Mercurial > repos > edward-kirton > hmmer
comparison hmmer.py @ 1:66f8262e1686
add datatype
author | eskirton@lbl.gov |
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date | Mon, 05 Mar 2012 22:51:04 -0800 |
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0:c16d8db9338a | 1:66f8262e1686 |
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1 """ | |
2 Hmmer classes | |
3 """ | |
4 | |
5 import data | |
6 import logging | |
7 import re | |
8 import string | |
9 from cgi import escape | |
10 from galaxy.datatypes.metadata import MetadataElement | |
11 from galaxy.datatypes import metadata | |
12 import galaxy.model | |
13 from galaxy import util | |
14 from sniff import * | |
15 | |
16 log = logging.getLogger(__name__) | |
17 | |
18 class Hmm( data.Text ): | |
19 """Class for hmmer database files""" | |
20 | |
21 file_ext = 'hmm' | |
22 | |
23 def init_meta( self, dataset, copy_from=None ): | |
24 data.Text.init_meta( self, dataset, copy_from=copy_from ) | |
25 | |
26 class HmmPressed( Hmm ): | |
27 """Class describing a hmmer database produced by hmmpress""" | |
28 | |
29 file_ext = 'hmmPressed' | |
30 composite_type='basic' | |
31 | |
32 MetadataElement( readonly=True, optional=True, visible=False, no_value=0 ) | |
33 | |
34 def __init__(self,**kwd): | |
35 data.Data.__init__(self, **kwd) | |
36 self.add_composite_file('hmm.h3m') | |
37 self.add_composite_file('hmm.h3i') | |
38 self.add_composite_file('hmm.h3f') | |
39 self.add_composite_file('hmm.h3p') | |
40 def set_peek( self, dataset, is_multi_byte=False ): | |
41 if not dataset.dataset.purged: | |
42 dataset.peek = "Folder of multiple files" | |
43 dataset.blurb = "Folder of multiple files" | |
44 else: | |
45 dataset.peek = 'file does not exist' | |
46 dataset.blurb = 'file purged from disk' | |
47 def display_peek( self, dataset ): | |
48 try: | |
49 return dataset.peek | |
50 except: | |
51 return "Folder of multiple files" | |
52 def get_mime(self): | |
53 """Returns the mime type of the datatype""" | |
54 return 'text/plain' |