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| author | zsloan | 2022-01-28 22:31:01 +0000 |
|---|---|---|
| committer | zsloan | 2022-03-16 14:41:09 -0500 |
| commit | e841dd524ee33386a47abb694dea90363de144b8 (patch) | |
| tree | 85a6acf3d4a8c271eac4e830cef41603da073c22 /wqflask | |
| parent | b50b0137bae82d4562f4d377cb7365293d3eed09 (diff) | |
| download | genenetwork2-e841dd524ee33386a47abb694dea90363de144b8.tar.gz | |
Add in-progress gen_ind_genofiles.py
gen_ind_genofiles.py is a command line script to generate genotype files for groups of
individuals/samples, taking a source .geno or .json file and a target 'dummy' .geno file as input
Diffstat (limited to 'wqflask')
| -rw-r--r-- | wqflask/maintenance/gen_ind_genofiles.py | 120 |
1 files changed, 120 insertions, 0 deletions
diff --git a/wqflask/maintenance/gen_ind_genofiles.py b/wqflask/maintenance/gen_ind_genofiles.py new file mode 100644 index 00000000..546bc60d --- /dev/null +++ b/wqflask/maintenance/gen_ind_genofiles.py @@ -0,0 +1,120 @@ +# 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
+
+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"),
+ 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
+ strain_genofile = args[1]
+
+ # Get genotypes from the source strain genofile
+ strain_genotypes(strain_genofile)
+
+ # 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]]
+
+def group_samples(target_group):
+ """
+ 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': zip(sample_list, 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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