def loadPecan(iFileHandle, renamer=firstWord): """ Load pecan alignment data. """ aln = Alignment() for h, s in FastaFile(iFileHandle): try: aln.add(renamer(h), s) except Exception, e: print e
#!/usr/bin/env python """ testTextIndex.py Author: Tony Papenfuss Date: Thu May 29 11:44:36 EST 2008 """ import os, sys from fasta import FastaFile filename = 'tumour_sample.fa' f = FastaFile(filename, indexed=True, clobber=True, method='pickle')
Author: Tony Papenfuss Date: Tue Mar 18 14:27:10 EST 2008 """ import os, sys def rule(): print '-' * 80 from fasta import FastaFile f = FastaFile('HSP100.fa') rule() print 'readOne' print f.readOne() print f.readOne() rule() print 'readAll' print f.readAll() rule() print 'Mapping' f.asMapping() print f rule() rule()
#!/usr/bin/env python """ testTextIndex.py Author: Tony Papenfuss Date: Thu May 29 11:44:36 EST 2008 """ import os, sys from fasta import FastaFile filename = 'tumour_sample.fa' f = FastaFile(filename, indexed=True, clobber=False, method='db') x = f[9000:9100]
def saveFasta(self, oFileHandle, **kw): writer = FastaFile(oFileHandle, 'w') for name in self.order: writer.write(name, self.seqDict[name]) writer.close()
#!/usr/bin/env python """ testTextIndex.py Author: Tony Papenfuss Date: Thu May 29 11:44:36 EST 2008 """ import os, sys from fasta import FastaFile filename = '/Users/papenfuss/databases/devil/transcriptome/reads/combined.fa' f = FastaFile(filename, indexed=True, clobber=True, method='text')