Hopefully corrected for the offset - issue EI-CoreBioinformatics#129

lucventurini · Oct 2, 2018 · 5191c28 · 5191c28
1 parent 8d34439
commit 5191c28
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Showing 2 changed files with 7 additions and 7 deletions.
diff --git a/Mikado/parsers/bed12.py b/Mikado/parsers/bed12.py
@@ -687,9 +687,9 @@ def expand(self, sequence, upstream, downstream, expand_orf=False, logger=create
 
         old_sequence = sequence[upstream:len(self) + upstream]
 
-        self.start_codon = str(old_sequence[self.thick_start + self.phase:self.thick_start + self.phase + 3]).upper()
+        self.start_codon = str(old_sequence[self.thick_start + self.phase -1 :self.thick_start + self.phase + 2]).upper()
         # last_codon_start = self.thick_end + ((self.thick_end - self.thick_start + 1 + self.phase) % 3 - 3)
-        self.stop_codon = str(old_sequence[self.thick_end - 2:self.thick_end + 1]).upper()
+        self.stop_codon = str(old_sequence[self.thick_end - 3:self.thick_end]).upper()
 
         assert 0 < len(self.stop_codon) <= 3, self.stop_codon
 

diff --git a/Mikado/tests/padding_test.bed12 b/Mikado/tests/padding_test.bed12
@@ -1,5 +1,5 @@
-44	1	61560	ID=mikado.44G2.2;coding=True;phase=0	85.0	+	69	61340	0	22	140,119,137,89,218,261,240,141,156,112,160,165,132,72,126,75,168,105,201,87,114,309	0,19637,20638,24654,26061,27238,28273,28974,29420,30474,32004,33291,34188,35466,42587,43055,44730,46583,50405,53556,59448,61250	
-44	1	61560	ID=mikado.44G2.3;coding=True;phase=0	79.0	+	69	61340	0	21	140,119,137,89,218,261,240,141,141,112,160,165,132,126,75,168,105,201,87,114,309	0,19637,20638,24654,26061,27238,28273,28974,29435,30474,32004,33291,34188,42587,43055,44730,46583,50405,53556,59448,61250	
-44	1	61560	ID=mikado.44G2.4;coding=True;phase=0	72.0	+	69	61340	0	21	140,119,137,89,218,261,240,171,141,112,160,165,132,126,75,168,105,201,87,114,309	0,19637,20638,24654,26061,27238,28273,28944,29435,30474,32004,33291,34188,42587,43055,44730,46583,50405,53556,59448,61250	
-44	1	62511	ID=mikado.44G2.1;coding=True;phase=0	85.0	+	69	61340	0	22	140,119,137,89,218,261,240,141,141,112,160,165,132,72,126,75,168,105,201,87,114,1260	0,19637,20638,24654,26061,27238,28273,28974,29435,30474,32004,33291,34188,35466,42587,43055,44730,46583,50405,53556,59448,61250	
-44	1	67118	ID=mikado.44G2.5;coding=True;phase=0	83.0	+	69	61340	0	24	140,119,137,89,218,261,240,141,141,112,160,165,132,72,126,75,168,105,201,87,114,1186,59,430	0,19637,20638,24654,26061,27238,28273,28974,29435,30474,32004,33291,34188,35466,42587,43055,44730,46583,50405,53556,59448,61250,63052,66687	
+44	1	61560	ID=mikado.44G2.2;coding=True;phase=0	85.0	+	70	61341	0	22	140,119,137,89,218,261,240,141,156,112,160,165,132,72,126,75,168,105,201,87,114,309	0,19637,20638,24654,26061,27238,28273,28974,29420,30474,32004,33291,34188,35466,42587,43055,44730,46583,50405,53556,59448,61250	
+44	1	61560	ID=mikado.44G2.3;coding=True;phase=0	79.0	+	70	61341	0	21	140,119,137,89,218,261,240,141,141,112,160,165,132,126,75,168,105,201,87,114,309	0,19637,20638,24654,26061,27238,28273,28974,29435,30474,32004,33291,34188,42587,43055,44730,46583,50405,53556,59448,61250	
+44	1	61560	ID=mikado.44G2.4;coding=True;phase=0	72.0	+	70	61341	0	21	140,119,137,89,218,261,240,171,141,112,160,165,132,126,75,168,105,201,87,114,309	0,19637,20638,24654,26061,27238,28273,28944,29435,30474,32004,33291,34188,42587,43055,44730,46583,50405,53556,59448,61250	
+44	1	62511	ID=mikado.44G2.1;coding=True;phase=0	85.0	+	70	61341	0	22	140,119,137,89,218,261,240,141,141,112,160,165,132,72,126,75,168,105,201,87,114,1260	0,19637,20638,24654,26061,27238,28273,28974,29435,30474,32004,33291,34188,35466,42587,43055,44730,46583,50405,53556,59448,61250	
+44	1	67118	ID=mikado.44G2.5;coding=True;phase=0	83.0	+	70	61341	0	24	140,119,137,89,218,261,240,141,141,112,160,165,132,72,126,75,168,105,201,87,114,1186,59,430	0,19637,20638,24654,26061,27238,28273,28974,29435,30474,32004,33291,34188,35466,42587,43055,44730,46583,50405,53556,59448,61250,63052,66687