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annotate mira.py @ 74:e30e2d1d17e7 draft

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planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/datatypes/mira_datatypes commit d4e11b67b826d88a69f81b7a208d23bddc8526a4
author peterjc
date Mon, 21 Jan 2019 12:18:07 -0500
parents ce83350d97de
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ce83350d97de planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/datatypes/mira_datatypes commit 37696a346fd171af564d7681e409603b4b93bf65
peterjc
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1 """MiraAssemblyFormat class for the 'mira' format within Galaxy."""
ce83350d97de planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/datatypes/mira_datatypes commit 37696a346fd171af564d7681e409603b4b93bf65
peterjc
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ce83350d97de planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/datatypes/mira_datatypes commit 37696a346fd171af564d7681e409603b4b93bf65
peterjc
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3 from galaxy.datatypes.data import Text
ce83350d97de planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/datatypes/mira_datatypes commit 37696a346fd171af564d7681e409603b4b93bf65
peterjc
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ce83350d97de planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/datatypes/mira_datatypes commit 37696a346fd171af564d7681e409603b4b93bf65
peterjc
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ce83350d97de planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/datatypes/mira_datatypes commit 37696a346fd171af564d7681e409603b4b93bf65
peterjc
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6 class MiraAssemblyFormat(Text):
ce83350d97de planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/datatypes/mira_datatypes commit 37696a346fd171af564d7681e409603b4b93bf65
peterjc
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7 """MIRA Assembly Format data."""
ce83350d97de planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/datatypes/mira_datatypes commit 37696a346fd171af564d7681e409603b4b93bf65
peterjc
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8
ce83350d97de planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/datatypes/mira_datatypes commit 37696a346fd171af564d7681e409603b4b93bf65
peterjc
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9 file_ext = "mira"
ce83350d97de planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/datatypes/mira_datatypes commit 37696a346fd171af564d7681e409603b4b93bf65
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ce83350d97de planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/datatypes/mira_datatypes commit 37696a346fd171af564d7681e409603b4b93bf65
peterjc
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11 def sniff(self, filename):
ce83350d97de planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/datatypes/mira_datatypes commit 37696a346fd171af564d7681e409603b4b93bf65
peterjc
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12 """Determine if the file is a MIRA Assembly Format file.
ce83350d97de planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/datatypes/mira_datatypes commit 37696a346fd171af564d7681e409603b4b93bf65
peterjc
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ce83350d97de planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/datatypes/mira_datatypes commit 37696a346fd171af564d7681e409603b4b93bf65
peterjc
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14 Note currently this only detects MIRA Assembly Format v2.0,
ce83350d97de planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/datatypes/mira_datatypes commit 37696a346fd171af564d7681e409603b4b93bf65
peterjc
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15 as used in MIRA v3.9 and v4.0.
ce83350d97de planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/datatypes/mira_datatypes commit 37696a346fd171af564d7681e409603b4b93bf65
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ce83350d97de planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/datatypes/mira_datatypes commit 37696a346fd171af564d7681e409603b4b93bf65
peterjc
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17 It does not detect MIRA Assembly Format v1 as used in both
ce83350d97de planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/datatypes/mira_datatypes commit 37696a346fd171af564d7681e409603b4b93bf65
peterjc
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18 MIRA v3.2 and v3.4.
ce83350d97de planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/datatypes/mira_datatypes commit 37696a346fd171af564d7681e409603b4b93bf65
peterjc
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19 """
ce83350d97de planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/datatypes/mira_datatypes commit 37696a346fd171af564d7681e409603b4b93bf65
peterjc
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20 h = open(filename)
ce83350d97de planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/datatypes/mira_datatypes commit 37696a346fd171af564d7681e409603b4b93bf65
peterjc
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21 line = h.readline()
ce83350d97de planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/datatypes/mira_datatypes commit 37696a346fd171af564d7681e409603b4b93bf65
peterjc
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22 if line.rstrip() != "@Version\t2\t0":
ce83350d97de planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/datatypes/mira_datatypes commit 37696a346fd171af564d7681e409603b4b93bf65
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23 h.close()
ce83350d97de planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/datatypes/mira_datatypes commit 37696a346fd171af564d7681e409603b4b93bf65
peterjc
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24 return False
ce83350d97de planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/datatypes/mira_datatypes commit 37696a346fd171af564d7681e409603b4b93bf65
peterjc
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25 line = h.readline()
ce83350d97de planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/datatypes/mira_datatypes commit 37696a346fd171af564d7681e409603b4b93bf65
peterjc
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26 if line.rstrip() != "@Program\tMIRALIB":
ce83350d97de planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/datatypes/mira_datatypes commit 37696a346fd171af564d7681e409603b4b93bf65
peterjc
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27 h.close()
ce83350d97de planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/datatypes/mira_datatypes commit 37696a346fd171af564d7681e409603b4b93bf65
peterjc
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28 return False
ce83350d97de planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/datatypes/mira_datatypes commit 37696a346fd171af564d7681e409603b4b93bf65
peterjc
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29 return True
ce83350d97de planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/datatypes/mira_datatypes commit 37696a346fd171af564d7681e409603b4b93bf65
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ce83350d97de planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/datatypes/mira_datatypes commit 37696a346fd171af564d7681e409603b4b93bf65
peterjc
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31 def merge(split_files, output_file):
ce83350d97de planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/datatypes/mira_datatypes commit 37696a346fd171af564d7681e409603b4b93bf65
peterjc
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32 """Merge MIRA assembly files (not implemented).
ce83350d97de planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/datatypes/mira_datatypes commit 37696a346fd171af564d7681e409603b4b93bf65
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ce83350d97de planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/datatypes/mira_datatypes commit 37696a346fd171af564d7681e409603b4b93bf65
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34 Merging multiple MIRA files is non-trivial and may not be possible...
ce83350d97de planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/datatypes/mira_datatypes commit 37696a346fd171af564d7681e409603b4b93bf65
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35 """
ce83350d97de planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/datatypes/mira_datatypes commit 37696a346fd171af564d7681e409603b4b93bf65
peterjc
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36 if len(split_files) == 1:
ce83350d97de planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/datatypes/mira_datatypes commit 37696a346fd171af564d7681e409603b4b93bf65
peterjc
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37 # For one file only, use base class method (move/copy)
ce83350d97de planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/datatypes/mira_datatypes commit 37696a346fd171af564d7681e409603b4b93bf65
peterjc
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38 return Text.merge(split_files, output_file)
ce83350d97de planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/datatypes/mira_datatypes commit 37696a346fd171af564d7681e409603b4b93bf65
peterjc
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39 if not split_files:
ce83350d97de planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/datatypes/mira_datatypes commit 37696a346fd171af564d7681e409603b4b93bf65
peterjc
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40 raise ValueError("Given no MIRA, %r, to merge into %s"
ce83350d97de planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/datatypes/mira_datatypes commit 37696a346fd171af564d7681e409603b4b93bf65
peterjc
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41 % (split_files, output_file))
ce83350d97de planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/datatypes/mira_datatypes commit 37696a346fd171af564d7681e409603b4b93bf65
peterjc
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42 raise NotImplementedError("Merging MIRA Assembly Files has not been implemented")
ce83350d97de planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/datatypes/mira_datatypes commit 37696a346fd171af564d7681e409603b4b93bf65
peterjc
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43 merge = staticmethod(merge)
ce83350d97de planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/datatypes/mira_datatypes commit 37696a346fd171af564d7681e409603b4b93bf65
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44
ce83350d97de planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/datatypes/mira_datatypes commit 37696a346fd171af564d7681e409603b4b93bf65
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45 def split(cls, input_datasets, subdir_generator_function, split_params):
ce83350d97de planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/datatypes/mira_datatypes commit 37696a346fd171af564d7681e409603b4b93bf65
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46 """Split a MIRA Assembly File (not implemented for now)."""
ce83350d97de planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/datatypes/mira_datatypes commit 37696a346fd171af564d7681e409603b4b93bf65
peterjc
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47 if split_params is None:
ce83350d97de planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/datatypes/mira_datatypes commit 37696a346fd171af564d7681e409603b4b93bf65
peterjc
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48 return None
ce83350d97de planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/datatypes/mira_datatypes commit 37696a346fd171af564d7681e409603b4b93bf65
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49 raise NotImplementedError("Can't yet split a MIRA Assembly Format file")
ce83350d97de planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/datatypes/mira_datatypes commit 37696a346fd171af564d7681e409603b4b93bf65
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50 merge = staticmethod(merge)