Пример #1
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 def testSamePrefixDifferentSuffixThreeReads(self):
     seq = '>hey\nagtcagtcagtc\n>you\nagttcctggtc\n>how\nagtcggtat'
     result = getPrefixAndSuffix(StringIO(seq))
     self.assertEqual(result, (3, 0))
Пример #2
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 def testDifferentPrefixSameSuffixThreeReads(self):
     seq = '>hey\nagtccttagatcg\n>you\ncgaatcg\n>how\natgacctcg'
     result = getPrefixAndSuffix(StringIO(seq))
     self.assertEqual(result, (0, 3))
Пример #3
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 def testTwoDifferentReads(self):
     seq = '>hey\nagtcagtcagtc\n>you\ntcctg'
     result = getPrefixAndSuffix(StringIO(seq))
     self.assertEqual(result, (0, 0))
Пример #4
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 def testSamePrefixAndSuffixTwoReads(self):
     seq = '>hey\nagtcagtcagtc\n>you\nagttcctggtc'
     result = getPrefixAndSuffix(StringIO(seq))
     self.assertEqual(result, (3, 3))
Пример #5
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 def testZeroInput(self):
     result = getPrefixAndSuffix(StringIO())
     self.assertEqual(result, (0, 0))
Пример #6
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 def testOneInput(self):
     seq = '>hey\nagtcagtcagtc'
     result = getPrefixAndSuffix(StringIO(seq))
     self.assertEqual(result, (12, 12))
Пример #7
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 def testSamePrefixDifferentSuffixThreeReads(self):
     seq = '>hey\nagtcagtcagtc\n>you\nagttcctggtc\n>how\nagtcggtat'
     result = getPrefixAndSuffix(StringIO(seq))
     self.assertEqual(result, (3, 0))
Пример #8
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 def testDifferentPrefixSameSuffixThreeReads(self):
     seq = '>hey\nagtccttagatcg\n>you\ncgaatcg\n>how\natgacctcg'
     result = getPrefixAndSuffix(StringIO(seq))
     self.assertEqual(result, (0, 3))
Пример #9
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 def testTwoDifferentReads(self):
     seq = '>hey\nagtcagtcagtc\n>you\ntcctg'
     result = getPrefixAndSuffix(StringIO(seq))
     self.assertEqual(result, (0, 0))
Пример #10
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 def testSamePrefixAndSuffixTwoReads(self):
     seq = '>hey\nagtcagtcagtc\n>you\nagttcctggtc'
     result = getPrefixAndSuffix(StringIO(seq))
     self.assertEqual(result, (3, 3))
Пример #11
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 def testOneInput(self):
     seq = '>hey\nagtcagtcagtc'
     result = getPrefixAndSuffix(StringIO(seq))
     self.assertEqual(result, (12, 12))
Пример #12
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 def testZeroInput(self):
     result = getPrefixAndSuffix(StringIO())
     self.assertEqual(result, (0, 0))
Пример #13
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#!/usr/bin/env python

from Bio import SeqIO
from dark.analyze_reads import getPrefixAndSuffix
from dark.analyze_reads import trimReads
import sys


if len(sys.argv) != 2:
    print >> sys.stderr, "getPrefixAndSuffix() takes exactly 1 argument"
    sys.exit(1)

else:
    filename = sys.argv[1]
    prefix, suffix = getPrefixAndSuffix(filename)

    print >>sys.stderr, "Prefix length %d, suffix length %d" % (prefix, suffix)

    SeqIO.write(trimReads(prefix, suffix, filename), sys.stdout, 'fasta')
Пример #14
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#!/usr/bin/env python

from __future__ import print_function

from Bio import SeqIO
from dark.analyze_reads import getPrefixAndSuffix
from dark.analyze_reads import trimReads
import sys


if len(sys.argv) != 2:
    print('getPrefixAndSuffix() takes exactly 1 argument', file=sys.stderr)
    sys.exit(1)

else:
    filename = sys.argv[1]
    prefix, suffix = getPrefixAndSuffix(filename)

    print('Prefix length %d, suffix length %d' % (prefix, suffix),
          file=sys.stderr)

    SeqIO.write(trimReads(prefix, suffix, filename), sys.stdout, 'fasta')
Пример #15
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 def testSamePrefixSameSuffixThreeReads(self):
     seq = ">hey\nagtccttagatcg\n>you\nagtcgaatcg\n>how\nagtaacctcg"
     result = getPrefixAndSuffix(StringIO(seq))
     self.assertEqual(result, (3, 3))