Minor changes/bug fixes

- Removed some unused code
- Strip marker genotype to avoid newline character at end
- Convert zip to list for marker genotypes
- Add typing to group_samples
- Rename strain_genofile to source_genofile

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)