"""PrimerDesign script using Primer3 by yong27, 2005-05-17

priming conditions refer to http://www.rfcgr.mrc.ac.uk/Software/EMBOSS/Apps/eprimer3.html """ import unittest, os, glob from cStringIO import StringIO from Bio import Fasta from Bio.Emboss import Primer

class PrimerDesigner:

• temp_dir = 'temp'

  def init(self, ifile):

  • self.fi = Fasta.Iterator(ifile, Fasta.RecordParser()) self.pg = None

  def getNextFasta(self):
  • return self.fi.next()
  def saveAllFastas(self):
  • self.cleanUp() os.mkdir(self.temp_dir) for fasta in self.fi:
    • fasta.title = fasta.title.replace(':','-')

      besid = ''.join(fasta.title.split()) file(os.path.join(self.temp_dir, besid), 'w').write(str(fasta))

  def cleanUp(self):
  • if os.path.exists(self.temp_dir):
    • for fname in os.listdir(self.temp_dir):
      • os.remove(os.path.join(self.temp_dir, fname))
      os.rmdir(self.temp_dir)
  def doPrimer3(self, **keywds):
  • self.saveAllFastas() for fname in os.listdir(self.temp_dir):
    • fname = os.path.join(self.temp_dir, fname) cmds = ['eprimer3'] cmds.extend(['-sequence', fname]) cmds.extend(['-outfile', fname+'.eprimer3']) for k,v in keywds.iteritems():
      • cmds.extend(['-'+k, v])
      os.system(' '.join(cmds))
    self.pg = self.primerGenerator()
  def getNextPrimer(self):
  • return self.pg.next()
  def primerGenerator(self):

  • ppser = Primer.Primer3Parser() for fname in glob.glob(os.path.join(self.temp_dir, '*.eprimer3')):

    • try:
      • primer = ppser.parse(file(fname)).primers[0]

      except IndexError:

      • continue
      yield (os.path.splitext(os.path.split(fname)[1])[0], primer)
  def getPrimerInfos(self, primer, direction):
  • seq = getattr(primer, direction+'_seq') tm = getattr(primer, direction+'_tm') return [direction, seq, str(tm), str(primer.size)]
  def writeXls(self, xfile):
  • for fname, primer in self.pg:

    • words = fname.split('') xfile.write('\t'.join(words+self.getPrimerInfos(primer, 'forward'))+'\n') xfile.write('\t'.join(words+self.getPrimerInfos(primer, 'reverse'))+'\n')

class BreakPrimerDesigner(PrimerDesigner):

• def init(self, ifile):

  • PrimerDesigner.init(self, ifile)

  def writeXls(self, xfile):
  • xfile.write('\t'.join([
    • 'BAC', 'BES', 'FPC start', 'FPC end', 'Human match', 'Direction', 'Primer sequence', 'Primer TM', 'Product size' ])+'\n')
    for fname, primer in self.pg:

    • besid, bacid, start, end, humanMatch = fname.split('') xfile.write('\t'.join([

      • bacid, besid, start, end, humanMatch, ]+self.getPrimerInfos(primer, 'forward'))+'\n')
      xfile.write('\t'.join([
      • bacid, besid, start, end, humanMatch, ]+self.getPrimerInfos(primer, 'reverse'))+'\n')

class ByunsBreakPrimerDesigner:

• def init(self, ifile):

  • self.pd = BreakPrimerDesigner(ifile) self.pd.doPrimer3(otm='55', mintm='53')

  def write(self, wfile):
  • self.pd.writeXls(wfile)

class TestPrimerDesigner(unittest.TestCase):

• def setUp(self):
  • inputFile = StringIO("""\

>bE78F16SP6 CH242-78F16 46 72 18:11487196-11487708 GGTTGATGGTTCCCTGGTTTCATAAAACCTCTCAGGAACATTAGACTATGTCCGTGGAGA GAAGTAAAACCCAATTATCCTCAGTGCCAGTAGTTTTTATGTCTCAGAAGAGATTCTGCT GGAAGGATCACTGGGCATTTCAAGATGTTTGGAAACACTGCACTGATGGAGTTATCCTCA GAGGGGTGTCATTAAATGTTTGTTTACGATTGTTGGTGGGTCTATCAAACCCACTTATTT CTGCCAGCGTTAGATTTTTGACTCAATTAGGAAAAAAAAAGTATTAGAGGGAACTAACTT TGCAGCAAAGGGCAGATACTCTTAGGTACTGAAAACTTGCTGAATTCTGTAGGAATAGGA ACCTTGGGAATTATGCTTCCGTAGGAGAAATAATCAGAAAGGTCATTTTAGTCACTTAGG AGTCTGTGGTGCCACTGGAATAATTAAAAACATGATAATTTAAACTGACTGTAGAGGTAA TGGAAGAAACATGAAATTTAGTTAGACTAGGGTAGTTGAGTTTGTTCAAAAATCAAATGG AAATCTTAGGGCACTACGGGAGCAGTTGAGAGTTGATCACAGCTGAGCAAGGCTGGTCTT CTTCCTGCAGGTCCCGGCACCTTTGAGGATCTGACAAAGGCTGGCTGTCTTCTCTCAAGA CAAGGGGCACGGGACCCCCAGTG >bE78F16T7 CH242-78F16 46 72 18:11085776-11086061 TTGCTCTAACAGCCCTGAAATCCCCTGCAGCAGATTACTCTGATATAGGANGAANNGGCC CCCNTTNCCNTTCACTGCTCTTTTTGACTTCCAAAAATAATATTCTGGCCCAGCTGTTCG GTCAGGGCCTCGGTTTATTTGTAGTTAGCCAGAGAGGGGACCATAAATGAAATTCAGATG CCGGGAGGGAGGAATGTCAGTCCTTCCAAATCCAACACTGAAAAGCCTTTCTTGTTTTTG AGCTGAATAAAGAACGTCGGGCAATGGAACTTTGACCCAACATGCCATCCAGTCCAAAGA GGAACGGCCAGAAAAAAGTGGACTTGTCTGGAGATGGTTCTCAGCCTCTAAGCCAGCCAG CTCAGTCCCTTGTTTTAGCCCCCAGGGTATCTGGGCAGCCACAGGTCTGAGACACCCTTG GTAGCTGAGGGCTCCCCTGGGCGCACAGGGCATGAGGGTGCCACCACGAAGAGGGGCCAC AGGGCCCTTTTGTCAGCAAACAGAGCCTGGGCTCCAGGCTCCAGGTCTTGCAACAAATCC CACCTCACC """)

• self.pd = PrimerDesigner(inputFile)

• def testGetNextFasta(self):
  • expected = "bE78F16SP6 CH242-78F16 46 72 18:11487196-11487708" self.assertEquals(expected, self.pd.getNextFasta().title) expected = "bE78F16T7 CH242-78F16 46 72 18:11085776-11086061" self.assertEquals(expected, self.pd.getNextFasta().title)
  def testSaveAllFastas(self):
  • self.pd.saveAllFastas()

    expected = ['bE78F16SP6CH242-78F16467218-11487196-11487708',

    • 'bE78F16T7CH242-78F16467218-11085776-11086061',

    • ]
    self.assertEquals(expected, os.listdir('temp'))
  def testDoPrimer3(self):
  • self.pd.doPrimer3()

    expected = ['bE78F16SP6CH242-78F16467218-11487196-11487708',

    • 'bE78F16T7CH242-78F16467218-11085776-11086061', 'bE78F16SP6CH242-78F16467218-11487196-11487708.eprimer3', 'bE78F16T7CH242-78F16467218-11085776-11086061.eprimer3',

    • ]
    expected.sort() self.assertEquals(expected, sorted(os.listdir('temp')))
  def testGetNextPrimer(self):
  • self.pd.doPrimer3() fname, primer = self.pd.getNextPrimer() self.assertEquals('TCTGTGGTGCCACTGGAATA', primer.forward_seq)

    self.assertEquals('bE78F16SP6CH242-78F16467218-11487196-11487708',fname)

  def testWriteXls(self):
  • self.pd.doPrimer3() xfile = StringIO() self.pd.writeXls(xfile) self.assertEquals('bE78F16SP6', xfile.getvalue().splitlines()[1].split('\t')[0])

if name=='main':

• unittest.main()