def test_squeeze_seq(self):
"""squeeze should collapse homopolymers to one nuc."""
seq = "AAAGGGAAACCCGGGA"
self.assertEqual(squeeze_seq(seq), "AGACGA")
self.assertEqual(squeeze_seq("AAAATATTTAGGC"), "ATATAGC")
self.assertEqual(squeeze_seq(""), "")
self.assertEqual(squeeze_seq("ATGCATGCATGC"), "ATGCATGCATGC")
def test_squeeze_seq(self):
"""squeeze should collapse homopolymers to one nuc."""
seq = "AAAGGGAAACCCGGGA"
self.assertEqual(squeeze_seq(seq), "AGACGA")
self.assertEqual(squeeze_seq("AAAATATTTAGGC"), "ATATAGC")
self.assertEqual(squeeze_seq(""), "")
self.assertEqual(squeeze_seq("ATGCATGCATGC"), "ATGCATGCATGC")
def prefix_filter_flowgrams(flowgrams, squeeze=False):
"""Filters flowgrams by common prefixes.
flowgrams: iterable source of flowgrams
squeeze: if True, collapse all poly-X to X
Returns prefix mapping.
"""
# collect flowgram sequences
if squeeze:
seqs = imap(
lambda f: (f.Name, squeeze_seq(str(f.toSeq(truncate=True)))),
flowgrams)
else:
seqs = imap(lambda f: (f.Name, str(f.toSeq(truncate=True))), flowgrams)
# equivalent but more efficient than
#seqs = [(f.Name, str(f.toSeq(truncate=True))) for f in flowgrams]
# get prefix mappings
mapping = build_prefix_map(seqs)
l = len(mapping)
orig_l = sum([len(a) for a in mapping.values()]) + l
return (l, orig_l, mapping)
def prefix_filter_flowgrams(flowgrams, squeeze=False):
"""Filters flowgrams by common prefixes.
flowgrams: iterable source of flowgrams
squeeze: if True, collapse all poly-X to X
Returns prefix mapping.
"""
# collect flowgram sequences
if squeeze:
seqs = imap(
lambda f: (f.Name, squeeze_seq(str(f.toSeq(truncate=True)))),
flowgrams)
else:
seqs = imap(lambda f: (f.Name, str(f.toSeq(truncate=True))), flowgrams)
# equivalent but more efficient than
#seqs = [(f.Name, str(f.toSeq(truncate=True))) for f in flowgrams]
# get prefix mappings
mapping = build_prefix_map(seqs)
l = len(mapping)
orig_l = sum([len(a) for a in mapping.values()]) + l
return (l, orig_l, mapping)