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)