diff options
Diffstat (limited to 'wqflask/base')
| -rw-r--r-- | wqflask/base/data_set.py | 23 |
1 files changed, 20 insertions, 3 deletions
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py index 9ca880d0..4a422ee4 100644 --- a/wqflask/base/data_set.py +++ b/wqflask/base/data_set.py @@ -169,8 +169,27 @@ class Markers(object): """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')) + try: - markers = json.load(json_data_fh) + markers = [] + with open(locate(name + "_snps.txt", 'r')) as bimbam_fh: + marker = {} + if len(bimbam_fh[0].split(", ")) > 2: + delimiter = ", " + elif len(bimbam_fh[0].split(",")) > 2: + delimiter = "," + elif len(bimbam_fh[0].split("\t")) > 2: + delimiter = "\t" + else: + delimiter = " " + for line in bimbam_fh: + marker['name'] = line.split(delimiter)[0] + marker['Mb'] + marker['chr'] = line.split(delimiter)[2] + marker['cM'] + markers.append(marker) + #try: + # markers = json.load(json_data_fh) except: markers = [] @@ -180,8 +199,6 @@ class Markers(object): marker['Mb'] = float(marker['Mb']) self.markers = markers - #logger.debug("self.markers:", self.markers) - def add_pvalues(self, p_values): logger.debug("length of self.markers:", len(self.markers)) |