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# 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
from typing import List
import MySQLdb
from wqflask import app
def 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
source_genofile = args[1]
# 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]]
# Generate the output .geno files
generate_new_genofiles(source_genofile, strain_genotypes(source_genofile), target_groups)
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, strain_genotypes, target_groups):
for group in target_groups:
base_samples = group_samples(source_genofile)
target_samples = group_samples(group)
strain_pos_map = map_strain_pos_to_target_group(base_samples, target_samples)
new_genofile = app.config.get("GENENETWORK_FILES") + "/genotype/_" + group
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 i, sample in enumerate(target_samples):
sample_strain = get_strain_for_sample(sample)
pos_map.append(base_samples.index(sample_strain))
return pos_map
def group_samples(target_group: str) -> List:
"""
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': list(zip(sample_list, [item.strip() for item in 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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