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annotate mira.py @ 84:8d7684a3346a draft

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planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/datatypes/mira_datatypes commit 89578746a1c5b29c84a173d8b2709f086f69a7b6
author peterjc
date Mon, 01 Jul 2019 13:28:59 -0400
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65ea1ef0181d planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/datatypes/mira_datatypes commit 89578746a1c5b29c84a173d8b2709f086f69a7b6
peterjc
parents:
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1 """MiraAssemblyFormat class for the 'mira' format within Galaxy."""
65ea1ef0181d planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/datatypes/mira_datatypes commit 89578746a1c5b29c84a173d8b2709f086f69a7b6
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65ea1ef0181d planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/datatypes/mira_datatypes commit 89578746a1c5b29c84a173d8b2709f086f69a7b6
peterjc
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3 from galaxy.datatypes.data import Text
65ea1ef0181d planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/datatypes/mira_datatypes commit 89578746a1c5b29c84a173d8b2709f086f69a7b6
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65ea1ef0181d planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/datatypes/mira_datatypes commit 89578746a1c5b29c84a173d8b2709f086f69a7b6
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65ea1ef0181d planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/datatypes/mira_datatypes commit 89578746a1c5b29c84a173d8b2709f086f69a7b6
peterjc
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6 class MiraAssemblyFormat(Text):
65ea1ef0181d planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/datatypes/mira_datatypes commit 89578746a1c5b29c84a173d8b2709f086f69a7b6
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7 """MIRA Assembly Format data."""
65ea1ef0181d planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/datatypes/mira_datatypes commit 89578746a1c5b29c84a173d8b2709f086f69a7b6
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65ea1ef0181d planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/datatypes/mira_datatypes commit 89578746a1c5b29c84a173d8b2709f086f69a7b6
peterjc
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9 file_ext = "mira"
65ea1ef0181d planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/datatypes/mira_datatypes commit 89578746a1c5b29c84a173d8b2709f086f69a7b6
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65ea1ef0181d planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/datatypes/mira_datatypes commit 89578746a1c5b29c84a173d8b2709f086f69a7b6
peterjc
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11 def sniff(self, filename):
65ea1ef0181d planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/datatypes/mira_datatypes commit 89578746a1c5b29c84a173d8b2709f086f69a7b6
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12 """Determine if the file is a MIRA Assembly Format file.
65ea1ef0181d planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/datatypes/mira_datatypes commit 89578746a1c5b29c84a173d8b2709f086f69a7b6
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65ea1ef0181d planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/datatypes/mira_datatypes commit 89578746a1c5b29c84a173d8b2709f086f69a7b6
peterjc
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14 Note currently this only detects MIRA Assembly Format v2.0,
65ea1ef0181d planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/datatypes/mira_datatypes commit 89578746a1c5b29c84a173d8b2709f086f69a7b6
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15 as used in MIRA v3.9 and v4.0.
65ea1ef0181d planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/datatypes/mira_datatypes commit 89578746a1c5b29c84a173d8b2709f086f69a7b6
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65ea1ef0181d planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/datatypes/mira_datatypes commit 89578746a1c5b29c84a173d8b2709f086f69a7b6
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17 It does not detect MIRA Assembly Format v1 as used in both
65ea1ef0181d planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/datatypes/mira_datatypes commit 89578746a1c5b29c84a173d8b2709f086f69a7b6
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18 MIRA v3.2 and v3.4.
65ea1ef0181d planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/datatypes/mira_datatypes commit 89578746a1c5b29c84a173d8b2709f086f69a7b6
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19 """
65ea1ef0181d planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/datatypes/mira_datatypes commit 89578746a1c5b29c84a173d8b2709f086f69a7b6
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20 h = open(filename)
65ea1ef0181d planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/datatypes/mira_datatypes commit 89578746a1c5b29c84a173d8b2709f086f69a7b6
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21 line = h.readline()
65ea1ef0181d planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/datatypes/mira_datatypes commit 89578746a1c5b29c84a173d8b2709f086f69a7b6
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22 if line.rstrip() != "@Version\t2\t0":
65ea1ef0181d planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/datatypes/mira_datatypes commit 89578746a1c5b29c84a173d8b2709f086f69a7b6
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23 h.close()
65ea1ef0181d planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/datatypes/mira_datatypes commit 89578746a1c5b29c84a173d8b2709f086f69a7b6
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24 return False
65ea1ef0181d planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/datatypes/mira_datatypes commit 89578746a1c5b29c84a173d8b2709f086f69a7b6
peterjc
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25 line = h.readline()
65ea1ef0181d planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/datatypes/mira_datatypes commit 89578746a1c5b29c84a173d8b2709f086f69a7b6
peterjc
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26 if line.rstrip() != "@Program\tMIRALIB":
65ea1ef0181d planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/datatypes/mira_datatypes commit 89578746a1c5b29c84a173d8b2709f086f69a7b6
peterjc
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27 h.close()
65ea1ef0181d planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/datatypes/mira_datatypes commit 89578746a1c5b29c84a173d8b2709f086f69a7b6
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28 return False
65ea1ef0181d planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/datatypes/mira_datatypes commit 89578746a1c5b29c84a173d8b2709f086f69a7b6
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29 return True
65ea1ef0181d planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/datatypes/mira_datatypes commit 89578746a1c5b29c84a173d8b2709f086f69a7b6
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65ea1ef0181d planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/datatypes/mira_datatypes commit 89578746a1c5b29c84a173d8b2709f086f69a7b6
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31 def merge(split_files, output_file):
65ea1ef0181d planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/datatypes/mira_datatypes commit 89578746a1c5b29c84a173d8b2709f086f69a7b6
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32 """Merge MIRA assembly files (not implemented).
65ea1ef0181d planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/datatypes/mira_datatypes commit 89578746a1c5b29c84a173d8b2709f086f69a7b6
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33
65ea1ef0181d planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/datatypes/mira_datatypes commit 89578746a1c5b29c84a173d8b2709f086f69a7b6
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34 Merging multiple MIRA files is non-trivial and may not be possible...
65ea1ef0181d planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/datatypes/mira_datatypes commit 89578746a1c5b29c84a173d8b2709f086f69a7b6
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35 """
65ea1ef0181d planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/datatypes/mira_datatypes commit 89578746a1c5b29c84a173d8b2709f086f69a7b6
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36 if len(split_files) == 1:
65ea1ef0181d planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/datatypes/mira_datatypes commit 89578746a1c5b29c84a173d8b2709f086f69a7b6
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37 # For one file only, use base class method (move/copy)
65ea1ef0181d planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/datatypes/mira_datatypes commit 89578746a1c5b29c84a173d8b2709f086f69a7b6
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38 return Text.merge(split_files, output_file)
65ea1ef0181d planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/datatypes/mira_datatypes commit 89578746a1c5b29c84a173d8b2709f086f69a7b6
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39 if not split_files:
65ea1ef0181d planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/datatypes/mira_datatypes commit 89578746a1c5b29c84a173d8b2709f086f69a7b6
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40 raise ValueError(
65ea1ef0181d planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/datatypes/mira_datatypes commit 89578746a1c5b29c84a173d8b2709f086f69a7b6
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41 "No MIRA files to merge, %r, into %r" % (split_files, output_file)
65ea1ef0181d planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/datatypes/mira_datatypes commit 89578746a1c5b29c84a173d8b2709f086f69a7b6
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42 )
65ea1ef0181d planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/datatypes/mira_datatypes commit 89578746a1c5b29c84a173d8b2709f086f69a7b6
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43 raise NotImplementedError(
65ea1ef0181d planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/datatypes/mira_datatypes commit 89578746a1c5b29c84a173d8b2709f086f69a7b6
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44 "Merging MIRA Assembly Files has not been implemented"
65ea1ef0181d planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/datatypes/mira_datatypes commit 89578746a1c5b29c84a173d8b2709f086f69a7b6
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45 )
65ea1ef0181d planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/datatypes/mira_datatypes commit 89578746a1c5b29c84a173d8b2709f086f69a7b6
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46
65ea1ef0181d planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/datatypes/mira_datatypes commit 89578746a1c5b29c84a173d8b2709f086f69a7b6
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47 merge = staticmethod(merge)
65ea1ef0181d planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/datatypes/mira_datatypes commit 89578746a1c5b29c84a173d8b2709f086f69a7b6
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48
65ea1ef0181d planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/datatypes/mira_datatypes commit 89578746a1c5b29c84a173d8b2709f086f69a7b6
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49 def split(cls, input_datasets, subdir_generator_function, split_params):
65ea1ef0181d planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/datatypes/mira_datatypes commit 89578746a1c5b29c84a173d8b2709f086f69a7b6
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50 """Split a MIRA Assembly File (not implemented for now)."""
65ea1ef0181d planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/datatypes/mira_datatypes commit 89578746a1c5b29c84a173d8b2709f086f69a7b6
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51 if split_params is None:
65ea1ef0181d planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/datatypes/mira_datatypes commit 89578746a1c5b29c84a173d8b2709f086f69a7b6
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52 return None
65ea1ef0181d planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/datatypes/mira_datatypes commit 89578746a1c5b29c84a173d8b2709f086f69a7b6
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53 raise NotImplementedError("Can't yet split a MIRA Assembly Format file")
65ea1ef0181d planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/datatypes/mira_datatypes commit 89578746a1c5b29c84a173d8b2709f086f69a7b6
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54
65ea1ef0181d planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/datatypes/mira_datatypes commit 89578746a1c5b29c84a173d8b2709f086f69a7b6
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55 merge = staticmethod(merge)