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comparison uniqprimer-0.5.0/primertools/fastaparser.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 1, 2011
3
4 @author: John L. Herndon
5 @contact: herndon@cs.colostate.edu
6 @organization: Colorado State University
7 @group: Computer Science Department, Asa Ben-Hur's laboratory
8 '''
9
10
11 import utils
12 import primersequence
13
14 from Bio import SeqIO
15 from Bio import Seq
16 from Bio import Alphabet
17
18 def parseFastaFileAsPrimerSequence( fileName ):
19
20 utils.logMessage("fastaparser::parseFastaFileAsPrimerSequence( )", "parsing fasta file {0}".format( fileName ) )
21 returnValue = { }
22
23 sequences = SeqIO.parse( open( fileName ), "fasta" )
24
25 for sequence in sequences:
26 seqdata = primersequence.PrimerSequence( sequence.id, len( sequence ), sequence.seq )
27 returnValue[ sequence.id ] = seqdata
28
29 utils.logMessage("fastaparser::parseFastaFileAsPrimerSequence( )", "read {0} sequences".format( len( returnValue.keys( ) ) ) )
30
31 return returnValue
32
33 def parseFastaFile( fileName ):
34 '''
35 parse a fasta file and return a list of Bio.Seq
36 '''
37 utils.logMessage("fastaparser::parseFastaFile( )", "parsing fasta file {0}".format( fileName ) )
38
39 sequences = SeqIO.parse( open( fileName ), "fasta" )
40
41 return sequences
42
43 def writeFastaFile( sequences, fileName ):
44 '''
45 write a set of sequences to a fasta file.
46 returns the name of the new file
47 '''
48
49 primerSequenceIdent = "primer_sequences"
50 utils.logMessage( "PrimerManager::writeFastaFile( )", "Writing {0} sequences to fasta file".format( len( sequences ) ) )
51 seqRecords = [ ]
52 i = 0
53 for sequence in sequences:
54 seqStr = str( reduce( lambda x, y: str( x )+str( y ), sequence) )
55 seqRecord = SeqIO.SeqRecord( Seq.Seq( seqStr, Alphabet.IUPAC.extended_dna ), id="seq_{0}".format( i ) )
56 seqRecords.append( seqRecord )
57 i += 1
58
59 SeqIO.write( seqRecords, open( fileName, "w" ), "fasta" )
60
61 utils.logMessage( "PrimerManager::writeFastaFile( )", "writing fasta file complete" )
62 return fileName
63