def testPrefixSuffix(self): seq = '>hey\nagtccgatcg' trimmed_seq = '>hey\nccga' result = trimReads(3, 3, StringIO(seq)) test_result = list(SeqIO.parse(StringIO(trimmed_seq), 'fasta')) self.assertEqual(list(map(str, tuple(result))), list(map(str, tuple(test_result))))
def testOneInput(self): result = trimReads(10, 10, StringIO()) test_result = list(SeqIO.parse(StringIO(), 'fasta')) self.assertEqual(list(map(str, tuple(result))), list(map(str, tuple(test_result))))
#!/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 testLongPrefixSuffix(self): seq = ">hey\nagtccgatcg" trimmed_seq = ">hey\n" result = trimReads(8, 4, StringIO(seq)) test_result = list(SeqIO.parse(StringIO(trimmed_seq), "fasta")) self.assertEqual(map(str, tuple(result)), map(str, tuple(test_result)))
def testZeroInput(self): result = trimReads(0, 0, StringIO()) test_result = list(SeqIO.parse(StringIO(), "fasta")) self.assertEqual(map(str, tuple(result)), map(str, tuple(test_result)))