1 files changed, 0 insertions, 96 deletions
diff --git a/wqflask/base/data_set/markers.py b/wqflask/base/data_set/markers.py
deleted file mode 100644
index 6f56445e..00000000
--- a/wqflask/base/data_set/markers.py
+++ /dev/null
@@ -1,96 +0,0 @@
-"Base Class: Markers - "
-
-import math
-
-from utility.tools import locate, flat_files
-
-class Markers:
-    """Todo: Build in cacheing so it saves us reading the same file more than once"""
-
-    def __init__(self, name):
-        json_data_fh = open(locate(name + ".json", 'genotype/json'))
-
-        markers = []
-        with open("%s/%s_snps.txt" % (flat_files('genotype/bimbam'), name), 'r') as bimbam_fh:
-            if len(bimbam_fh.readline().split(", ")) > 2:
-                delimiter = ", "
-            elif len(bimbam_fh.readline().split(",")) > 2:
-                delimiter = ","
-            elif len(bimbam_fh.readline().split("\t")) > 2:
-                delimiter = "\t"
-            else:
-                delimiter = " "
-            for line in bimbam_fh:
-                marker = {}
-                marker['name'] = line.split(delimiter)[0].rstrip()
-                marker['Mb'] = float(line.split(delimiter)[
-                                     1].rstrip()) / 1000000
-                marker['chr'] = line.split(delimiter)[2].rstrip()
-                markers.append(marker)
-
-        for marker in markers:
-            if (marker['chr'] != "X") and (marker['chr'] != "Y") and (marker['chr'] != "M"):
-                marker['chr'] = int(marker['chr'])
-            marker['Mb'] = float(marker['Mb'])
-
-        self.markers = markers
-
-    def add_pvalues(self, p_values):
-        if isinstance(p_values, list):
-            # THIS IS only needed for the case when we are limiting the number of p-values calculated
-            # if len(self.markers) > len(p_values):
-            #    self.markers = self.markers[:len(p_values)]
-
-            for marker, p_value in zip(self.markers, p_values):
-                if not p_value:
-                    continue
-                marker['p_value'] = float(p_value)
-                if math.isnan(marker['p_value']) or marker['p_value'] <= 0:
-                    marker['lod_score'] = 0
-                    marker['lrs_value'] = 0
-                else:
-                    marker['lod_score'] = -math.log10(marker['p_value'])
-                    # Using -log(p) for the LRS; need to ask Rob how he wants to get LRS from p-values
-                    marker['lrs_value'] = -math.log10(marker['p_value']) * 4.61
-        elif isinstance(p_values, dict):
-            filtered_markers = []
-            for marker in self.markers:
-                if marker['name'] in p_values:
-                    marker['p_value'] = p_values[marker['name']]
-                    if math.isnan(marker['p_value']) or (marker['p_value'] <= 0):
-                        marker['lod_score'] = 0
-                        marker['lrs_value'] = 0
-                    else:
-                        marker['lod_score'] = -math.log10(marker['p_value'])
-                        # Using -log(p) for the LRS; need to ask Rob how he wants to get LRS from p-values
-                        marker['lrs_value'] = - \
-                            math.log10(marker['p_value']) * 4.61
-                    filtered_markers.append(marker)
-            self.markers = filtered_markers
-
-
-class HumanMarkers(Markers):
-    "Markers for humans ..."
-
-    def __init__(self, name, specified_markers=[]):
-        marker_data_fh = open(flat_files('mapping') + '/' + name + '.bim')
-        self.markers = []
-        for line in marker_data_fh:
-            splat = line.strip().split()
-            if len(specified_markers) > 0:
-                if splat[1] in specified_markers:
-                    marker = {}
-                    marker['chr'] = int(splat[0])
-                    marker['name'] = splat[1]
-                    marker['Mb'] = float(splat[3]) / 1000000
-                else:
-                    continue
-            else:
-                marker = {}
-                marker['chr'] = int(splat[0])
-                marker['name'] = splat[1]
-                marker['Mb'] = float(splat[3]) / 1000000
-            self.markers.append(marker)
-
-    def add_pvalues(self, p_values):
-        super(HumanMarkers, self).add_pvalues(p_values)