Mercurial > repos > yufei-luo > s_mart

comparison commons/pyRepetUnit/profilesDB/ProfilesDatabankUtils.py @ 18:94ab73e8a190

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author m-zytnicki
date Mon, 29 Apr 2013 03:20:15 -0400
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17:b0e8584489e6 18:94ab73e8a190
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 )