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comparison uniqprimer-0.5.0/primertools/excludefilemanager.py @ 3:3249d78ecfc2 draft

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author dereeper
date Mon, 03 Jan 2022 09:56:55 +0000
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2:7e0438dad4e9 3:3249d78ecfc2
1 '''
2 Created on Jan 16, 2011
3
4 @author: jlh
5 '''
6 import utils
7 import fastaparser
8 from Bio import SeqIO
9 import os
10
11 class ExcludeFileManager( object ):
12 '''
13 A class to manage fasta files to be excluded
14 '''
15
16 def __init__( self ):
17 """
18 Initialize the ExcludeFileManager
19 """
20 self.excludeFiles = [ ]
21 self.outputFile = ""
22
23 def getOutputFileName( self ):
24 """
25 get the name of the file combined-sequence fasta file
26 """
27 return self.outputFile
28
29 def addExcludeFile( self, excludeFile ):
30 """
31 add a file to be managed by the ExcludeFileManager
32 """
33
34 if os.path.exists( excludeFile ) == False:
35 utils.logMessage( "ExcludeFileManager::addExcludeFile( )", "exclude file not found: {0}".format( excludeFile ) )
36 raise utils.NoFileFoundException( excludeFile )
37
38 utils.logMessage( "ExcludeFileManager::addExcludeFile( )", "adding exclude file {0}".format( excludeFile ) )
39 self.excludeFiles.append( excludeFile )
40
41 def buildOutputFileName( self ):
42 """
43 build a unique file name to store the combined output sequences to
44 """
45 self.outputFile = utils.getTemporaryDirectory( ) + "/combined_exlude.ffn"
46 utils.logMessage( "ExcludeFileManager::buildOutputFileName( )", " exclude file: {0}".format( self.outputFile ) )
47
48 def exportSequences( self ):
49 """
50 combine all exclude files into a single exclude file
51 """
52
53 utils.logMessage( "ExcludeFileManager::exportSequences( )", "parsing exclude sequences")
54
55 #read all exclude file sequences into memory
56 sequences = [ ]
57 for excludeFile in self.excludeFiles:
58 sequences.extend( fastaparser.parseFastaFile( excludeFile ) )
59
60 utils.logMessage( "ExcludeFileManager::exportSequences( )", "finished parsing, writing to a common file" )
61
62 self.buildOutputFileName( )
63 #combine the sequences and write them to a file
64
65 SeqIO.write( sequences, open( self.outputFile, "w" ), "fasta" )
66
67 utils.logMessage( "ExcludeFileManager::exportSequences( )", "All sequences exported" )
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