Mercurial > repos > yufei-luo > s_mart
comparison commons/pyRepetUnit/profilesDB/ProfilesDatabankUtils.py @ 18:94ab73e8a190
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author | m-zytnicki |
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date | Mon, 29 Apr 2013 03:20:15 -0400 |
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17:b0e8584489e6 | 18:94ab73e8a190 |
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1 """ | |
2 Utility to handle a databank of HMM profiles. | |
3 """ | |
4 | |
5 import sys | |
6 from commons.pyRepetUnit.profilesDB.Profiles import Profiles | |
7 from commons.pyRepetUnit.profilesDB.ProfilesDatabank import ProfilesDatabank | |
8 from commons.core.utils.FileUtils import FileUtils | |
9 | |
10 class ProfilesDatabankUtils: | |
11 """ | |
12 Utility to handle a databank of HMM profiles. | |
13 """ | |
14 | |
15 def read( inFileName, verbose=0 ): | |
16 """ | |
17 Read a file in Pfam format and return a L[ProfilesDatabank<commons.core.ProfilesDatabank>} instance. | |
18 @param inFileName: name of the input file | |
19 @type inFileName: string | |
20 @param verbose: verbosity level | |
21 @type verbose: integer | |
22 """ | |
23 if verbose > 0: print "reading file '%s'..." % ( inFileName ); sys.stdout.flush() | |
24 | |
25 | |
26 if FileUtils.isEmpty(inFileName): | |
27 return (None) | |
28 profilesInstance = Profiles() | |
29 profilesDBInstance = ProfilesDatabank() | |
30 f = open( inFileName , "r") | |
31 while profilesInstance.read( f ): | |
32 profilesDBInstance.append( profilesInstance ) | |
33 profilesInstance = Profiles() | |
34 f.close() | |
35 if verbose > 0: print "file '%s' is loaded" % ( inFileName ); sys.stdout.flush() | |
36 return (profilesDBInstance) | |
37 | |
38 read = staticmethod( read ) |