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comparison capture_kits.py @ 1:a0f4b5618eee default tip

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abstracted capture kits
author Yusuf Ali <ali@yusuf.email>
date Wed, 25 Mar 2015 15:47:16 -0600
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0:6b2e640c8c6d 1:a0f4b5618eee
1 import os
2 import re
3 import sys
4 import operator
5 import csv
6 from galaxy import config
7
8 # get tool-data path
9 configur = config.Configuration()
10 kitDir = configur.resolve_path("tool-data")
11
12 # determine if config file exists
13 if not os.path.exists( kitDir + "/depth_report.loc" ):
14 kitDir = "/export/achri_galaxy/dbs/CaptureKits/";
15 else:
16 with open(kitDir + "/depth_report.loc", "r") as tsv:
17 for line in csv.reader(tsv, delimiter="\t"):
18 if line[0] == 'capture_kits_dir':
19 kitDir = line[1]
20
21 def kit_fileOptions():
22 list = os.listdir(kitDir);
23 list.sort()
24 pattern = re.compile('(.*)$')
25 fileOptions = [(s) for s in list if os.path.exists(kitDir + s)]
26 ds = [pattern.match(s) for s in fileOptions]
27 datasets = [(m.group(1), m.group(1), False) for m in ds if m]
28 return datasets
29