diff options
| -rw-r--r-- | wqflask/maintenance/gen_ind_genofiles.py | 19 |
1 files changed, 8 insertions, 11 deletions
diff --git a/wqflask/maintenance/gen_ind_genofiles.py b/wqflask/maintenance/gen_ind_genofiles.py index 546bc60d..ec0fcd55 100644 --- a/wqflask/maintenance/gen_ind_genofiles.py +++ b/wqflask/maintenance/gen_ind_genofiles.py @@ -1,17 +1,14 @@ # 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 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"),
@@ -22,10 +19,7 @@ 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)
+ 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
@@ -35,13 +29,16 @@ def main(args): else:
target_groups = [args[2]]
-def group_samples(target_group):
+ # Generate the output .geno files
+ generate_new_genofiles(strain_genotypes(source_genofile), target_groups)
+
+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\
+ file_location = app.config.get("GENENETWORK_FILES") + "/genotype/" + target_group
if ".geno" not in target_group:
file_location += ".geno"
@@ -109,7 +106,7 @@ def strain_genotypes(strain_genofile: str) -> List: '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:])
+ 'genotypes': list(zip(sample_list, [item.strip() for item in line_items][geno_start_col:]))
}
marker_genotypes.append(this_marker)
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