Fix landmark definitions for HIV to be 1-based, as part of #589.

cfe-lab · Jun 17, 2021 · d786b28 · d786b28
1 parent f7ea48f
commit d786b28
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Showing 6 changed files with 170 additions and 120 deletions.
diff --git a/micall/data/landmark_reader.py b/micall/data/landmark_reader.py
@@ -57,12 +57,12 @@ def get_gene(self,
                 continue
             region_copy = dict(region)
             if 'end' not in region_copy:
-                region_copy['end'] = regions[i+1]['start']
+                region_copy['end'] = regions[i+1]['start']-1
             break
         else:
             raise ValueError(f'Landmarks not found for gene {gene_name!r} in '
                              f'{coordinates}.')
-        if drop_stop_codon:
+        if drop_stop_codon and region_copy.get('stop') != 'N':
             region_copy['end'] -= 3
         return region_copy
 

diff --git a/micall/data/landmark_references.yaml b/micall/data/landmark_references.yaml
@@ -2,153 +2,160 @@
 - seed_pattern: HIV.*
   coordinates: HIV1-B-FR-K03455-seed
   landmarks:
+    # 1-based, inclusive positions in HXB2, including stop codons.
     - {name: "5' LTR", start: 1, end: 634, frame: 0, colour: darkgrey}
-    - {name: gag, full_name: HIV1B-gag, start: 789, end: 2289, frame: 0, colour: lightblue}
-    - {name: vif, full_name: HIV1B-vif, start: 5040, end: 5616, frame: 0, colour: steelblue}
-    - {name: tat, start: 8379, end: 8469, frame: 0, colour: plum}
-    - {name: nef, full_name: HIV1B-nef, start: 8796, end: 9414, frame: 0, colour: mediumaquamarine}
-    - {name: tat, start: 5831, end: 6045, frame: 1, colour: plum}
-    - {name: vpu, full_name: HIV1B-vpu, start: 6061, end: 6307, frame: 1, colour: red}
-    - {name: rev, start: 8379, end: 8653, frame: 1, colour: yellowgreen}
+    - {name: gag, full_name: HIV1B-gag, start: 790, end: 2292, frame: 0, colour: lightblue}
+    - {name: vif, full_name: HIV1B-vif, start: 5041, end: 5619, frame: 0, colour: steelblue}
+
+    # Actually starts at 8379, spliced to the end of tat in the middle of a codon.
+    - {name: tat, full_name: tat2, start: 8380, end: 8469, frame: 0, colour: plum}
+
+    - {name: nef, full_name: HIV1B-nef, start: 8797, end: 9417, frame: 0, colour: mediumaquamarine}
+    - {name: tat, start: 5831, end: 6049, frame: 1, colour: plum}
+    - {name: vpu, full_name: HIV1B-vpu, start: 6062, end: 6310, frame: 1, colour: red}
+
+    # Actually starts at 8379, spliced to the end of rev in the middle of a codon.
+    - {name: rev, full_name: rev2, start: 8378, end: 8653, frame: 1, colour: yellowgreen}
+
     - {name: "3' LTR", start: 9086, end: 9719, frame: 1, colour: darkgrey}
     - {name: pol, start: 2085, end: 5096, frame: 2, colour: orange}
-    - {name: vpr, full_name: HIV1B-vpr, start: 5558, end: 5847, frame: 2, colour: turquoise}
-    - {name: rev, start: 5970, end: 6045, frame: 2, colour: yellowgreen}
+    - {name: vpr, full_name: HIV1B-vpr, start: 5559, end: 5850, frame: 2, colour: turquoise}
+    - {name: rev, start: 5970, end: 6048, frame: 2, colour: yellowgreen, stop: N}
     - {name: env, start: 6225, end: 8795, frame: 2, colour: salmon}
-    - {name: PR, start: 2252, end: 2549, frame: 3, colour: orange}
-    - {name: RT, start: 2549, end: 3869, frame: 3, colour: darkorange}
-    - {name: INT, start: 4229, end: 5093, frame: 3, colour: orange}
-    - {name: V3, full_name: V3LOOP, start: 7109, end: 7217, frame: 3, colour: salmon}
-    - {name: GP41, start: 7757, end: 8792, frame: 3, colour: salmon}
-    - {name: GP120, start: 6224, end: 7757, frame: 3}  # Not displayed.
+    - {name: PR, start: 2253, end: 2549, frame: 3, colour: orange, stop: N}
+    - {name: RT, start: 2550, end: 3869, frame: 3, colour: darkorange, stop: N}
+    - {name: INT, start: 4230, end: 5096, frame: 3, colour: orange}
+    - {name: V3, full_name: V3LOOP, start: 7110, end: 7217, frame: 3, colour: salmon, stop: N}
+    - {name: GP41, start: 7758, end: 8795, frame: 3, colour: salmon}
+    - {name: GP120, start: 6225, end: 7757, frame: 3, stop: N}  # Not displayed.
 - seed_pattern: HCV-1b
   coordinates: HCV-1b
   prefix: HCV1B-Con1-
   landmarks:
     - {name: "5'", start: 1, colour: darkgrey}
-    - {name: C, full_name: Core, start: 342, colour: '#1f77b4'}
-    - {name: E1, start: 915, colour: '#ff7f0e'}
-    - {name: E2, start: 1491, colour: '#2ca02c'}
-    - {name: p7, start: 2580, colour: '#d62728'}
-    - {name: NS2, start: 2769, colour: '#9467bd'}
-    - {name: NS3, start: 3420, colour: '#8c564b'}
+    - {name: C, full_name: Core, start: 342, colour: '#1f77b4', stop: N}
+    - {name: E1, start: 915, colour: '#ff7f0e', stop: N}
+    - {name: E2, start: 1491, colour: '#2ca02c', stop: N}
+    - {name: p7, start: 2580, colour: '#d62728', stop: N}
+    - {name: NS2, start: 2769, colour: '#9467bd', stop: N}
+    - {name: NS3, start: 3420, colour: '#8c564b', stop: N}
     # Reverse order to avoid NS4a's label getting cut off.
-    - {name: NS4b, start: 5475, colour: '#7f7f7f'}
-    - {name: NS4a, start: 5313, colour: '#e377c2'}
-    - {name: NS5a, start: 6258, colour: '#bcbd22'}
-    - {name: NS5b, start: 7599, colour: '#17becf'}
+    - {name: NS4b, start: 5475, colour: '#7f7f7f', stop: N}
+    - {name: NS4a, start: 5313, colour: '#e377c2', stop: N}
+    - {name: NS5a, start: 6258, colour: '#bcbd22', stop: N}
+    - {name: NS5b, start: 7599, colour: '#17becf', stop: N}
     - {name: "3'", start: 9372, end: 9646, colour: darkgrey}
 - seed_pattern: HCV-1.*
   coordinates: HCV-1a
   prefix: HCV1A-H77-
   landmarks:
     - {name: "5'", start: 1, colour: darkgrey}
-    - {name: C, full_name: Core, start: 342, colour: '#1f77b4'}
-    - {name: E1, start: 915, colour: '#ff7f0e'}
-    - {name: E2, start: 1491, colour: '#2ca02c'}
-    - {name: p7, start: 2580, colour: '#d62728'}
-    - {name: NS2, start: 2769, colour: '#9467bd'}
-    - {name: NS3, start: 3420, colour: '#8c564b'}
-    - {name: NS4b, start: 5475, colour: '#7f7f7f'}
-    - {name: NS4a, start: 5313, colour: '#e377c2'}
-    - {name: NS5a, start: 6258, colour: '#bcbd22'}
-    - {name: NS5b, start: 7602, colour: '#17becf'}
+    - {name: C, full_name: Core, start: 342, colour: '#1f77b4', stop: N}
+    - {name: E1, start: 915, colour: '#ff7f0e', stop: N}
+    - {name: E2, start: 1491, colour: '#2ca02c', stop: N}
+    - {name: p7, start: 2580, colour: '#d62728', stop: N}
+    - {name: NS2, start: 2769, colour: '#9467bd', stop: N}
+    - {name: NS3, start: 3420, colour: '#8c564b', stop: N}
+    - {name: NS4b, start: 5475, colour: '#7f7f7f', stop: N}
+    - {name: NS4a, start: 5313, colour: '#e377c2', stop: N}
+    - {name: NS5a, start: 6258, colour: '#bcbd22', stop: N}
+    - {name: NS5b, start: 7602, colour: '#17becf', stop: N}
     - {name: "3'", start: 9375, end: 9646, colour: darkgrey}
 - seed_pattern: HCV-2.*
   coordinates: HCV-2a
   prefix: HCV2-JFH-1-
   landmarks:
     - {name: "5'", start: 1, colour: darkgrey}
-    - {name: C, full_name: Core, start: 341, colour: '#1f77b4'}
-    - {name: E1, start: 914, colour: '#ff7f0e'}
-    - {name: E2, start: 1490, colour: '#2ca02c'}
-    - {name: p7, start: 2591, colour: '#d62728'}
-    - {name: NS2, start: 2780, colour: '#9467bd'}
-    - {name: NS3, start: 3431, colour: '#8c564b'}
-    - {name: NS4b, start: 5486, colour: '#7f7f7f'}
-    - {name: NS4a, start: 5324, colour: '#e377c2'}
-    - {name: NS5a, start: 6269, colour: '#bcbd22'}
-    - {name: NS5b, start: 7667, colour: '#17becf'}
+    - {name: C, full_name: Core, start: 341, colour: '#1f77b4', stop: N}
+    - {name: E1, start: 914, colour: '#ff7f0e', stop: N}
+    - {name: E2, start: 1490, colour: '#2ca02c', stop: N}
+    - {name: p7, start: 2591, colour: '#d62728', stop: N}
+    - {name: NS2, start: 2780, colour: '#9467bd', stop: N}
+    - {name: NS3, start: 3431, colour: '#8c564b', stop: N}
+    - {name: NS4b, start: 5486, colour: '#7f7f7f', stop: N}
+    - {name: NS4a, start: 5324, colour: '#e377c2', stop: N}
+    - {name: NS5a, start: 6269, colour: '#bcbd22', stop: N}
+    - {name: NS5b, start: 7667, colour: '#17becf', stop: N}
     - {name: "3'", start: 9441, end: 9646, colour: darkgrey}
 - seed_pattern: HCV-3.*
   coordinates: HCV-3a
   prefix: HCV3-S52-
   landmarks:
     - {name: "5'", start: 1, colour: darkgrey}
-    - {name: C, full_name: Core, start: 340, colour: '#1f77b4'}
-    - {name: E1, start: 913, colour: '#ff7f0e'}
-    - {name: E2, start: 1489, colour: '#2ca02c'}
-    - {name: p7, start: 2596, colour: '#d62728'}
-    - {name: NS2, start: 2785, colour: '#9467bd'}
-    - {name: NS3, start: 3436, colour: '#8c564b'}
-    - {name: NS4b, start: 5491, colour: '#7f7f7f'}
-    - {name: NS4a, start: 5329, colour: '#e377c2'}
-    - {name: NS5a, start: 6274, colour: '#bcbd22'}
-    - {name: NS5b, start: 7630, colour: '#17becf'}
+    - {name: C, full_name: Core, start: 340, colour: '#1f77b4', stop: N}
+    - {name: E1, start: 913, colour: '#ff7f0e', stop: N}
+    - {name: E2, start: 1489, colour: '#2ca02c', stop: N}
+    - {name: p7, start: 2596, colour: '#d62728', stop: N}
+    - {name: NS2, start: 2785, colour: '#9467bd', stop: N}
+    - {name: NS3, start: 3436, colour: '#8c564b', stop: N}
+    - {name: NS4b, start: 5491, colour: '#7f7f7f', stop: N}
+    - {name: NS4a, start: 5329, colour: '#e377c2', stop: N}
+    - {name: NS5a, start: 6274, colour: '#bcbd22', stop: N}
+    - {name: NS5b, start: 7630, colour: '#17becf', stop: N}
     - {name: "3'", start: 9404, end: 9646, colour: darkgrey}
 - seed_pattern: HCV-4.*
   coordinates: HCV-4a
   prefix: HCV4-ED43-
   landmarks:
     - {name: "5'", start: 1, colour: darkgrey}
-    - {name: C, full_name: Core, start: 341, colour: '#1f77b4'}
-    - {name: E1, start: 914, colour: '#ff7f0e'}
-    - {name: E2, start: 1490, colour: '#2ca02c'}
-    - {name: p7, start: 2579, colour: '#d62728'}
-    - {name: NS2, start: 2768, colour: '#9467bd'}
-    - {name: NS3, start: 3419, colour: '#8c564b'}
-    - {name: NS4b, start: 5474, colour: '#7f7f7f'}
-    - {name: NS4a, start: 5312, colour: '#e377c2'}
-    - {name: NS5a, start: 6257, colour: '#bcbd22'}
-    - {name: NS5b, start: 7592, colour: '#17becf'}
+    - {name: C, full_name: Core, start: 341, colour: '#1f77b4', stop: N}
+    - {name: E1, start: 914, colour: '#ff7f0e', stop: N}
+    - {name: E2, start: 1490, colour: '#2ca02c', stop: N}
+    - {name: p7, start: 2579, colour: '#d62728', stop: N}
+    - {name: NS2, start: 2768, colour: '#9467bd', stop: N}
+    - {name: NS3, start: 3419, colour: '#8c564b', stop: N}
+    - {name: NS4b, start: 5474, colour: '#7f7f7f', stop: N}
+    - {name: NS4a, start: 5312, colour: '#e377c2', stop: N}
+    - {name: NS5a, start: 6257, colour: '#bcbd22', stop: N}
+    - {name: NS5b, start: 7592, colour: '#17becf', stop: N}
     - {name: "3'", start: 9366, end: 9646, colour: darkgrey}
 - seed_pattern: HCV-5.*
   coordinates: HCV-5a
   prefix: HCV5-SA13-
   landmarks:
     - {name: "5'", start: 1, colour: darkgrey}
-    - {name: C, full_name: Core, start: 247, colour: '#1f77b4'}
-    - {name: E1, start: 820, colour: '#ff7f0e'}
-    - {name: E2, start: 1396, colour: '#2ca02c'}
-    - {name: p7, start: 2488, colour: '#d62728'}
-    - {name: NS2, start: 2677, colour: '#9467bd'}
-    - {name: NS3, start: 3328, colour: '#8c564b'}
-    - {name: NS4b, start: 5383, colour: '#7f7f7f'}
-    - {name: NS4a, start: 5221, colour: '#e377c2'}
-    - {name: NS5a, start: 6166, colour: '#bcbd22'}
-    - {name: NS5b, start: 7516, colour: '#17becf'}
+    - {name: C, full_name: Core, start: 247, colour: '#1f77b4', stop: N}
+    - {name: E1, start: 820, colour: '#ff7f0e', stop: N}
+    - {name: E2, start: 1396, colour: '#2ca02c', stop: N}
+    - {name: p7, start: 2488, colour: '#d62728', stop: N}
+    - {name: NS2, start: 2677, colour: '#9467bd', stop: N}
+    - {name: NS3, start: 3328, colour: '#8c564b', stop: N}
+    - {name: NS4b, start: 5383, colour: '#7f7f7f', stop: N}
+    - {name: NS4a, start: 5221, colour: '#e377c2', stop: N}
+    - {name: NS5a, start: 6166, colour: '#bcbd22', stop: N}
+    - {name: NS5b, start: 7516, colour: '#17becf', stop: N}
     - {name: "3'", start: 9289, end: 9646, colour: darkgrey}
 - seed_pattern: HCV-6.*
   coordinates: HCV-6a
   prefix: HCV6-EUHK2-
   landmarks:
     - {name: "5'", start: 1, colour: darkgrey}
-    - {name: C, full_name: Core, start: 284, colour: '#1f77b4'}
-    - {name: E1, start: 857, colour: '#ff7f0e'}
-    - {name: E2, start: 1433, colour: '#2ca02c'}
-    - {name: p7, start: 2534, colour: '#d62728'}
-    - {name: NS2, start: 2723, colour: '#9467bd'}
-    - {name: NS3, start: 3374, colour: '#8c564b'}
-    - {name: NS4b, start: 5429, colour: '#7f7f7f'}
-    - {name: NS4a, start: 5267, colour: '#e377c2'}
-    - {name: NS5a, start: 6212, colour: '#bcbd22'}
-    - {name: NS5b, start: 7565, colour: '#17becf'}
+    - {name: C, full_name: Core, start: 284, colour: '#1f77b4', stop: N}
+    - {name: E1, start: 857, colour: '#ff7f0e', stop: N}
+    - {name: E2, start: 1433, colour: '#2ca02c', stop: N}
+    - {name: p7, start: 2534, colour: '#d62728', stop: N}
+    - {name: NS2, start: 2723, colour: '#9467bd', stop: N}
+    - {name: NS3, start: 3374, colour: '#8c564b', stop: N}
+    - {name: NS4b, start: 5429, colour: '#7f7f7f', stop: N}
+    - {name: NS4a, start: 5267, colour: '#e377c2', stop: N}
+    - {name: NS5a, start: 6212, colour: '#bcbd22', stop: N}
+    - {name: NS5b, start: 7565, colour: '#17becf', stop: N}
     - {name: "3'", start: 9339, end: 9646, colour: darkgrey}
 - seed_pattern: HCV-7.*
   coordinates: HCV-7a
   prefix: HCV7-QC69-
   landmarks:
     - {name: "5'", start: 1, colour: darkgrey}
-    - {name: C, full_name: Core, start: 309, colour: '#1f77b4'}
-    - {name: E1, start: 882, colour: '#ff7f0e'}
-    - {name: E2, start: 1458, colour: '#2ca02c'}
-    - {name: p7, start: 2559, colour: '#d62728'}
-    - {name: NS2, start: 2748, colour: '#9467bd'}
-    - {name: NS3, start: 3399, colour: '#8c564b'}
-    - {name: NS4b, start: 5454, colour: '#7f7f7f'}
-    - {name: NS4a, start: 5292, colour: '#e377c2'}
-    - {name: NS5a, start: 6237, colour: '#bcbd22'}
-    - {name: NS5b, start: 7575, colour: '#17becf'}
+    - {name: C, full_name: Core, start: 309, colour: '#1f77b4', stop: N}
+    - {name: E1, start: 882, colour: '#ff7f0e', stop: N}
+    - {name: E2, start: 1458, colour: '#2ca02c', stop: N}
+    - {name: p7, start: 2559, colour: '#d62728', stop: N}
+    - {name: NS2, start: 2748, colour: '#9467bd', stop: N}
+    - {name: NS3, start: 3399, colour: '#8c564b', stop: N}
+    - {name: NS4b, start: 5454, colour: '#7f7f7f', stop: N}
+    - {name: NS4a, start: 5292, colour: '#e377c2', stop: N}
+    - {name: NS5a, start: 6237, colour: '#bcbd22', stop: N}
+    - {name: NS5b, start: 7575, colour: '#17becf', stop: N}
     - {name: "3'", start: 9349, end: 9646, colour: darkgrey}
 - seed_pattern: HLA-B-seed
   coordinates: HLA-B-seed

diff --git a/micall/tests/test_landmark_reader.py b/micall/tests/test_landmark_reader.py
@@ -47,7 +47,7 @@ def test_gene_without_end():
 """)
     expected_gene = dict(name='gene2',
                          start=789,
-                         end=5040,
+                         end=5039,
                          frame=0,
                          colour='lightblue')
     reader = LandmarkReader.load(landmarks_yaml)
@@ -59,10 +59,11 @@ def test_gene_without_end():
 
 def test_load_defaults():
     expected_gene = dict(name='PR',
-                         start=2252,
+                         start=2253,
                          end=2549,
                          frame=3,
-                         colour='orange')
+                         colour='orange',
+                         stop='N')
     reader = LandmarkReader.load()
 
     gene = reader.get_gene('HIV1-B-FR-K03455-seed', 'PR', drop_stop_codon=False)
@@ -82,7 +83,7 @@ def test_gene_with_prefix():
 """)
     expected_gene = dict(name='gene2',
                          start=789,
-                         end=5040,
+                         end=5039,
                          frame=0,
                          colour='lightblue')
     reader = LandmarkReader.load(landmarks_yaml)
@@ -103,7 +104,7 @@ def test_gene_drop_stop_codon():
 """)
     expected_gene = dict(name='gene2',
                          start=789,
-                         end=5037,
+                         end=5036,
                          frame=0,
                          colour='lightblue')
     reader = LandmarkReader.load(landmarks_yaml)
@@ -113,6 +114,28 @@ def test_gene_drop_stop_codon():
     assert gene == expected_gene
 
 
+def test_gene_no_stop_codon():
+    landmarks_yaml = StringIO("""\
+- seed_pattern: R1
+  coordinates: R1-seed
+  landmarks:
+    - {name: gene1, start: 1, frame: 0, colour: darkgrey}
+    - {name: gene2, start: 789, frame: 0, colour: lightblue, stop: N}
+    - {name: gene3, start: 5040, end: 5616, frame: 0, colour: steelblue}
+""")
+    expected_gene = dict(name='gene2',
+                         start=789,
+                         end=5039,
+                         frame=0,
+                         colour='lightblue',
+                         stop='N')
+    reader = LandmarkReader.load(landmarks_yaml)
+
+    gene = reader.get_gene('R1-seed', 'gene2', drop_stop_codon=True)
+
+    assert gene == expected_gene
+
+
 def test_gene_missing_prefix():
     landmarks_yaml = StringIO("""\
 - seed_pattern: R1
@@ -143,7 +166,7 @@ def test_gene_with_full_name():
     expected_gene = dict(name='2',
                          full_name='gene2',
                          start=789,
-                         end=5040,
+                         end=5039,
                          frame=0,
                          colour='lightblue')
     reader = LandmarkReader.load(landmarks_yaml)

diff --git a/micall/tests/test_plot_contigs.py b/micall/tests/test_plot_contigs.py
@@ -812,10 +812,10 @@ def test_plot_genome_coverage_blast_aligns_refs():
 1,HIV1-G-CM-KP718923-seed,300,1,90,1,10,1653,1662
 """)
     expected_figure = """\
-5' LTR[1-634], gag[789-2289], vif[5040-5616], tat[8379-8469], nef[8796-9414]
-tat[5831-6045], vpu[6061-6307], rev[8379-8653], 3' LTR[9086-9719]
-pol[2085-5096], vpr[5558-5847], rev[5970-6045], env[6225-8795]
-PR[2252-2549], RT[2549-3869], INT[4229-5093], V3[7109-7217], GP41[7757-8792]
+5' LTR[1-634], gag[790-2292], vif[5041-5619], tat[8380-8469], nef[8797-9417]
+tat[5831-6049], vpu[6062-6310], rev[8378-8653], 3' LTR[9086-9719]
+pol[2085-5096], vpr[5559-5850], rev[5970-6048], env[6225-8795]
+PR[2253-2549], RT[2550-3869], INT[4230-5096], V3[7110-7217], GP41[7758-8795]
 2261--1.1->2270
 2261--1.1->2270
 Coverage 5x10
@@ -849,10 +849,10 @@ def test_plot_genome_coverage_g2p():
 HIV1-CON-XX-Consensus-seed,HIV1-B-FR-K03455-seed,1,6,7201,7206
 """)
     expected_figure = """\
-5' LTR[1-634], gag[789-2289], vif[5040-5616], tat[8379-8469], nef[8796-9414]
-tat[5831-6045], vpu[6061-6307], rev[8379-8653], 3' LTR[9086-9719]
-pol[2085-5096], vpr[5558-5847], rev[5970-6045], env[6225-8795]
-PR[2252-2549], RT[2549-3869], INT[4229-5093], V3[7109-7217], GP41[7757-8792]
+5' LTR[1-634], gag[790-2292], vif[5041-5619], tat[8380-8469], nef[8797-9417]
+tat[5831-6049], vpu[6062-6310], rev[8378-8653], 3' LTR[9086-9719]
+pol[2085-5096], vpr[5559-5850], rev[5970-6048], env[6225-8795]
+PR[2253-2549], RT[2550-3869], INT[4230-5096], V3[7110-7217], GP41[7758-8795]
 2261--1.1->2266
 Coverage 100x6
 [7201-7206], HIV1-CON-XX-Consensus-seed - depth 100(1-9719)

diff --git a/micall/utils/consensus_aligner.py b/micall/utils/consensus_aligner.py
@@ -191,12 +191,12 @@ def start_contig(self,
         self.coordinate_name = coordinate_name
         coordinate_seq = self.projects.getReference(coordinate_name)
         aligner = Aligner(seq=coordinate_seq, preset='map-ont')
-        self.alignments = list(aligner.map(consensus))
-        if self.alignments or 10_000 < len(consensus):
+        self.alignments = list(aligner.map(self.consensus))
+        if self.alignments or 10_000 < len(self.consensus):
             self.algorithm = 'minimap2'
         else:
             self.algorithm = 'gotoh'
-            self.align_gotoh(coordinate_seq, consensus)
+            self.align_gotoh(coordinate_seq, self.consensus)
         self.alignments = [alignment
                            for alignment in self.alignments
                            if alignment.is_primary]