Merge branch 'testing' into bug/fix_rqtl_covariates

1 files changed, 77 insertions, 76 deletions

diff --git a/wqflask/utility/genofile_parser.py b/wqflask/utility/genofile_parser.py
index 0b736176..86d9823e 100644
--- a/wqflask/utility/genofile_parser.py
+++ b/wqflask/utility/genofile_parser.py
@@ -12,88 +12,89 @@ import simplejson as json
 
 from pprint import pformat as pf
 
-class Marker(object):
-  def __init__(self):
-    self.name = None
-    self.chr = None
-    self.cM = None
-    self.Mb = None
-    self.genotypes = []
 
+class Marker:
+    def __init__(self):
+        self.name = None
+        self.chr = None
+        self.cM = None
+        self.Mb = None
+        self.genotypes = []
 
-class ConvertGenoFile(object):
 
-  def __init__(self, input_file):
-    self.mb_exists = False
-    self.cm_exists = False
-    self.markers = []
+class ConvertGenoFile:
 
-    self.latest_row_pos = None
-    self.latest_col_pos = None
+    def __init__(self, input_file):
+        self.mb_exists = False
+        self.cm_exists = False
+        self.markers = []
 
-    self.latest_row_value = None
-    self.latest_col_value = None
-    self.input_fh = open(input_file)
-    print("!!!!!!!!!!!!!!!!PARSER!!!!!!!!!!!!!!!!!!")
-    self.haplotype_notation = {
-      '@mat': "1",
-      '@pat': "2",
-      '@het': "-999",
-      '@unk': "-999"
-    }
-    self.configurations = {}
+        self.latest_row_pos = None
+        self.latest_col_pos = None
 
-  def process_rows(self):
-    for self.latest_row_pos, row in enumerate(self.input_fh):
-        self.latest_row_value = row
-        # Take care of headers
-        if not row.strip():
-            continue
-        if row.startswith('#'):
-            continue
-        if row.startswith('Chr'):
-            if 'Mb' in row.split():
-                self.mb_exists = True
-            if 'cM' in row.split():
-                self.cm_exists = True
-            skip = 2 + self.cm_exists + self.mb_exists
-            self.individuals = row.split()[skip:]
-            continue
-        if row.startswith('@'):
-            key, _separater, value = row.partition(':')
-            key = key.strip()
-            value = value.strip()
-            if key in self.haplotype_notation:
-                self.configurations[value] = self.haplotype_notation[key]
-            continue
-        if not len(self.configurations):
-            raise EmptyConfigurations
-        yield row
+        self.latest_row_value = None
+        self.latest_col_value = None
+        self.input_fh = open(input_file)
+        print("!!!!!!!!!!!!!!!!PARSER!!!!!!!!!!!!!!!!!!")
+        self.haplotype_notation = {
+            '@mat': "1",
+            '@pat': "2",
+            '@het': "-999",
+            '@unk': "-999"
+        }
+        self.configurations = {}
 
-  def process_csv(self):
-    for row in self.process_rows():
-      row_items = row.split("\t")
+    def process_rows(self):
+        for self.latest_row_pos, row in enumerate(self.input_fh):
+            self.latest_row_value = row
+            # Take care of headers
+            if not row.strip():
+                continue
+            if row.startswith('#'):
+                continue
+            if row.startswith('Chr'):
+                if 'Mb' in row.split():
+                    self.mb_exists = True
+                if 'cM' in row.split():
+                    self.cm_exists = True
+                skip = 2 + self.cm_exists + self.mb_exists
+                self.individuals = row.split()[skip:]
+                continue
+            if row.startswith('@'):
+                key, _separater, value = row.partition(':')
+                key = key.strip()
+                value = value.strip()
+                if key in self.haplotype_notation:
+                    self.configurations[value] = self.haplotype_notation[key]
+                continue
+            if not len(self.configurations):
+                raise EmptyConfigurations
+            yield row
 
-      this_marker = Marker()
-      this_marker.name = row_items[1]
-      this_marker.chr = row_items[0]
-      if self.cm_exists and self.mb_exists:
-        this_marker.cM = row_items[2]
-        this_marker.Mb = row_items[3]
-        genotypes = row_items[4:]
-      elif self.cm_exists:
-          this_marker.cM = row_items[2]
-          genotypes = row_items[3:]
-      elif self.mb_exists:
-          this_marker.Mb = row_items[2]
-          genotypes = row_items[3:]
-      else:
-        genotypes = row_items[2:]
-      for item_count, genotype in enumerate(genotypes):
-        if genotype.upper().strip() in self.configurations:
-          this_marker.genotypes.append(self.configurations[genotype.upper().strip()])
-        else:
-          print("WARNING:", genotype.upper())
-          this_marker.genotypes.append("NA")
-      self.markers.append(this_marker.__dict__)
+    def process_csv(self):
+        for row in self.process_rows():
+            row_items = row.split("\t")
 
+            this_marker = Marker()
+            this_marker.name = row_items[1]
+            this_marker.chr = row_items[0]
+            if self.cm_exists and self.mb_exists:
+                this_marker.cM = row_items[2]
+                this_marker.Mb = row_items[3]
+                genotypes = row_items[4:]
+            elif self.cm_exists:
+                this_marker.cM = row_items[2]
+                genotypes = row_items[3:]
+            elif self.mb_exists:
+                this_marker.Mb = row_items[2]
+                genotypes = row_items[3:]
+            else:
+                genotypes = row_items[2:]
+            for item_count, genotype in enumerate(genotypes):
+                if genotype.upper().strip() in self.configurations:
+                    this_marker.genotypes.append(
+                        self.configurations[genotype.upper().strip()])
+                else:
+                    print("WARNING:", genotype.upper())
+                    this_marker.genotypes.append("NA")
+            self.markers.append(this_marker.__dict__)