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1 """
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2 MiraAssemblyFormat class for the 'mira' format within Galaxy
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3 """
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4
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5 from galaxy.datatypes.data import Text
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6
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7
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8 class MiraAssemblyFormat(Text):
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9 """MIRA Assembly Format data"""
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10 file_ext = "mira"
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11
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12 def sniff( self, filename ):
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13 """Determines whether the file is a MIRA Assembly Format file.
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14
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15 Note currently this only detects MIRA Assembly Format v2.0,
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16 as used in MIRA v3.9 and v4.0.
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17
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18 It does not detect MIRA Assembly Format v1 as used in both
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19 MIRA v3.2 and v3.4.
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20 """
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21 h = open(filename)
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22 line = h.readline()
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23 if line.rstrip() != "@Version\t2\t0":
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24 h.close()
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25 return False
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26 line = h.readline()
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27 if line.rstrip() != "@Program\tMIRALIB":
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28 h.close()
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29 return False
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30 return True
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31
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32 def merge(split_files, output_file):
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33 """Merging multiple MIRA files is non-trivial and may not be possible..."""
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34 if len(split_files) == 1:
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35 #For one file only, use base class method (move/copy)
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36 return Text.merge(split_files, output_file)
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37 if not split_files:
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38 raise ValueError("Given no MIRA, %r, to merge into %s" \
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39 % (split_files, output_file))
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40 raise NotImplementedError("Merging MIRA Assembly Files has not been implemented")
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41 merge = staticmethod(merge)
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42
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43 def split( cls, input_datasets, subdir_generator_function, split_params):
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44 """Split a MIRA Assembly File (not implemented for now)."""
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45 if split_params is None:
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46 return None
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47 raise NotImplementedError("Can't yet split a MIRA Assembly Format file")
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48 merge = staticmethod(merge)
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