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1 '''
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2 Created on Jan 16, 2011
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3
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4 @author: jlh
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5 '''
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6 import utils
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7 import fastaparser
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8 from Bio import SeqIO
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9 import os
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10
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11 class ExcludeFileManager( object ):
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12 '''
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13 A class to manage fasta files to be excluded
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14 '''
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15
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16 def __init__( self ):
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17 """
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18 Initialize the ExcludeFileManager
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19 """
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20 self.excludeFiles = [ ]
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21 self.outputFile = ""
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22
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23 def getOutputFileName( self ):
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24 """
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25 get the name of the file combined-sequence fasta file
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26 """
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27 return self.outputFile
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28
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29 def addExcludeFile( self, excludeFile ):
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30 """
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31 add a file to be managed by the ExcludeFileManager
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32 """
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33
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34 if os.path.exists( excludeFile ) == False:
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35 utils.logMessage( "ExcludeFileManager::addExcludeFile( )", "exclude file not found: {0}".format( excludeFile ) )
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36 raise utils.NoFileFoundException( excludeFile )
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37
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38 utils.logMessage( "ExcludeFileManager::addExcludeFile( )", "adding exclude file {0}".format( excludeFile ) )
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39 self.excludeFiles.append( excludeFile )
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40
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41 def buildOutputFileName( self ):
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42 """
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43 build a unique file name to store the combined output sequences to
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44 """
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45 self.outputFile = utils.getTemporaryDirectory( ) + "/combined_exlude.ffn"
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46 utils.logMessage( "ExcludeFileManager::buildOutputFileName( )", " exclude file: {0}".format( self.outputFile ) )
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47
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48 def exportSequences( self ):
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49 """
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50 combine all exclude files into a single exclude file
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51 """
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52
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53 utils.logMessage( "ExcludeFileManager::exportSequences( )", "parsing exclude sequences")
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54
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55 #read all exclude file sequences into memory
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56 sequences = [ ]
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57 for excludeFile in self.excludeFiles:
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58 sequences.extend( fastaparser.parseFastaFile( excludeFile ) )
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59
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60 utils.logMessage( "ExcludeFileManager::exportSequences( )", "finished parsing, writing to a common file" )
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61
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62 self.buildOutputFileName( )
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63 #combine the sequences and write them to a file
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64
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65 SeqIO.write( sequences, open( self.outputFile, "w" ), "fasta" )
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66
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67 utils.logMessage( "ExcludeFileManager::exportSequences( )", "All sequences exported" )
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68
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