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1 import sys
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2 import os
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3 import re
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4
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5 def get_field_samples_options(dataset):
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6 options = []
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7 line=os.popen("grep '#CHROM' %s"%dataset.file_name).read()[:-1].split('\t')
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8 index=line.index('FORMAT')
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9 for opt in line[index+1:] :
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10 options.append((opt,opt, True))
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11 return options
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12
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13 def get_field_chrs_options(dataset):
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14 options = []
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15 chrs=os.popen("grep '##contig' %s"%dataset.file_name).read()[:-1].split('\n')
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16 for line in chrs:
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17 opt=re.search('^##contig=<ID=(\w+),length=',line).group(1)
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18 options.append((opt,opt, True))
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19 return options
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20
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