|
0
|
1 import os
|
|
|
2 import re
|
|
|
3 import csv
|
|
|
4 import operator
|
|
|
5 from galaxy import config
|
|
|
6
|
|
|
7 # get tool-data path
|
|
|
8 configur = config.Configuration()
|
|
|
9 kitDir = configur.resolve_path("tool-data")
|
|
|
10
|
|
|
11 # determine if config file exists
|
|
|
12 if not os.path.exists( kitDir + "/hgvs_annotate.loc" ):
|
|
|
13 kitDir = "/export/geno_tmp/achri/dbs/";
|
|
|
14 else:
|
|
|
15 with open(kitDir + "/hgvs_annotate.loc", "r") as tsv:
|
|
|
16 for line in csv.reader(tsv, delimiter="\t"):
|
|
|
17 if line[0] == 'pathways_dbs':
|
|
|
18 kitDir = line[1]
|
|
|
19
|
|
|
20
|
|
|
21 polyPhenDir = kitDir
|
|
|
22 def PolyPhen_fileOptions():
|
|
|
23 list = os.listdir(polyPhenDir);
|
|
|
24 list.sort()
|
|
|
25 pattern = re.compile('polyphen_(.*)\.txt.gz$')
|
|
|
26 fileOptions = [(s) for s in list if os.path.exists(polyPhenDir + s)]
|
|
|
27 ds = [pattern.match(s) for s in fileOptions]
|
|
|
28 datasets = [(m.group(1), m.group(1), False) for m in ds if m]
|
|
|
29 return datasets
|
