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1 import os
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2 import re
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3 import sys
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4 import operator
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5 import csv
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6 from galaxy import config
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7
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8 # get tool-data path
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9 configur = config.Configuration()
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10 kitDir = configur.resolve_path("tool-data")
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11
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12 # determine if config file exists
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13 if not os.path.exists( kitDir + "/report_poor_coverage" ):
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14 kitDir = "/export/achri_galaxy/dbs/CaptureKits/";
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15 else:
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16 with open(kitDir + "/report_poor_coverage", "r") as tsv:
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17 for line in csv.reader(tsv, delimiter="\t"):
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18 if line[0] == 'capturekits_directory':
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19 kitDir = line[1]
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20
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21 def kit_fileOptions():
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22 list = os.listdir(kitDir);
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23 list.sort()
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24 pattern = re.compile('(.*)$')
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25 fileOptions = [(s) for s in list if os.path.exists(kitDir + 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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29
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