def testLengthOne(self):
"""
A FASTA list with just one item gets de-duped to the same one item.
"""
reads = Reads()
reads.add(Read('id', 'GGG'))
self.assertEqual(list(dedupFasta(reads)), [Read('id', 'GGG')])
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(dedupFasta([s1])), [s1])
def testLengthOne(self):
"""
A FASTA list with just one item gets de-duped to the same one item.
"""
reads = Reads()
reads.add(Read('id', 'GGG'))
self.assertEqual(list(dedupFasta(reads)), [Read('id', 'GGG')])
def testRemovalOfIdenticalSequences(self):
"""
A list with 2 copies of the same seq is de-duped to have 1 copy.
"""
reads = Reads()
reads.add(Read('id', 'GGG'))
reads.add(Read('id', 'GGG'))
self.assertEqual(list(dedupFasta(reads)), [Read('id', 'GGG')])
def testRemovalOfIdenticalSequences(self):
"""
A list with 2 copies of the same seq is de-duped to have 1 copy.
"""
reads = Reads()
reads.add(Read('id', 'GGG'))
reads.add(Read('id', 'GGG'))
self.assertEqual(list(dedupFasta(reads)), [Read('id', 'GGG')])
def testRemovalOfIdenticalSequencesWithDifferingIds(self):
"""
A list with 2 copies of the same seq is de-duped to have 1 copy,
including when the read ids differ.
"""
reads = Reads()
reads.add(Read('id1', 'GGG'))
reads.add(Read('id2', 'GGG'))
self.assertEqual(list(dedupFasta(reads)), [Read('id1', 'GGG')])
def testRemovalOfIdenticalSequencesWithDifferingIds(self):
"""
A list with 2 copies of the same seq is de-duped to have 1 copy,
including when the read ids differ.
"""
reads = Reads()
reads.add(Read('id1', 'GGG'))
reads.add(Read('id2', 'GGG'))
self.assertEqual(list(dedupFasta(reads)), [Read('id1', 'GGG')])
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(dedupFasta([s1, s2])), [s1])
def testEmpty(self):
"""An empty FASTA list gets de-duped to an empty list."""
self.assertEqual(list(dedupFasta([])), [])
def testEmpty(self):
"""
An empty FASTA list gets de-duped to an empty list.
"""
self.assertEqual(list(dedupFasta([])), [])
