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-rw-r--r--wqflask/maintenance/gen_ind_genofiles.py234
1 files changed, 117 insertions, 117 deletions
diff --git a/wqflask/maintenance/gen_ind_genofiles.py b/wqflask/maintenance/gen_ind_genofiles.py
index ec0fcd55..abca4a4a 100644
--- a/wqflask/maintenance/gen_ind_genofiles.py
+++ b/wqflask/maintenance/gen_ind_genofiles.py
@@ -1,117 +1,117 @@
-# 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
-
-from gn3.db.datasets import retrieve_group_samples
-
-def db_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(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
- 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)
+# 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
+
+from gn3.db.datasets import retrieve_group_samples
+
+def db_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(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
+ 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)
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-22 22:04:47 +0000