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