Do not rename reverse complemented sequences

Donaim · Donaim · commit d77e5a01ec80 · 2024-07-12T14:28:10.000-07:00
diff --git a/src/cfeintact/aligned_sequence.py b/src/cfeintact/aligned_sequence.py
@@ -39,7 +39,7 @@ def coordinate_mapping(self):
 
     def reverse(self):
         newthis = SeqRecord(Seq.reverse_complement(self.this.seq),
-                            id=(self.this.id or "*Unknown*") + "[REVERSE_COMPLEMENT]",
+                            id=self.this.id,
                             name=self.this.name
                             )
 
diff --git a/tests/expected-results-edgy/errors.json b/tests/expected-results-edgy/errors.json
@@ -1195,7 +1195,7 @@
             "orf": null
         }
     ],
-    "Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455.CfE.BUT.REVERSECOMPLEMENTED[REVERSE_COMPLEMENT]": [],
+    "Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455.CfE.BUT.REVERSECOMPLEMENTED": [],
     "Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455.CfE.BUT.REVERSED": [
         {
             "qseqid": "Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455.CfE.BUT.REVERSED",
@@ -1420,7 +1420,7 @@
             "orf": null
         }
     ],
-    "Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455.CfE.BUT.WITH-XS[REVERSE_COMPLEMENT]": [
+    "Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455.CfE.BUT.WITH-XS": [
         {
             "qseqid": "Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455.CfE.BUT.WITH-XS",
             "error": "UnknownNucleotide",
@@ -1664,15 +1664,15 @@
             "orf": null
         }
     ],
-    "Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455.CfE.BUT.WITH-BAD-SYMBOLS[REVERSE_COMPLEMENT]": [
+    "Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455.CfE.BUT.WITH-BAD-SYMBOLS": [
         {
             "qseqid": "Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455.CfE.BUT.WITH-BAD-SYMBOLS",
             "error": "UnknownNucleotide",
             "message": "Sequence contains invalid nucleotides: >1>#>@> (start: 45, end: 51).",
             "orf": null
         }
     ],
-    "Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455.CfE.BUT.WITH-DASHES[REVERSE_COMPLEMENT]": [
+    "Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455.CfE.BUT.WITH-DASHES": [
         {
             "qseqid": "Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455.CfE.BUT.WITH-DASHES",
             "error": "UnknownNucleotide",
diff --git a/tests/expected-results-edgy/holistic.json b/tests/expected-results-edgy/holistic.json
@@ -103,7 +103,7 @@
         "orfs_end": 8368,
         "blast_n_conseqs": 0
     },
-    "Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455.CfE.BUT.REVERSECOMPLEMENTED[REVERSE_COMPLEMENT]": {
+    "Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455.CfE.BUT.REVERSECOMPLEMENTED": {
         "intact": true,
         "qlen": 9718,
         "hypermutation_probablility": 0.0,
@@ -129,7 +129,7 @@
         "orfs_end": 8368,
         "blast_n_conseqs": 0
     },
-    "Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455.CfE.BUT.WITH-XS[REVERSE_COMPLEMENT]": {
+    "Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455.CfE.BUT.WITH-XS": {
         "intact": false,
         "qlen": 9711,
         "hypermutation_probablility": 0.0,
@@ -155,7 +155,7 @@
         "orfs_end": 8368,
         "blast_n_conseqs": 0
     },
-    "Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455.CfE.BUT.WITH-BAD-SYMBOLS[REVERSE_COMPLEMENT]": {
+    "Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455.CfE.BUT.WITH-BAD-SYMBOLS": {
         "intact": false,
         "qlen": 9711,
         "hypermutation_probablility": 0.0,
@@ -168,7 +168,7 @@
         "orfs_end": 8793,
         "blast_n_conseqs": 3
     },
-    "Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455.CfE.BUT.WITH-DASHES[REVERSE_COMPLEMENT]": {
+    "Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455.CfE.BUT.WITH-DASHES": {
         "intact": false,
         "qlen": 9711,
         "hypermutation_probablility": 0.0,
diff --git a/tests/expected-results-edgy/intact.fasta b/tests/expected-results-edgy/intact.fasta
@@ -324,7 +324,7 @@ CTGGGGAGTGGCGAGCCCTCAGATCCTGCATATAAGCAGCTGCTTTTTGCCTGTACTGGG
 TCTCTCTGGTTAGACCAGATCTGAGCCTGGGAGCTCTCTGGCTAACTAGGGAACCCACTG
 CTTAAGCCTCAATAAAGCTTGCCTTGAGTGCTTCAAGTAGTGTGTGCCCGTCTGTTGTGT
 GACTCTGGTAACTAGAGATCCCTCAGACCCTTTTAGTCAGTGTGGAAAATCTCTAGCA
->Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455.CfE.BUT.REVERSECOMPLEMENTED[REVERSE_COMPLEMENT] <unknown description>
+>Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455.CfE.BUT.REVERSECOMPLEMENTED <unknown description>
 TGGAAGGGCTAATTCACTCCCAACGAAGACAAGATATCCTTGATCTGTGGATCTACCACA
 CACAAGGCTACTTCCCTGATTAGCAGAACTACACACCAGGGCCAGGGATCAGATATCCAC
 TGACCTTTGGATGGTGCTACAAGCTAGTACCAGTTGAGCCAGAGAAGTTAGAAGAAGCCA
diff --git a/tests/expected-results-edgy/nonintact.fasta b/tests/expected-results-edgy/nonintact.fasta
@@ -332,7 +332,7 @@ CCCAGTAGGTAAGGTACGTCCGAGTGTCCCACATTGTTCGACCACAAGAGAGGAAACAAC
 CGAAGAAGATTGAAGAGACCGAGTTGACCATGATCGAACATCGTGGTAGGTTTCCAGTCA
 CCTATAGACTAGGGACCGGGACCACACATCAAGACGATTAGTCCCTTCATCGGAACACAC
 ACCATCTAGGTGTCTAGTTCCTATAGAACAGAAGCAACCCTCACTTAATCGGGAAGGT
->Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455.CfE.BUT.WITH-XS[REVERSE_COMPLEMENT] <unknown description>
+>Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455.CfE.BUT.WITH-XS <unknown description>
 TGGAAGGGCTAATTCACTCCCAACGAAGACAAGATATCCTTGATCTGTGGATCTACCACA
 CACAAGGCTACTTCCCTGATTAGCAGAACTACACACCAGGGCCAGGGATCAGATATCCAC
 TGACCTTTGGATGGTGCTACAAGCTAGTACCAGTTGAGCCAGAGAAGTTAGAAGAAGCCA
@@ -497,7 +497,7 @@ CTTAAGCCTCAATAAAGCTTGCCTTGAGTGCTTCAAGTAGTGTGTGCCCGTCTGTTGTGT
 GACTCTAGAGATCCCTCAGACCCTTTTAGTCAGTGTGGAAAATCTCTAGCA
 >small-sequence-with-xs <unknown description>
 ATCTCTAGAGTC
->Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455.CfE.BUT.WITH-BAD-SYMBOLS[REVERSE_COMPLEMENT] <unknown description>
+>Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455.CfE.BUT.WITH-BAD-SYMBOLS <unknown description>
 TGGAAGGGCTAATTCACTCCCAACGAAGACAAGATATCCTTGATCTGTGGATCTACCACA
 CACAAGGCTACTTCCCTGATTAGCAGAACTACACACCAGGGCCAGGGATCAGATATCCAC
 TGACCTTTGGATGGTGCTACAAGCTAGTACCAGTTGAGCCAGAGAAGTTAGAAGAAGCCA
@@ -660,7 +660,7 @@ CTGGGGAGTGGCGAGCCCTCAGATCCTGCATATAAGCAGCTGCTTTTTGCCTGTACTGGG
 TCTCTCTGGTTAGACCAGATCTGAGCCTGGGAGCTCTCTGGCTAACTAGGGAACCCACTG
 CTTAAGCCTCAATAAAGCTTGCCTTGAGTGCTTCAAGTAGTGTGTGCCCGTCTGTTGTGT
 GACTCTAGAGATCCCTCAGACCCTTTTAGTCAGTGTGGAAAATCTCTAGCA
->Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455.CfE.BUT.WITH-DASHES[REVERSE_COMPLEMENT] <unknown description>
+>Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455.CfE.BUT.WITH-DASHES <unknown description>
 TGGAAGGGCTAATTCACTCCCAACGAAGACAAGATATCCTTGATCTGTGGATCTACCACA
 CACAAGGCTACTTCCCTGATTAGCAGAACTACACACCAGGGCCAGGGATCAGATATCCAC
 TGACCTTTGGATGGTGCTACAAGCTAGTACCAGTTGAGCCAGAGAAGTTAGAAGAAGCCA
diff --git a/tests/expected-results-edgy/orfs.json b/tests/expected-results-edgy/orfs.json
@@ -1335,7 +1335,7 @@
             "subtype_nucleotides": "TTTTTTAGGGAAAATTTGGCCTTCCAACAAGGGAAGGCCGGGGAATTTTCCTCAGAGCAGACCAGAGCCAACAGCCCCACCAGCAGAAAACTGGGGGATGGGGGAAGAGATAACGGGGGAAGAGATAACCTCCTTACCGAAGCAGGAGCAGAAAGACAAGGAACATCCTCCTCCTTTAGTTTCCCTCAAATCACTCTTTGGCAACGACCCCTTGTCACAGTAAAAATAGGAGGACAGCTGAAAGAAGCTCTATTAGATACAGGAGCAGATGATACAGTATTAGAAGATATAAATTTGCCAGGAAAATGGAAACCAAAAATGATAGGGGGAATTGGAGGTTTTATCAAGGTAAAGCAATATGATCAGATACTTATAGAAATCTGTGGAAAAAAGGCTATAGGTACAGTATTAGTAGGACCTACACCTGTCAACATAATTGGACGAAATATGTTGACTCAGATTGGTTGTACTTTAAATTTCCCAATTAGTCCTATTGACACTGTACCAGTAACATTAAAGCCAGGAATGGATGGACCAAAGGTTAAACAGTGGCCATTGACAGAAGAAAAAATAAAAGCATTAACAGAAATTTGTAAAGAGATGGAAGAGGAAGGAAAAATCTCAAAAATTGGGCCTGAAAATCCATACAATACTCCAGTATTTGCTATAAAGAAAAAGGACAGCACCAAATGGAGGAAATTAGTAGATTTCAGAGAGCTCAATAAAAGAACTCAGGACTTTTGGGAAGTTCAATTAGGAATACCGCATCCAGCAGGTTTAAAAAAGAAAAAATCAGTAACAGTACTAGATGTGGGAGATGCATATTTTTCAGTTCCTTTAGATGAAAGCTTTAGAAAGTATACTGCATTCACCATACCTAGTATAAACAATGAGACACCAGGAATCAGATATCAGTACAATGTGCTGCCACAGGGATGGAAAGGATCACCGGCAATATTCCAGAGTAGCATGACAAAAATCTTAGAGCCCTTTAGAATAAAAAATCCAGAAATGGTTATCTATCAATACAAGGATGACTTGTATGTAGGATCTGATTTAGAAATAGGGCAGCACAGAACAAAAATAGAGGAGCTAAGAGCTCATCTATTGAGCTGGGGATTTACTACACCAGACAAAAAGCATCAGAAGGAACCTCCATTCCTTTGGATGGGATATGAACTCCATCCTGACAGATGGACAGTCCAGCCTATAGAACTGCCAGAAAAAGACAGCTGGACTGTCAATGATATACAGAAATTAGTGGGAAAACTAAATTGGGCAAGTCAAATTTATGCAGGGATTAAGGTAAAGCAACTGTGTAAACTCCTCAGGGGAGCTAAAGCACTAACAGACATAGTACCACTGACTGAAGAAGCAGAATTAGAGTTGGCAGAGAACAGGGAGATTCTAAAAACCCCTGTGCATGGAGTATATTATGACCCATCAAAAGACTTAGTAGCAGAAGTACAGAAACAAGGGCAGGACCAATGGACATATCAAATTTATCAAGAGCCATTTAAAAATCTAAAAACAGGAAAATATGCCAGAAGAGGGTCTGCTCACACTAATGATGTAAGACAATTAACAGAAGTGGTGCAAAAAGTAGCCACAGAAAGCATAGTAATATGGGGAAAGACCCCTAAATTTAGACTACCCATACAAAGAGAAACATGGGAAACATGGTGGATGGAGTATTGGCAGGCTACCTGGATTCCTGAATGGGAGTTTGTTAATACCCCTCCTCTAGTAAAATTATGGTACCAATTAGAAAAAGACCCCATAGTAGGAGCAGAGACTTTCTATGTAGATGGGGCAGCTAGTAGGGAGACTAAGCTAGGAAAAGCAGGGTATGTCACTGACAGAGGAAGACAAAAGGTAGTTTCCCTAACTGAGACAACAAATCAAAAGACTGAATTACATGCGATCCATTTAGCCTTGCAGGATTCAGGATCAGAAGTAAATATAGTAACAGACTCACAATATGCATTAGGAATCATTCAGGCACAACCAGACAGGAGTGAATCAGAAGTAGTCAACCAAATAATAGAGGAGCTAATAAAAAAGGAGAAAGTCTACCTGTCATGGGTACCAGCACACAAGGGGATTGGAGGAAATGAACAAGTAGATAAATTAGTCAGTTCAGGAATCAGGAAGGTGCTATTTTTAGATGGGATAGATAAGGCTCAAGAAGAACATGAAAGATATCACAGCAATTGGAGAACAATGGCTAGTGATTTTAATTTGCCACCTATAGTAGCAAAGGAAATAGTAACCAACTGTGATAAATGTCAACTAAAAGGGGAAGCTATGCATGGACAAGTAGACTGTAGTCCAGGGATATGGCAATTAGATTGCACACATCTAGAAGGAAAAGTCATCCTGGTAGCAGTCCACGTGGCCAGTGGATATATAGAAGCAGAAGTTATCCCAGCAGAAACAGGACAGGAGACAGCATACTTTCTGCTAAAACTAGCAGGAAGATGGCCAGTAAAAGTAATACACACAGACAACGGTAGCAATTTCACCAGCGCTGCAGTTAAAGCAGCCTGTTGGTGGGCCAATGTCCAACAGGAATTTGGGATCCCCTACAATCCCCAAAGTCAAGGAGTAGTAGAATCTATGAATAAGGAATTAAAGAAAATCATAGGGCAGGTAAGAGAGCAAGCTGAACACCTTAAAACAGCAGTACAAATGGCAGTATTCATTCACAATTTTAAAAGAAAAGGGGGGATTGGGGGGTACAGTGCAGGGGAAAGAATAATAGACATAATAGCAACAGACATACAAACTAAAGAATTACAAAAACAAATTACAAAAATTCAAAATTTTCGGGTTTATTACAGGGACAGCAGAGACCCAATTTGGAAAGGACCAGCAAAACTACTCTGGAAAGGTGAAGGGGCAGTAGTAATACAAGACAATAGTGATATAAAAGTAGTACCAAGAAGAAAAGCAAAGATCATTAGGGATTATGGAAAACAGATGGCAGGTGATGATTGTGTGGCAGGTAGACAGGATGAGGATTAG"
         }
     ],
-    "Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455.CfE.BUT.REVERSECOMPLEMENTED[REVERSE_COMPLEMENT]": [
+    "Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455.CfE.BUT.REVERSECOMPLEMENTED": [
         {
             "name": "gag",
             "start": 789,
@@ -1669,7 +1669,7 @@
             "subtype_nucleotides": "ATGGGAAGTAAGTGGTCAAAAAGTAGCATAGTGGGATGGCCTCAGGTCAGGGAAAAAATAAAGCAAACTCCTCCAGCAACAGAAGGAGTAGGAGCAGTATCTCAAGATCTAGATAAACATGGAGCAATAACAAGTAGTAATATAGATAATGCTGATTGTGTCTGGCTGAGAGCACAAGAGGACGAGGAGGTAGGCTTTCCAGTCATGCCGCAGGTACCTCTAAGACCAATGACTTATAAGGGAGCTTTTGATCTTAGCTTCTTTTTAAAAGAAAAGGGGGGACTGGATGGGCTAATTTACTCCAAGAAAAGACAAGAGATCCTTGACTTATGGGTCTATAATACACAAGGCTTCTTCCCTGATTGGCAAAACTACACACCAGGGCCAGGGATCAGATTCCCACTGTGTTTTGGATGGTGCTTCAAGCTAGTACCAGTTGACCAAAGAGAAGTAGAGGAGGACAACAAAGGAGAAAACAACTGCCTGTTACACCCCATGAGCCAGCATGGAATAGAGGACGAAGAAAGAGAAGTGCTGATGTGGAAGTTTGACAGTGCCCTAGCACGAAAACACGTAGCCCGAGAACAGCATCCAGAGTACTATAAAGACTGCTGA"
         }
     ],
-    "Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455.CfE.BUT.WITH-XS[REVERSE_COMPLEMENT]": [
+    "Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455.CfE.BUT.WITH-XS": [
         {
             "name": "gag",
             "start": 789,
@@ -2003,7 +2003,7 @@
             "subtype_nucleotides": "ATGGCAGGAAGAAGCGGAAGCACCGACGAGGAACTCCTCAGAGCAGTAAGGATCATCAAAATCCTATACCAAAGCA"
         }
     ],
-    "Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455.CfE.BUT.WITH-BAD-SYMBOLS[REVERSE_COMPLEMENT]": [
+    "Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455.CfE.BUT.WITH-BAD-SYMBOLS": [
         {
             "name": "gag",
             "start": 789,
@@ -2170,7 +2170,7 @@
             "subtype_nucleotides": "ATGGGTGGCAAGTGGTCAAAAAGTAGTGTGATTGGATGGCCTACTGTAAGGGAAAGAATGAGACGAGCTGAGCCAGCAGCAGATAGGGTGGGAGCAGCATCTCGAGACCTGGAAAAACATGGAGCAATCACAAGTAGCAATACAGCAGCTACCAATGCTGCTTGTGCCTGGCTAGAAGCACAAGAGGAGGAGGAGGTGGGTTTTCCAGTCACACCTCAGGTACCTTTAAGACCAATGACTTACAAGGCAGCTGTAGATCTTAGCCACTTTTTAAAAGAAAAGGGGGGACTGGAAGGGCTAATTCACTCCCAAAGAAGACAAGATATCCTTGATCTGTGGATCTACCACACACAAGGCTACTTCCCTGATTGGCAGAACTACACACCAGGGCCAGGGGTCAGATATCCACTGACCTTTGGATGGTGCTACAAGCTAGTACCAGTTGAGCCAGATAAGATAGAAGAGGCCAATAAAGGAGAGAACACCAGCTTGTTACACCCTGTGAGCCTGCATGGGATGGATGACCCGGAGAGAGAAGTGTTAGAGTGGAGGTTTGACAGCCGCCTAGCATTTCATCACGTGGCCCGAGAGCTGCATCCGGAGTACTTCAAGAACTGCTGA"
         }
     ],
-    "Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455.CfE.BUT.WITH-DASHES[REVERSE_COMPLEMENT]": [
+    "Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455.CfE.BUT.WITH-DASHES": [
         {
             "name": "gag",
             "start": 789,

Original file line number	Diff line number	Diff line change
`@@ -39,7 +39,7 @@ def coordinate_mapping(self):`
`39`	`39`
`40`	`40`	`def reverse(self):`
`41`	`41`	`newthis = SeqRecord(Seq.reverse_complement(self.this.seq),`
`42`		`- id=(self.this.id or "Unknown") + "[REVERSE_COMPLEMENT]",`
	`42`	`+ id=self.this.id,`
`43`	`43`	`name=self.this.name`
`44`	`44`	`)`
`45`	`45`
Original file line number	Diff line number	Diff line change
`@@ -1195,7 +1195,7 @@`
`1195`	`1195`	`"orf": null`
`1196`	`1196`	`}`
`1197`	`1197`	`],`
`1198`		`- "Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455.CfE.BUT.REVERSECOMPLEMENTED[REVERSE_COMPLEMENT]": [],`
	`1198`	`+ "Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455.CfE.BUT.REVERSECOMPLEMENTED": [],`
`1199`	`1199`	`"Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455.CfE.BUT.REVERSED": [`
`1200`	`1200`	`{`
`1201`	`1201`	`"qseqid": "Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455.CfE.BUT.REVERSED",`
`@@ -1420,7 +1420,7 @@`
`1420`	`1420`	`"orf": null`
`1421`	`1421`	`}`
`1422`	`1422`	`],`
`1423`		`- "Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455.CfE.BUT.WITH-XS[REVERSE_COMPLEMENT]": [`
	`1423`	`+ "Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455.CfE.BUT.WITH-XS": [`
`1424`	`1424`	`{`
`1425`	`1425`	`"qseqid": "Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455.CfE.BUT.WITH-XS",`
`1426`	`1426`	`"error": "UnknownNucleotide",`
`@@ -1664,15 +1664,15 @@`
`1664`	`1664`	`"orf": null`
`1665`	`1665`	`}`
`1666`	`1666`	`],`
`1667`		`- "Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455.CfE.BUT.WITH-BAD-SYMBOLS[REVERSE_COMPLEMENT]": [`
	`1667`	`+ "Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455.CfE.BUT.WITH-BAD-SYMBOLS": [`
`1668`	`1668`	`{`
`1669`	`1669`	`"qseqid": "Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455.CfE.BUT.WITH-BAD-SYMBOLS",`
`1670`	`1670`	`"error": "UnknownNucleotide",`
`1671`	`1671`	`"message": "Sequence contains invalid nucleotides: >1>#>@> (start: 45, end: 51).",`
`1672`	`1672`	`"orf": null`
`1673`	`1673`	`}`
`1674`	`1674`	`],`
`1675`		`- "Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455.CfE.BUT.WITH-DASHES[REVERSE_COMPLEMENT]": [`
	`1675`	`+ "Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455.CfE.BUT.WITH-DASHES": [`
`1676`	`1676`	`{`
`1677`	`1677`	`"qseqid": "Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455.CfE.BUT.WITH-DASHES",`
`1678`	`1678`	`"error": "UnknownNucleotide",`
Original file line number	Diff line number	Diff line change
`@@ -1335,7 +1335,7 @@`
`1335`	`1335`	"subtype_nucleotides": "TTTTTTAGGGAAAATTTGGCCTTCCAACAAGGGAAGGCCGGGGAATTTTCCTCAGAGCAGACCAGAGCCAACAGCCCCACCAGCAGAAAACTGGGGGATGGGGGAAGAGATAACGGGGGAAGAGATAACCTCCTTACCGAAGCAGGAGCAGAAAGACAAGGAACATCCTCCTCCTTTAGTTTCCCTCAAATCACTCTTTGGCAACGACCCCTTGTCACAGTAAAAATAGGAGGACAGCTGAAAGAAGCTCTATTAGATACAGGAGCAGATGATACAGTATTAGAAGATATAAATTTGCCAGGAAAATGGAAACCAAAAATGATAGGGGGAATTGGAGGTTTTATCAAGGTAAAGCAATATGATCAGATACTTATAGAAATCTGTGGAAAAAAGGCTATAGGTACAGTATTAGTAGGACCTACACCTGTCAACATAATTGGACGAAATATGTTGACTCAGATTGGTTGTACTTTAAATTTCCCAATTAGTCCTATTGACACTGTACCAGTAACATTAAAGCCAGGAATGGATGGACCAAAGGTTAAACAGTGGCCATTGACAGAAGAAAAAATAAAAGCATTAACAGAAATTTGTAAAGAGATGGAAGAGGAAGGAAAAATCTCAAAAATTGGGCCTGAAAATCCATACAATACTCCAGTATTTGCTATAAAGAAAAAGGACAGCACCAAATGGAGGAAATTAGTAGATTTCAGAGAGCTCAATAAAAGAACTCAGGACTTTTGGGAAGTTCAATTAGGAATACCGCATCCAGCAGGTTTAAAAAAGAAAAAATCAGTAACAGTACTAGATGTGGGAGATGCATATTTTTCAGTTCCTTTAGATGAAAGCTTTAGAAAGTATACTGCATTCACCATACCTAGTATAAACAATGAGACACCAGGAATCAGATATCAGTACAATGTGCTGCCACAGGGATGGAAAGGATCACCGGCAATATTCCAGAGTAGCATGACAAAAATCTTAGAGCCCTTTAGAATAAAAAATCCAGAAATGGTTATCTATCAATACAAGGATGACTTGTATGTAGGATCTGATTTAGAAATAGGGCAGCACAGAACAAAAATAGAGGAGCTAAGAGCTCATCTATTGAGCTGGGGATTTACTACACCAGACAAAAAGCATCAGAAGGAACCTCCATTCCTTTGGATGGGATATGAACTCCATCCTGACAGATGGACAGTCCAGCCTATAGAACTGCCAGAAAAAGACAGCTGGACTGTCAATGATATACAGAAATTAGTGGGAAAACTAAATTGGGCAAGTCAAATTTATGCAGGGATTAAGGTAAAGCAACTGTGTAAACTCCTCAGGGGAGCTAAAGCACTAACAGACATAGTACCACTGACTGAAGAAGCAGAATTAGAGTTGGCAGAGAACAGGGAGATTCTAAAAACCCCTGTGCATGGAGTATATTATGACCCATCAAAAGACTTAGTAGCAGAAGTACAGAAACAAGGGCAGGACCAATGGACATATCAAATTTATCAAGAGCCATTTAAAAATCTAAAAACAGGAAAATATGCCAGAAGAGGGTCTGCTCACACTAATGATGTAAGACAATTAACAGAAGTGGTGCAAAAAGTAGCCACAGAAAGCATAGTAATATGGGGAAAGACCCCTAAATTTAGACTACCCATACAAAGAGAAACATGGGAAACATGGTGGATGGAGTATTGGCAGGCTACCTGGATTCCTGAATGGGAGTTTGTTAATACCCCTCCTCTAGTAAAATTATGGTACCAATTAGAAAAAGACCCCATAGTAGGAGCAGAGACTTTCTATGTAGATGGGGCAGCTAGTAGGGAGACTAAGCTAGGAAAAGCAGGGTATGTCACTGACAGAGGAAGACAAAAGGTAGTTTCCCTAACTGAGACAACAAATCAAAAGACTGAATTACATGCGATCCATTTAGCCTTGCAGGATTCAGGATCAGAAGTAAATATAGTAACAGACTCACAATATGCATTAGGAATCATTCAGGCACAACCAGACAGGAGTGAATCAGAAGTAGTCAACCAAATAATAGAGGAGCTAATAAAAAAGGAGAAAGTCTACCTGTCATGGGTACCAGCACACAAGGGGATTGGAGGAAATGAACAAGTAGATAAATTAGTCAGTTCAGGAATCAGGAAGGTGCTATTTTTAGATGGGATAGATAAGGCTCAAGAAGAACATGAAAGATATCACAGCAATTGGAGAACAATGGCTAGTGATTTTAATTTGCCACCTATAGTAGCAAAGGAAATAGTAACCAACTGTGATAAATGTCAACTAAAAGGGGAAGCTATGCATGGACAAGTAGACTGTAGTCCAGGGATATGGCAATTAGATTGCACACATCTAGAAGGAAAAGTCATCCTGGTAGCAGTCCACGTGGCCAGTGGATATATAGAAGCAGAAGTTATCCCAGCAGAAACAGGACAGGAGACAGCATACTTTCTGCTAAAACTAGCAGGAAGATGGCCAGTAAAAGTAATACACACAGACAACGGTAGCAATTTCACCAGCGCTGCAGTTAAAGCAGCCTGTTGGTGGGCCAATGTCCAACAGGAATTTGGGATCCCCTACAATCCCCAAAGTCAAGGAGTAGTAGAATCTATGAATAAGGAATTAAAGAAAATCATAGGGCAGGTAAGAGAGCAAGCTGAACACCTTAAAACAGCAGTACAAATGGCAGTATTCATTCACAATTTTAAAAGAAAAGGGGGGATTGGGGGGTACAGTGCAGGGGAAAGAATAATAGACATAATAGCAACAGACATACAAACTAAAGAATTACAAAAACAAATTACAAAAATTCAAAATTTTCGGGTTTATTACAGGGACAGCAGAGACCCAATTTGGAAAGGACCAGCAAAACTACTCTGGAAAGGTGAAGGGGCAGTAGTAATACAAGACAATAGTGATATAAAAGTAGTACCAAGAAGAAAAGCAAAGATCATTAGGGATTATGGAAAACAGATGGCAGGTGATGATTGTGTGGCAGGTAGACAGGATGAGGATTAG"
`1336`	`1336`	`}`
`1337`	`1337`	`],`
`1338`		`- "Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455.CfE.BUT.REVERSECOMPLEMENTED[REVERSE_COMPLEMENT]": [`
	`1338`	`+ "Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455.CfE.BUT.REVERSECOMPLEMENTED": [`
`1339`	`1339`	`{`
`1340`	`1340`	`"name": "gag",`
`1341`	`1341`	`"start": 789,`
`@@ -1669,7 +1669,7 @@`
`1669`	`1669`	"subtype_nucleotides": "ATGGGAAGTAAGTGGTCAAAAAGTAGCATAGTGGGATGGCCTCAGGTCAGGGAAAAAATAAAGCAAACTCCTCCAGCAACAGAAGGAGTAGGAGCAGTATCTCAAGATCTAGATAAACATGGAGCAATAACAAGTAGTAATATAGATAATGCTGATTGTGTCTGGCTGAGAGCACAAGAGGACGAGGAGGTAGGCTTTCCAGTCATGCCGCAGGTACCTCTAAGACCAATGACTTATAAGGGAGCTTTTGATCTTAGCTTCTTTTTAAAAGAAAAGGGGGGACTGGATGGGCTAATTTACTCCAAGAAAAGACAAGAGATCCTTGACTTATGGGTCTATAATACACAAGGCTTCTTCCCTGATTGGCAAAACTACACACCAGGGCCAGGGATCAGATTCCCACTGTGTTTTGGATGGTGCTTCAAGCTAGTACCAGTTGACCAAAGAGAAGTAGAGGAGGACAACAAAGGAGAAAACAACTGCCTGTTACACCCCATGAGCCAGCATGGAATAGAGGACGAAGAAAGAGAAGTGCTGATGTGGAAGTTTGACAGTGCCCTAGCACGAAAACACGTAGCCCGAGAACAGCATCCAGAGTACTATAAAGACTGCTGA"
`1670`	`1670`	`}`
`1671`	`1671`	`],`
`1672`		`- "Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455.CfE.BUT.WITH-XS[REVERSE_COMPLEMENT]": [`
	`1672`	`+ "Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455.CfE.BUT.WITH-XS": [`
`1673`	`1673`	`{`
`1674`	`1674`	`"name": "gag",`
`1675`	`1675`	`"start": 789,`
`@@ -2003,7 +2003,7 @@`
`2003`	`2003`	`"subtype_nucleotides": "ATGGCAGGAAGAAGCGGAAGCACCGACGAGGAACTCCTCAGAGCAGTAAGGATCATCAAAATCCTATACCAAAGCA"`
`2004`	`2004`	`}`
`2005`	`2005`	`],`
`2006`		`- "Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455.CfE.BUT.WITH-BAD-SYMBOLS[REVERSE_COMPLEMENT]": [`
	`2006`	`+ "Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455.CfE.BUT.WITH-BAD-SYMBOLS": [`
`2007`	`2007`	`{`
`2008`	`2008`	`"name": "gag",`
`2009`	`2009`	`"start": 789,`
`@@ -2170,7 +2170,7 @@`
`2170`	`2170`	"subtype_nucleotides": "ATGGGTGGCAAGTGGTCAAAAAGTAGTGTGATTGGATGGCCTACTGTAAGGGAAAGAATGAGACGAGCTGAGCCAGCAGCAGATAGGGTGGGAGCAGCATCTCGAGACCTGGAAAAACATGGAGCAATCACAAGTAGCAATACAGCAGCTACCAATGCTGCTTGTGCCTGGCTAGAAGCACAAGAGGAGGAGGAGGTGGGTTTTCCAGTCACACCTCAGGTACCTTTAAGACCAATGACTTACAAGGCAGCTGTAGATCTTAGCCACTTTTTAAAAGAAAAGGGGGGACTGGAAGGGCTAATTCACTCCCAAAGAAGACAAGATATCCTTGATCTGTGGATCTACCACACACAAGGCTACTTCCCTGATTGGCAGAACTACACACCAGGGCCAGGGGTCAGATATCCACTGACCTTTGGATGGTGCTACAAGCTAGTACCAGTTGAGCCAGATAAGATAGAAGAGGCCAATAAAGGAGAGAACACCAGCTTGTTACACCCTGTGAGCCTGCATGGGATGGATGACCCGGAGAGAGAAGTGTTAGAGTGGAGGTTTGACAGCCGCCTAGCATTTCATCACGTGGCCCGAGAGCTGCATCCGGAGTACTTCAAGAACTGCTGA"
`2171`	`2171`	`}`
`2172`	`2172`	`],`
`2173`		`- "Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455.CfE.BUT.WITH-DASHES[REVERSE_COMPLEMENT]": [`
	`2173`	`+ "Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455.CfE.BUT.WITH-DASHES": [`
`2174`	`2174`	`{`
`2175`	`2175`	`"name": "gag",`
`2176`	`2176`	`"start": 789,`