Mercurial > repos > cpt > cpt_putative_usp
comparison cpt.py @ 4:da1be0114755 draft default tip
planemo upload commit 471832a126aa25d903becae9a074a6b7b1ff7092-dirty
| author | cpt |
|---|---|
| date | Fri, 20 Sep 2024 04:02:16 +0000 |
| parents | f7afd1480d0f |
| children |
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| 3:76a3830e9cb1 | 4:da1be0114755 |
|---|---|
| 146 for match in self.re_stops.finditer(s, overlapped=True): | 146 for match in self.re_stops.finditer(s, overlapped=True): |
| 147 index = match.start() + 3 | 147 index = match.start() + 3 |
| 148 if index % 3 != 0: | 148 if index % 3 != 0: |
| 149 continue | 149 continue |
| 150 n = s[start:index] | 150 n = s[start:index] |
| 151 for (offset, n, t) in self.start_chop_and_trans(n): | 151 for offset, n, t in self.start_chop_and_trans(n): |
| 152 if n and len(t) >= self.min_len: | 152 if n and len(t) >= self.min_len: |
| 153 yield start + offset, n, t | 153 yield start + offset, n, t |
| 154 start = index | 154 start = index |
| 155 | 155 |
| 156 def putative_genes_in_sequence(self, nuc_seq): | 156 def putative_genes_in_sequence(self, nuc_seq): |
| 293 for match in self.re_stops.finditer(s, overlapped=True): | 293 for match in self.re_stops.finditer(s, overlapped=True): |
| 294 index = match.start() + 3 | 294 index = match.start() + 3 |
| 295 if index % 3 != 0: | 295 if index % 3 != 0: |
| 296 continue | 296 continue |
| 297 n = s[start:index] | 297 n = s[start:index] |
| 298 for (offset, n, t) in self.start_chop_and_trans(n): | 298 for offset, n, t in self.start_chop_and_trans(n): |
| 299 if n and len(t) >= self.min_len: | 299 if n and len(t) >= self.min_len: |
| 300 yield start + offset, n, t | 300 yield start + offset, n, t |
| 301 start = index | 301 start = index |
| 302 | 302 |
| 303 def putative_genes_in_sequence(self, nuc_seq): | 303 def putative_genes_in_sequence(self, nuc_seq): |