def _trim_all_ab1s(self, ab1_files): print 'Trimming %d ab1 files' % len(ab1_files) original_list = [abi.Trace(fname) for fname in ab1_files] for trace in original_list: trimmed = self._trim(trace) if trimmed is not None: yield trimmed
def trim_single_file(self, fname): ''' Trim a single file and save it to fasta format. Do nothing if the trimmed trace fails any validation rule.''' original = abi.Trace(fname) trimmed = self._trim(original) if trimmed is not None: out_fname = fname.split('.')[-2] + '_trimmed.fas' self._save_fasta(trimmed, out_fname)
def __init__(self, filename): unittest.TestCase.__init__(self, methodName='runTest') self.filename = filename self.abif = abifpy.Trace(self.filename) self.trimmed_seq = self.abif.trim(self.abif.seq) self.untrimmed_seq = self.abif.seq
def __init__(self, filename): unittest.TestCase.__init__(self, methodName='runTest') self.filename = filename self.abif = abifpy.Trace(self.filename)
#!/usr/bin/env python # demo.py # demo script for using abifpy to write fasta files from trace files import abifpy import glob counter = 0 print "Working..." for trace in glob.iglob('*.ab1'): abifpy.Trace(trace, trimming=True).export() counter += 1 print "Done! Processed {0} trace files.".format(counter)