Example #1
0
 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
Example #2
0
 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
Example #3
0
 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
Example #4
0
 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'))