diff options
Diffstat (limited to 'wqflask/base/data_set/markers.py')
| -rw-r--r-- | wqflask/base/data_set/markers.py | 10 |
1 files changed, 6 insertions, 4 deletions
diff --git a/wqflask/base/data_set/markers.py b/wqflask/base/data_set/markers.py index 6f56445e..2fa7cce0 100644 --- a/wqflask/base/data_set/markers.py +++ b/wqflask/base/data_set/markers.py @@ -2,16 +2,18 @@ import math -from utility.tools import locate, flat_files +from flask import current_app as app + +from utility.configuration 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')) + json_data_fh = open(locate(app, name + ".json", 'genotype/json')) markers = [] - with open("%s/%s_snps.txt" % (flat_files('genotype/bimbam'), name), 'r') as bimbam_fh: + with open("%s/%s_snps.txt" % (flat_files(app, 'genotype/bimbam'), name), 'r') as bimbam_fh: if len(bimbam_fh.readline().split(", ")) > 2: delimiter = ", " elif len(bimbam_fh.readline().split(",")) > 2: @@ -73,7 +75,7 @@ class HumanMarkers(Markers): "Markers for humans ..." def __init__(self, name, specified_markers=[]): - marker_data_fh = open(flat_files('mapping') + '/' + name + '.bim') + marker_data_fh = open(flat_files(app, 'mapping') + '/' + name + '.bim') self.markers = [] for line in marker_data_fh: splat = line.strip().split() |