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annotate mira.py @ 54:2bd1f1175fb2 draft

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planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/datatypes/mira_datatypes commit 206259620376b322fc8ed99a6efdd3712f38764b
author peterjc
date Wed, 11 Jul 2018 12:34:20 -0400
parents 94e05a9e3957
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54
2bd1f1175fb2 planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/datatypes/mira_datatypes commit 206259620376b322fc8ed99a6efdd3712f38764b
peterjc
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1 """MiraAssemblyFormat class for the 'mira' format within Galaxy."""
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94e05a9e3957 planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/datatypes/mira_datatypes commit fd979d17340cde155de176604744831d9597c6b6
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94e05a9e3957 planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/datatypes/mira_datatypes commit fd979d17340cde155de176604744831d9597c6b6
peterjc
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3 from galaxy.datatypes.data import Text
94e05a9e3957 planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/datatypes/mira_datatypes commit fd979d17340cde155de176604744831d9597c6b6
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94e05a9e3957 planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/datatypes/mira_datatypes commit fd979d17340cde155de176604744831d9597c6b6
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94e05a9e3957 planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/datatypes/mira_datatypes commit fd979d17340cde155de176604744831d9597c6b6
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6 class MiraAssemblyFormat(Text):
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2bd1f1175fb2 planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/datatypes/mira_datatypes commit 206259620376b322fc8ed99a6efdd3712f38764b
peterjc
parents: 3
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7 """MIRA Assembly Format data."""
2bd1f1175fb2 planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/datatypes/mira_datatypes commit 206259620376b322fc8ed99a6efdd3712f38764b
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parents: 3
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8
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94e05a9e3957 planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/datatypes/mira_datatypes commit fd979d17340cde155de176604744831d9597c6b6
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9 file_ext = "mira"
94e05a9e3957 planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/datatypes/mira_datatypes commit fd979d17340cde155de176604744831d9597c6b6
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94e05a9e3957 planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/datatypes/mira_datatypes commit fd979d17340cde155de176604744831d9597c6b6
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11 def sniff(self, filename):
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2bd1f1175fb2 planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/datatypes/mira_datatypes commit 206259620376b322fc8ed99a6efdd3712f38764b
peterjc
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12 """Determine if the file is a MIRA Assembly Format file.
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94e05a9e3957 planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/datatypes/mira_datatypes commit fd979d17340cde155de176604744831d9597c6b6
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94e05a9e3957 planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/datatypes/mira_datatypes commit fd979d17340cde155de176604744831d9597c6b6
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14 Note currently this only detects MIRA Assembly Format v2.0,
94e05a9e3957 planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/datatypes/mira_datatypes commit fd979d17340cde155de176604744831d9597c6b6
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15 as used in MIRA v3.9 and v4.0.
94e05a9e3957 planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/datatypes/mira_datatypes commit fd979d17340cde155de176604744831d9597c6b6
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94e05a9e3957 planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/datatypes/mira_datatypes commit fd979d17340cde155de176604744831d9597c6b6
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17 It does not detect MIRA Assembly Format v1 as used in both
94e05a9e3957 planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/datatypes/mira_datatypes commit fd979d17340cde155de176604744831d9597c6b6
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18 MIRA v3.2 and v3.4.
94e05a9e3957 planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/datatypes/mira_datatypes commit fd979d17340cde155de176604744831d9597c6b6
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19 """
94e05a9e3957 planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/datatypes/mira_datatypes commit fd979d17340cde155de176604744831d9597c6b6
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20 h = open(filename)
94e05a9e3957 planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/datatypes/mira_datatypes commit fd979d17340cde155de176604744831d9597c6b6
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21 line = h.readline()
94e05a9e3957 planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/datatypes/mira_datatypes commit fd979d17340cde155de176604744831d9597c6b6
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22 if line.rstrip() != "@Version\t2\t0":
94e05a9e3957 planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/datatypes/mira_datatypes commit fd979d17340cde155de176604744831d9597c6b6
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23 h.close()
94e05a9e3957 planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/datatypes/mira_datatypes commit fd979d17340cde155de176604744831d9597c6b6
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24 return False
94e05a9e3957 planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/datatypes/mira_datatypes commit fd979d17340cde155de176604744831d9597c6b6
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25 line = h.readline()
94e05a9e3957 planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/datatypes/mira_datatypes commit fd979d17340cde155de176604744831d9597c6b6
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26 if line.rstrip() != "@Program\tMIRALIB":
94e05a9e3957 planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/datatypes/mira_datatypes commit fd979d17340cde155de176604744831d9597c6b6
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27 h.close()
94e05a9e3957 planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/datatypes/mira_datatypes commit fd979d17340cde155de176604744831d9597c6b6
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28 return False
94e05a9e3957 planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/datatypes/mira_datatypes commit fd979d17340cde155de176604744831d9597c6b6
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29 return True
94e05a9e3957 planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/datatypes/mira_datatypes commit fd979d17340cde155de176604744831d9597c6b6
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94e05a9e3957 planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/datatypes/mira_datatypes commit fd979d17340cde155de176604744831d9597c6b6
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31 def merge(split_files, output_file):
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2bd1f1175fb2 planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/datatypes/mira_datatypes commit 206259620376b322fc8ed99a6efdd3712f38764b
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32 """Merge MIRA assembly files (not implemented).
2bd1f1175fb2 planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/datatypes/mira_datatypes commit 206259620376b322fc8ed99a6efdd3712f38764b
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2bd1f1175fb2 planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/datatypes/mira_datatypes commit 206259620376b322fc8ed99a6efdd3712f38764b
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34 Merging multiple MIRA files is non-trivial and may not be possible...
2bd1f1175fb2 planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/datatypes/mira_datatypes commit 206259620376b322fc8ed99a6efdd3712f38764b
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35 """
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36 if len(split_files) == 1:
94e05a9e3957 planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/datatypes/mira_datatypes commit fd979d17340cde155de176604744831d9597c6b6
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37 # For one file only, use base class method (move/copy)
94e05a9e3957 planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/datatypes/mira_datatypes commit fd979d17340cde155de176604744831d9597c6b6
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38 return Text.merge(split_files, output_file)
94e05a9e3957 planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/datatypes/mira_datatypes commit fd979d17340cde155de176604744831d9597c6b6
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39 if not split_files:
94e05a9e3957 planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/datatypes/mira_datatypes commit fd979d17340cde155de176604744831d9597c6b6
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40 raise ValueError("Given no MIRA, %r, to merge into %s"
94e05a9e3957 planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/datatypes/mira_datatypes commit fd979d17340cde155de176604744831d9597c6b6
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41 % (split_files, output_file))
94e05a9e3957 planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/datatypes/mira_datatypes commit fd979d17340cde155de176604744831d9597c6b6
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42 raise NotImplementedError("Merging MIRA Assembly Files has not been implemented")
94e05a9e3957 planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/datatypes/mira_datatypes commit fd979d17340cde155de176604744831d9597c6b6
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43 merge = staticmethod(merge)
94e05a9e3957 planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/datatypes/mira_datatypes commit fd979d17340cde155de176604744831d9597c6b6
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94e05a9e3957 planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/datatypes/mira_datatypes commit fd979d17340cde155de176604744831d9597c6b6
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45 def split(cls, input_datasets, subdir_generator_function, split_params):
94e05a9e3957 planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/datatypes/mira_datatypes commit fd979d17340cde155de176604744831d9597c6b6
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46 """Split a MIRA Assembly File (not implemented for now)."""
94e05a9e3957 planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/datatypes/mira_datatypes commit fd979d17340cde155de176604744831d9597c6b6
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47 if split_params is None:
94e05a9e3957 planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/datatypes/mira_datatypes commit fd979d17340cde155de176604744831d9597c6b6
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48 return None
94e05a9e3957 planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/datatypes/mira_datatypes commit fd979d17340cde155de176604744831d9597c6b6
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49 raise NotImplementedError("Can't yet split a MIRA Assembly Format file")
94e05a9e3957 planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/datatypes/mira_datatypes commit fd979d17340cde155de176604744831d9597c6b6
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50 merge = staticmethod(merge)