Mercurial > repos > cpt > cpt_putative_usp

comparison cpt.py @ 4:da1be0114755 draft default tip

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planemo upload commit 471832a126aa25d903becae9a074a6b7b1ff7092-dirty
author cpt
date Fri, 20 Sep 2024 04:02:16 +0000
parents f7afd1480d0f
children
comparison
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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):