line.split(":")[1]
elif "@pat" in line:
geno_dict['pat'] = line.split(":")[1]
elif "@het" in line:
geno_dict['het'] = line.split(":")[1]
elif "@unk" in line:
geno_dict['unk'] = line.split(":")[1]
# 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:]
}
marker_genotypes.append(this_marker)
geno_dict['genotypes'] = marker_genotypes
return geno_dict
if __name__ == "__main__":
print("command line arguments:\n\t%s" % sys.argv)
main(sys.argv)
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