def testLengthOne(self):
"""
A FASTA list with just one item gets de-duped to the same one item.
"""
seq = '>hey\nagtcagtcagtc'
s1 = SeqIO.read(StringIO(seq), 'fasta')
self.assertEqual(list(dePrefixAndSuffixFasta([s1])), [s1])
def testLengthOne(self):
"""
A FASTA list with just one item gets de-duped to the same one item.
"""
seq = '>hey\nagtcagtcagtc'
s1 = SeqIO.read(StringIO(seq), 'fasta')
self.assertEqual(list(dePrefixAndSuffixFasta([s1])), [s1])
def testRemovalOfSuffix(self):
"""
A sequence that is a suffix of another is removed.
"""
s1 = SeqIO.read(StringIO('>s1\nagtcagtcagtc'), 'fasta')
s2 = SeqIO.read(StringIO('>s2\ncagtc'), 'fasta')
self.assertEqual(list(dePrefixAndSuffixFasta([s1, s2])), [s1])
def testRemovalOfSuffix(self):
"""
A sequence that is a suffix of another is removed.
"""
s1 = SeqIO.read(StringIO('>s1\nagtcagtcagtc'), 'fasta')
s2 = SeqIO.read(StringIO('>s2\ncagtc'), 'fasta')
self.assertEqual(list(dePrefixAndSuffixFasta([s1, s2])), [s1])
def testOrderIndependent(self):
"""
A sequence that is a prefix of another is removed when it appears
first.
"""
s1 = SeqIO.read(StringIO('>s1\nagtcag'), 'fasta')
s2 = SeqIO.read(StringIO('>s2\nagtcagtcagtc'), 'fasta')
self.assertEqual(list(dePrefixAndSuffixFasta([s1, s2])), [s2])
def testRemovalOfIdenticalSequences(self):
"""
A list with 2 copies of the same seq is de-duped to have 1 copy.
"""
seq = '>hey\nagtcagtcagtc'
s1 = SeqIO.read(StringIO(seq), 'fasta')
s2 = SeqIO.read(StringIO(seq), 'fasta')
self.assertEqual(list(dePrefixAndSuffixFasta([s1, s2])), [s1])
def testOrderIndependent(self):
"""
A sequence that is a prefix of another is removed when it appears
first.
"""
s1 = SeqIO.read(StringIO('>s1\nagtcag'), 'fasta')
s2 = SeqIO.read(StringIO('>s2\nagtcagtcagtc'), 'fasta')
self.assertEqual(list(dePrefixAndSuffixFasta([s1, s2])), [s2])
def testRemovalOfIdenticalSequences(self):
"""
A list with 2 copies of the same seq is de-duped to have 1 copy.
"""
seq = '>hey\nagtcagtcagtc'
s1 = SeqIO.read(StringIO(seq), 'fasta')
s2 = SeqIO.read(StringIO(seq), 'fasta')
self.assertEqual(list(dePrefixAndSuffixFasta([s1, s2])), [s1])
def testRemovalOfPrefixSuffixAndDuplicate(self):
"""
Prefixes, suffixes, and duplicates should collectively all be removed.
"""
s1 = SeqIO.read(StringIO('>s1\nagtcagtcagtc'), 'fasta')
s2 = SeqIO.read(StringIO('>s2\nagtcagtcagtc'), 'fasta')
s3 = SeqIO.read(StringIO('>s3\nagtcagt'), 'fasta')
s4 = SeqIO.read(StringIO('>s4\ntcagtc'), 'fasta')
self.assertEqual(list(dePrefixAndSuffixFasta([s1, s2, s3, s4])), [s1])
def testRemovalOfPrefixSuffixAndDuplicate(self):
"""
Prefixes, suffixes, and duplicates should collectively all be removed.
"""
s1 = SeqIO.read(StringIO('>s1\nagtcagtcagtc'), 'fasta')
s2 = SeqIO.read(StringIO('>s2\nagtcagtcagtc'), 'fasta')
s3 = SeqIO.read(StringIO('>s3\nagtcagt'), 'fasta')
s4 = SeqIO.read(StringIO('>s4\ntcagtc'), 'fasta')
self.assertEqual(list(dePrefixAndSuffixFasta([s1, s2, s3, s4])), [s1])
def testEmpty(self):
"""An empty FASTA list gets de-duped to an empty list."""
self.assertEqual(list(dePrefixAndSuffixFasta([])), [])
def testEmpty(self):
"""
An empty FASTA list gets de-duped to an empty list.
"""
self.assertEqual(list(dePrefixAndSuffixFasta([])), [])
