Python get_quals_dict Examples

Example #1

File: gen_dicts_for_qual_stats.py Project: jnesme/oligotyping

#!/usr/bin/env python

# get me some alignments and qual scores:
#
# python $me.py fasta.fa fasta.qual
#

import sys
import cPickle

from Oligotyping.utils.utils import get_quals_dict

alignment_file = sys.argv[1]
quals_file = sys.argv[2]

quals_dict = get_quals_dict(quals_file, alignment_file)

cPickle.dump(quals_dict, open(alignment_file + '-QUALS-DICT', 'w'))

print 'output file:'
print '  - "%s"' % (alignment_file + '-QUALS-DICT')

Example #2

File: _weightedEntropy.py Project: zjzace/oligotyping

 def test_01_RunWeightedEntropy(self):
     output_file = os.path.join(self.output_directory_path, 'entropy.txt')
     QD = get_quals_dict(self.qual_scores_file, self.alignment, output_file_path = os.path.join(self.output_directory_path, 'QUALS_DICT'), verbose = False)
     QSD = get_qual_stats_dict(QD, output_file_path = os.path.join(self.output_directory_path, 'QUAL_STATS_DICT'), verbose = False)
     entropy_analysis(self.alignment, output_file = output_file, verbose = False, weighted = True, qual_stats_dict = QSD)
     self.assertTrue(files_are_the_same(self.expected_result, output_file))