def make_seqs(seqs):
"""prepare the input sequences for feeding into meme.
This means only taking the unique sequences and their reverse
complement if desired"""
meme_input_seqs = []
for locseq in seqs.values():
seq = locseq[1]
util.add_if_unique(meme_input_seqs, seq)
if use_revcomp:
util.add_if_unique(meme_input_seqs, st.revcomp(seq))
return meme_input_seqs
def make_seqs(seqs):
"""prepare the input sequences for feeding into meme.
This means only taking the unique sequences and their reverse
complement if desired"""
meme_input_seqs = []
for locseq in seqs.values():
seq = locseq[1]
if seq not in meme_input_seqs:
meme_input_seqs.append(seq)
if use_revcomp:
revseq = st.revcomp(seq)
if revseq not in meme_input_seqs:
meme_input_seqs.append(revseq)
return meme_input_seqs
def make_seqs(seqs):
"""prepare the input sequences for feeding into meme.
This means only taking the unique sequences and their reverse
complement if desired"""
meme_input_seqs = []
for locseq in seqs.values():
seq = locseq[1]
if seq not in meme_input_seqs:
meme_input_seqs.append(seq)
if use_revcomp:
revseq = st.revcomp(seq)
if revseq not in meme_input_seqs:
meme_input_seqs.append(revseq)
return meme_input_seqs
def test_revcomp(self):
"""test revcomp function"""
self.assertEquals("GNCAT", st.revcomp('ATGNC'))
self.assertEquals("GNCAT", st.revcomp('atgnc'))
def test_revcomp(self):
"""test revcomp function"""
self.assertEquals("GNCAT", st.revcomp('ATGNC'))
self.assertEquals("GNCAT", st.revcomp('atgnc'))