Mercurial > repos > yusuf > hgvs_annotate

comparison gerp_datasets.py @ 0:40dd2e7ee63a default tip

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initial commit
author Yusuf Ali <ali@yusuf.email>
date Wed, 25 Mar 2015 16:00:12 -0600
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-1:000000000000 0:40dd2e7ee63a
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/gerp/";
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] == 'gerp_path':
18 kitDir = line[1]
19
20 gerpDir = kitDir;
21 def GERP_fileOptions():
22 list = os.listdir(gerpDir);
23 list.sort()
24 pattern = re.compile('.*\d+')
25 fileOptions = [(s) for s in list if os.path.exists(gerpDir + s)]
26 datasets = [(s, s, False) for s in fileOptions if pattern.match(s)]
27 return datasets