diff options
Diffstat (limited to 'wqflask')
| -rwxr-xr-x | wqflask/base/data_set.py | 11 |
1 files changed, 4 insertions, 7 deletions
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py index ab8554a0..16bc4ba4 100755 --- a/wqflask/base/data_set.py +++ b/wqflask/base/data_set.py @@ -74,16 +74,12 @@ class Markers(object): self.markers = json.load(json_data_fh) def add_pvalues(self, p_values): - print("length of self.markers:", len(self.markers)) - print("length of p_values:", len(p_values)) - # 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 itertools.izip(self.markers, p_values): marker['p_value'] = p_value - print("p_value is:", marker['p_value']) 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 @@ -99,9 +95,9 @@ class HumanMarkers(Markers): for line in marker_data_fh: splat = line.strip().split() marker = {} - marker['chr'] = int(splat[0]) + marker['chr'] = splat[0] marker['name'] = splat[1] - marker['Mb'] = float(splat[3]) / 1000000 + marker['Mb'] = str(float(splat[3]) / 1000000) self.markers.append(marker) #print("markers is: ", pf(self.markers)) @@ -122,7 +118,8 @@ class HumanMarkers(Markers): with Bench("deleting markers"): markers = [] for marker in self.markers: - if not marker['Mb'] <= 0 and not marker['chr'] == 0: + #if not float(marker['Mb']) <= 0 or not float(marker['chr']) == 0: + if float(marker['Mb']) > 0 and marker['chr'] != "0": markers.append(marker) self.markers = markers |