Python summarize_reads Examples

Example #1

File: test_summarize.py Project: sophiemathias/dark-matter

 def testMedianFourStrings(self):
     seq = '>hey\nagtcagtcagtc\n>you\nacctg\n>how\natgggtc\n>are\n\
     atggctattgaactgtatct'
     result = summarize_reads(StringIO(seq), 'fasta')
     self.assertEqual(result['median_length'], 9.5)

Example #2

File: test_summarize.py Project: sophiemathias/dark-matter

 def testMedianOneString(self):
     seq = '>hey\nagtcagtcagtc'
     result = summarize_reads(StringIO(seq), 'fasta')
     self.assertEqual(result['median_length'], 12)

Example #3

File: test_summarize.py Project: sophiemathias/dark-matter

 def testMedianThreeStrings(self):
     seq = '>hey\nagtcagtcagtc\n>you\nacctg\n>how\natgggtc'
     result = summarize_reads(StringIO(seq), 'fasta')
     self.assertEqual(result['median_length'], 7)

Example #4

File: test_summarize.py Project: sophiemathias/dark-matter

 def testMinLengthListTwoStrings(self):
     seq = '>hey\nagtcagtcagtc\n>you\nacctg'
     result = summarize_reads(StringIO(seq), 'fasta')
     self.assertEqual(result['min_length'], 5)

Example #5

File: test_summarize.py Project: sophiemathias/dark-matter

 def testMedianEmptyInput(self):
     result = summarize_reads(StringIO(), 'fasta')
     self.assertEqual(result['median_length'], 0)

Example #6

File: test_summarize.py Project: sophiemathias/dark-matter

 def testBaseCountsTwoReads(self):
     seq = '>hey\nagtcagtcagtc\n>you\nacctg'
     result = summarize_reads(StringIO(seq), 'fasta')
     self.assertEqual(result['base_counts'],
                      {'a': 4, 'c': 5, 't': 4, 'g': 4})

Example #7

File: test_summarize.py Project: sophiemathias/dark-matter

 def testMinLengthListEmptyInput(self):
     result = summarize_reads(StringIO(), 'fasta')
     self.assertEqual(result['min_length'], 0)

Example #8

File: test_summarize.py Project: sophiemathias/dark-matter

 def testBaseCountsEmptyImput(self):
     result = summarize_reads(StringIO(), 'fasta')
     self.assertEqual(result['base_counts'], {})

Example #9

File: test_summarize.py Project: sophiemathias/dark-matter

 def testBaseCountsOneRead(self):
     seq = '>hey\nagtcagtcagtc'
     result = summarize_reads(StringIO(seq), 'fasta')
     self.assertEqual(result['base_counts'],
                      {'a': 3, 'c': 3, 't': 3, 'g': 3})

Example #10

File: test_summarize.py Project: sophiemathias/dark-matter

 def testTotalLengthOneString(self):
     seq = '>hey\nagtcagtcagtc'
     result = summarize_reads(StringIO(seq), 'fasta')
     self.assertEqual(result['total_length'], 12)

Example #11

File: test_summarize.py Project: sophiemathias/dark-matter

 def testTotalLengthTwoStrings(self):
     seq = '>hey\nagtcagtcagtc\n>you\nacctg'
     result = summarize_reads(StringIO(seq), 'fasta')
     self.assertEqual(result['total_length'], 17)

Example #12

File: test_summarize.py Project: sophiemathias/dark-matter

 def testTotalLengthEmptyInput(self):
     result = summarize_reads(StringIO(), 'fasta')
     self.assertEqual(result['total_length'], 0)

Example #13

File: test_summarize.py Project: sophiemathias/dark-matter

 def testReadNumberTwoSequencesCount(self):
     seq = '>hey\nagtcagtcagtc\n>you\nacctg'
     result = summarize_reads(StringIO(seq), 'fasta')
     self.assertEqual(result['read_number'], 2)

Example #14

File: test_summarize.py Project: sophiemathias/dark-matter

 def testReadNumberOneSequenceCount(self):
     seq = '>hey\nagtcagtcagtc'
     result = summarize_reads(StringIO(seq), 'fasta')
     self.assertEqual(result['read_number'], 1)

Example #15

File: test_summarize.py Project: sophiemathias/dark-matter

 def testReadNumberEmptyInput(self):
     result = summarize_reads(StringIO(), 'fasta')
     self.assertEqual(result['read_number'], 0)

Example #16

File: summarize-reads.py Project: sophiemathias/dark-matter

#!/usr/bin/env python

from dark.summarize import summarize_reads
import sys


if len(sys.argv) > 2:
    print >>sys.stderr, "Usage: %s file.fasta / file.fastq" % sys.argv[0]
    sys.exit(1)

else:
    filename = sys.argv[1]
    if filename.endswith('a'):
        filetype = 'fasta'
    else:
        filetype = 'fastq'

    result = summarize_reads(filename, filetype)

    print "Number of reads:", result["read_number"]
    print "Total length: %s bases" % result["total_length"]
    print "The average read length: %s bases" % result["average_length"]
    print "Longest read:", result["max_length"]
    print "Shortest read:", result["min_length"]
    print "Median length:", result["median_length"]

    for base, count in result["base_counts"].items():
        print "%s: Total: %s; Average per read: %s" % (
            base, count, count / result["read_number"])