bring anchorna on par with sugar commit 856f335

rnajena · Oct 24, 2024 · 49982b6 · 49982b6
1 parent 47f3bc0
commit 49982b6
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Showing 3 changed files with 7 additions and 9 deletions.
diff --git a/anchorna/cli.py b/anchorna/cli.py
@@ -222,15 +222,12 @@ def _cmd_view(fname_anchor, fname, mode='aa', align=None, score_use_fluke=None):
             else:
                 offsets_cds = None
             if offsets_cds == offsets:
-                # seqs = seqs[:, 'cds']
-                # seqs.data = [seq.get('cds', gap='-') for seq in seqs]
-                seqs = seqs.get((slice(None), 'cds'), gap='-')
+                seqs = seqs.sl(gap='-')[:, 'cds']
                 if mode == 'aa':
                     seqs = seqs.translate(complete=True, final_stop=False)
             else:
                 for seq in seqs:
-                    seq.get(slice(offsets[seq.id], None), gap='-', inplace=True)
-                    #seq.data = seq.data[offsets[seq.id]:]
+                    seq.sl(gap='-', inplace=True)[offsets[seq.id]:]
                 if mode == 'aa':
                     seqs = seqs.translate(complete=True)
         if align:

diff --git a/anchorna/io.py b/anchorna/io.py
@@ -180,8 +180,9 @@ def export_dialign(anchors, seqids, mode='aa', score_use_fluke=None):
                 continue
             assert f.len == f0.len
             start = _apply_mode(f.start, f.offset, mode)
+            len_ = _apply_mode(f.len, f.offset, mode, islen=True)
             content.append(
-                f'{i+1} {j+1} {start0+1} {start+1} {f.len} {f.score}\n'
+                f'{i+1} {j+1} {start0+1} {start+1} {len_} {f.score}\n'
                 )
     return ''.join(content)
 

diff --git a/anchorna/tests/test_anchorna.py b/anchorna/tests/test_anchorna.py
@@ -135,7 +135,7 @@ def test_anchorna_workflow_subset():
         seqs2 = cutout(seqs, anchors, 'start+10', 'a5^-5')
         seqs3 = cutout(seqs, anchors, 'a5^-5', '*>')
         seqs4 = cutout(seqs, anchors, '*>', 'end')
-        assert str(seqs[0, 10:]) == str(seqs2[0] + seqs3[0] + seqs4[0])
+        assert str(seqs[0, 10:]) == seqs2[0].data + seqs3[0].data + seqs4[0].data
 
         fname = tmpdir / 'pesti_test_cutout.sjson'
         assert '' == check(f'anchorna cutout anchors.gff a0> a2< -o {fname}')
@@ -184,7 +184,7 @@ def test_anchorna_workflow_subset_poor():
         seqs2 = cutout(seqs, anchors, 'start+10', 'a5^-5')
         seqs3 = cutout(seqs, anchors, 'a5^-5', '*>')
         seqs4 = cutout(seqs, anchors, '*>', 'end')
-        assert str(seqs[0, 10:]) == str(seqs2[0] + seqs3[0] + seqs4[0])
+        assert str(seqs[0, 10:]) == seqs2[0].data + seqs3[0].data + seqs4[0].data
 
         _fix_open_log_file_on_windows()
 
@@ -225,7 +225,7 @@ def test_anchorna_workflow_subset_no_cds():
         seqs2 = cutout(seqs, anchors, 'start+10', 'a5^-5')
         seqs3 = cutout(seqs, anchors, 'a5^-5', '*>')
         seqs4 = cutout(seqs, anchors, '*>', 'end')
-        assert str(seqs[0, 10:]) == str(seqs2[0] + seqs3[0] + seqs4[0])
+        assert str(seqs[0, 10:]) == seqs2[0].data + seqs3[0].data + seqs4[0].data
 
         _fix_open_log_file_on_windows()