Change EOL from CRLF to LF

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)