Merge branch 'testing' of https://github.com/genenetwork/genenetwork2 into production

1 files changed, 12 insertions, 65 deletions

diff --git a/wqflask/maintenance/convert_geno_to_bimbam.py b/wqflask/maintenance/convert_geno_to_bimbam.py
index 05006d5c..45522705 100644
--- a/wqflask/maintenance/convert_geno_to_bimbam.py
+++ b/wqflask/maintenance/convert_geno_to_bimbam.py
@@ -17,17 +17,12 @@ import glob
 import traceback
 import gzip
 
-#import numpy as np
-#from pyLMM import lmm
-
 import simplejson as json
 
 from pprint import pformat as pf
 
 class EmptyConfigurations(Exception): pass
 
-        
-
 class Marker(object):
     def __init__(self):
         self.name = None
@@ -39,47 +34,34 @@ class Marker(object):
 class ConvertGenoFile(object):
 
     def __init__(self, input_file, output_files):
-        
         self.input_file = input_file
         self.output_files = output_files
-        
+
         self.mb_exists = False
         self.cm_exists = False
         self.markers = []
-        
+
         self.latest_row_pos = None
         self.latest_col_pos = None
-        
+
         self.latest_row_value = None
         self.latest_col_value = None
-        
-    def convert(self):
 
+    def convert(self):
         self.haplotype_notation = {
             '@mat': "1",
             '@pat': "0",
             '@het': "0.5",
             '@unk': "NA"
             }
-        
+
         self.configurations = {}
-        #self.skipped_cols = 3
-        
-        #if self.input_file.endswith(".geno.gz"):
-        #    print("self.input_file: ", self.input_file)
-        #    self.input_fh = gzip.open(self.input_file)
-        #else:
         self.input_fh = open(self.input_file)
-        
-        with open(self.output_files[0], "w") as self.geno_fh:
-            #if self.file_type == "geno":
-            self.process_csv()
-            #elif self.file_type == "snps":
-            #    self.process_snps_file()
 
+        self.process_csv()
 
     def process_csv(self):
-        for row_count, row in enumerate(self.process_rows()):
+        for row in self.process_rows():
             row_items = row.split("\t")
 
             this_marker = Marker()
@@ -102,53 +84,30 @@ class ConvertGenoFile(object):
                     this_marker.genotypes.append(self.configurations[genotype.upper().strip()])
                 else:
                     this_marker.genotypes.append("NA")
-                
-            #print("this_marker is:", pf(this_marker.__dict__))   
-            #if this_marker.chr == "14":
+
             self.markers.append(this_marker.__dict__)
 
         self.write_to_bimbam()    
-            
-        # with open(self.output_file, 'w') as fh:
-            # json.dump(self.markers, fh, indent="   ", sort_keys=True)
-                
-                # print('configurations:', str(configurations))
-                #self.latest_col_pos = item_count + self.skipped_cols
-                #self.latest_col_value = item
-                
-                #if item_count != 0:
-                #    self.output_fh.write(" ")
-                #self.output_fh.write(self.configurations[item.upper()])
-                    
-            #self.output_fh.write("\n")
 
     def write_to_bimbam(self):
         with open(self.output_files[0], "w") as geno_fh:
-            # geno_fh.write(str(len(self.sample_list)) + "\n")
-            # geno_fh.write("2\n")
-            # geno_fh.write("IND")
-            # for sample in self.sample_list:
-                # geno_fh.write(" " + sample)
-            # geno_fh.write("\n")
             for marker in self.markers:
                 geno_fh.write(marker['name'])
                 geno_fh.write(", X, Y")
                 geno_fh.write(", " + ", ".join(marker['genotypes']))
                 geno_fh.write("\n")
-                
-        #pheno_fh = open(self.output_files[1], 'w')
+
         with open(self.output_files[1], "w") as pheno_fh:
             for sample in self.sample_list:
                 pheno_fh.write("1\n")
-        
+
         with open(self.output_files[2], "w") as snp_fh:
             for marker in self.markers:
                 if self.mb_exists:
                     snp_fh.write(marker['name'] +", " + str(int(float(marker['Mb'])*1000000)) + ", " + marker['chr'] + "\n")
                 else:
                     snp_fh.write(marker['name'] +", " + str(int(float(marker['cM'])*1000000)) + ", " + marker['chr'] + "\n")
-        
-            
+
     def get_sample_list(self, row_contents):
         self.sample_list = []
         if self.mb_exists:
@@ -164,8 +123,6 @@ class ConvertGenoFile(object):
     
     def process_rows(self):
         for self.latest_row_pos, row in enumerate(self.input_fh):
-            #if self.input_file.endswith(".geno.gz"):
-            #    print("row: ", row)
             self.latest_row_value = row
             # Take care of headers
             if not row.strip():
@@ -208,10 +165,8 @@ class ConvertGenoFile(object):
                 convertob.convert()
             except EmptyConfigurations as why:
                 print("  No config info? Continuing...")
-                #excepted = True
                 continue
             except Exception as why:
-
                 print("  Exception:", why)
                 print(traceback.print_exc())
                 print("    Found in row %s at tabular column %s" % (convertob.latest_row_pos,
@@ -219,12 +174,6 @@ class ConvertGenoFile(object):
                 print("    Column is:", convertob.latest_col_value)
                 print("    Row is:", convertob.latest_row_value)
                 break
-            
-    #def process_snps_file(cls, snps_file, new_directory):
-    #    output_file = os.path.join(new_directory, "mouse_families.json")
-    #    print("%s -> %s" % (snps_file, output_file))
-    #    convertob = ConvertGenoFile(input_file, output_file)
-
 
 if __name__=="__main__":
     Old_Geno_Directory = """/home/zas1024/genotype_files/genotype/"""
@@ -234,6 +183,4 @@ if __name__=="__main__":
     #convertob = ConvertGenoFile("/home/zas1024/gene/genotype_files/genotypes/SRxSHRSPF2.geno", "/home/zas1024/gene/genotype_files/new_genotypes/SRxSHRSPF2.json")
     #convertob.convert()
     ConvertGenoFile.process_all(Old_Geno_Directory, New_Geno_Directory)
-    #ConvertGenoFiles(Geno_Directory)
-    
-    #process_csv(Input_File, Output_File)
\ No newline at end of file
+    #ConvertGenoFiles(Geno_Directory)
\ No newline at end of file