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Uploaded v0.0.1, previously only on the Test Tool Shed
author peterjc
date Fri, 21 Nov 2014 06:38:46 -0500
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-1:000000000000 0:ddd2e3362c5e
1 """
2 MiraAssemblyFormat class for the 'mira' format within Galaxy
3 """
4
5 from galaxy.datatypes.data import Text
6
7
8 class MiraAssemblyFormat(Text):
9 """MIRA Assembly Format data"""
10 file_ext = "mira"
11
12 def sniff( self, filename ):
13 """Determines whether the file is a MIRA Assembly Format file.
14
15 Note currently this only detects MIRA Assembly Format v2.0,
16 as used in MIRA v3.9 and v4.0.
17
18 It does not detect MIRA Assembly Format v1 as used in both
19 MIRA v3.2 and v3.4.
20 """
21 h = open(filename)
22 line = h.readline()
23 if line.rstrip() != "@Version\t2\t0":
24 h.close()
25 return False
26 line = h.readline()
27 if line.rstrip() != "@Program\tMIRALIB":
28 h.close()
29 return False
30 return True
31
32 def merge(split_files, output_file):
33 """Merging multiple MIRA files is non-trivial and may not be possible..."""
34 if len(split_files) == 1:
35 #For one file only, use base class method (move/copy)
36 return Text.merge(split_files, output_file)
37 if not split_files:
38 raise ValueError("Given no MIRA, %r, to merge into %s" \
39 % (split_files, output_file))
40 raise NotImplementedError("Merging MIRA Assembly Files has not been implemented")
41 merge = staticmethod(merge)
42
43 def split( cls, input_datasets, subdir_generator_function, split_params):
44 """Split a MIRA Assembly File (not implemented for now)."""
45 if split_params is None:
46 return None
47 raise NotImplementedError("Can't yet split a MIRA Assembly Format file")
48 merge = staticmethod(merge)