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1 '''
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2 Created on Jan 1, 2011
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3
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4 @author: John L. Herndon
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5 @contact: herndon@cs.colostate.edu
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6 @organization: Colorado State University
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7 @group: Computer Science Department, Asa Ben-Hur's laboratory
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8 '''
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9
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10
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11 import utils
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12 import primersequence
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13
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14 from Bio import SeqIO
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15 from Bio import Seq
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16 from Bio import Alphabet
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17
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18 def parseFastaFileAsPrimerSequence( fileName ):
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19
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20 utils.logMessage("fastaparser::parseFastaFileAsPrimerSequence( )", "parsing fasta file {0}".format( fileName ) )
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21 returnValue = { }
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22
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23 sequences = SeqIO.parse( open( fileName ), "fasta" )
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24
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25 for sequence in sequences:
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26 seqdata = primersequence.PrimerSequence( sequence.id, len( sequence ), sequence.seq )
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27 returnValue[ sequence.id ] = seqdata
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28
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29 utils.logMessage("fastaparser::parseFastaFileAsPrimerSequence( )", "read {0} sequences".format( len( returnValue.keys( ) ) ) )
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30
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31 return returnValue
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32
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33 def parseFastaFile( fileName ):
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34 '''
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35 parse a fasta file and return a list of Bio.Seq
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36 '''
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37 utils.logMessage("fastaparser::parseFastaFile( )", "parsing fasta file {0}".format( fileName ) )
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38
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39 sequences = SeqIO.parse( open( fileName ), "fasta" )
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40
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41 return sequences
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42
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43 def writeFastaFile( sequences, fileName ):
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44 '''
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45 write a set of sequences to a fasta file.
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46 returns the name of the new file
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47 '''
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48
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49 primerSequenceIdent = "primer_sequences"
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50 utils.logMessage( "PrimerManager::writeFastaFile( )", "Writing {0} sequences to fasta file".format( len( sequences ) ) )
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51 seqRecords = [ ]
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52 i = 0
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53 for sequence in sequences:
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54 seqStr = str( reduce( lambda x, y: str( x )+str( y ), sequence) )
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55 seqRecord = SeqIO.SeqRecord( Seq.Seq( seqStr, Alphabet.IUPAC.extended_dna ), id="seq_{0}".format( i ) )
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56 seqRecords.append( seqRecord )
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57 i += 1
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58
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59 SeqIO.write( seqRecords, open( fileName, "w" ), "fasta" )
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60
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61 utils.logMessage( "PrimerManager::writeFastaFile( )", "writing fasta file complete" )
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62 return fileName
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63 |
