Mercurial > repos > yusuf > hgvs_annotate

comparison polyphen_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/";
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