def testSamePrefixDifferentSuffixThreeReads(self): seq = '>hey\nagtcagtcagtc\n>you\nagttcctggtc\n>how\nagtcggtat' result = getPrefixAndSuffix(StringIO(seq)) self.assertEqual(result, (3, 0))
def testDifferentPrefixSameSuffixThreeReads(self): seq = '>hey\nagtccttagatcg\n>you\ncgaatcg\n>how\natgacctcg' result = getPrefixAndSuffix(StringIO(seq)) self.assertEqual(result, (0, 3))
def testTwoDifferentReads(self): seq = '>hey\nagtcagtcagtc\n>you\ntcctg' result = getPrefixAndSuffix(StringIO(seq)) self.assertEqual(result, (0, 0))
def testSamePrefixAndSuffixTwoReads(self): seq = '>hey\nagtcagtcagtc\n>you\nagttcctggtc' result = getPrefixAndSuffix(StringIO(seq)) self.assertEqual(result, (3, 3))
def testZeroInput(self): result = getPrefixAndSuffix(StringIO()) self.assertEqual(result, (0, 0))
def testOneInput(self): seq = '>hey\nagtcagtcagtc' result = getPrefixAndSuffix(StringIO(seq)) self.assertEqual(result, (12, 12))
#!/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')
#!/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')
def testSamePrefixSameSuffixThreeReads(self): seq = ">hey\nagtccttagatcg\n>you\nagtcgaatcg\n>how\nagtaacctcg" result = getPrefixAndSuffix(StringIO(seq)) self.assertEqual(result, (3, 3))