Issue 73 (#74)

* changes in grammar and test

* re-run pipeline

* extra manual changes

grammar.py

@@ -135,7 +135,7 @@ def check_multiple_positions_dont_exist(groups, gene, seq_type):
         # This is only valid for cases with two aminoacids or more (not to clash with amino_acid_insertion)
         'regex': f'(?<=\\b)({aa}{aa}+)-?(\d+)-?({aa}+)(?=\\b)',
         'apply_syntax': lambda g: '-'.join(g).upper(),
-        'check_invalid': lambda g: f'lengths don\'t match: {g[0]}-{g[2]}' if len(g[0]) != len(g[2]) else '',
+        'check_invalid': lambda g: '',
         'check_sequence': lambda g, gg: check_sequence_multiple_pos(g, gg, 'peptide'),
         'coordinate_indexes': (1,)
     },
@@ -237,7 +237,7 @@ def format_negatives(input_list: list[str], indexes: list[int]):
         # Note the use of positive and negative lookahead / lookbehind for dashes to include both cases
         'regex': f'({nt}{nt}+)-?((?<=-)(?:-?\d+|\(-\d+\))(?=-)|(?<!-)(?:-?\d+|\(-\d+\))(?!-))-?({nt}+)(?=\\b)',
         'apply_syntax': lambda g: ('-'.join(format_negatives(g, [1]))).upper().replace('U', 'T'),
-        'check_invalid': lambda g: f'lengths don\'t match: {g[0]}-{g[2]}' if len(g[0]) != len(g[2]) else '',
+        'check_invalid': lambda g: '',
         'check_sequence': lambda g, gg: check_sequence_multiple_pos(g, gg, 'dna')
     },
     {

manual_fixes_pombase/allele_manual_changes_formatted.tsv

@@ -14,6 +14,14 @@ SPBC6B1.05c	atg7-m1	W227*	nonsense_mutation	PMID:26696398			partial_amino_acid_d
 SPAC1486.02c	dsc2-V160*	V160*	nonsense_mutation	PMID:28821619			partial_amino_acid_deletion			
 SPBC19C2.09	sre1-Q802*	Q802*	nonsense_mutation	PMID:28821619			partial_amino_acid_deletion			
 SPBC4F6.15c	rad23-1	Q232*	nonsense_mutation	PMID:8621070			partial_amino_acid_deletion			
+SPBC16A3.09c	ufd1-I210HRLstop	210->stop	nonsense_mutation	PMID:25658828	I210*		partial_amino_acid_deletion	
+SPAC110.02	pds5-G755V-STOP	AA755->Stop	nonsense_mutation	PMID:28438891	G755*		partial_amino_acid_deletion	
+SPAC110.02	pds5-K686-STOP	AA686->stop	nonsense_mutation	PMID:28438891	K686*		partial_amino_acid_deletion	
+SPAC56F8.06c	alg10-183-stop	183-stop	nonsense_mutation	PMID:30389790	N184*		partial_amino_acid_deletion	
+SPAC17H9.04c	dri1-W46X	aa46->stop	nonsense_mutation	PMID:33946513	W38*		partial_amino_acid_deletion	revision 8403, complement(2009905..2011719)
+SPAC3G9.04	ssu72-Gln57Stop	aa57->stop	nonsense_mutation	PMID:34967420	Q57*		partial_amino_acid_deletion	
+SPBC3B9.11c	ctf1 Tyr260Stop	aa260stop	nonsense_mutation	PMID:34967420	Y260*		partial_amino_acid_deletion	
+SPCC18B5.03	wee1-112	opal	nonsense_mutation	PMID:7262540,PMID:10392445	unknown opal		partial_amino_acid_deletion	very special case, in which they know that it is a nonsense mutation, because they crossed "the original mutants with sup3-5, an efficient suppressor of opal nonsense alleles"
 SPBC28F2.12	rpb1-CTD-S2A(5-16),CTDdelta(17-29)	CTD-S2A(5-16),CTDdelta(17-29)	amino_acid_deletion_and_mutation	PMID:17502918	CTD-S2A(r5-r16)delta(r17-r29)	rpb1-CTD-S2A(r5-r16)delta(r17-r29)				
 SPBC28F2.12	rpb1-CTD-S2E(5-16)	CTD-S2E(5-16)	amino_acid_mutation	PMID:17502918	CTD-S2E(r5-r16)	rpb1-CTD-S2E(r5-r16)
 SPBC28F2.12	rpb1-CTDdelta(11-29)	CTDdelta(11-29)	amino_acid_mutation	PMID:17502918	CTD-delta(r11-r29)	rpb1-CTD-delta(r11-r29)	partial_amino_acid_deletion

manual_fixes_pombase/get_cannot_fix_formatted.py

@@ -1,7 +1,7 @@
 import pandas
 
 all_alleles = pandas.read_csv('../data/alleles.tsv', sep='\t', na_filter=False)
-data = pandas.read_csv('../results/allele_cannot_fix_sequence_errors.tsv', sep='\t', na_filter=False)
+data = pandas.read_csv('../results/allele_cannot_fix_other_errors.tsv', sep='\t', na_filter=False)
 
 already_fixed = pandas.concat([
     pandas.read_csv('manual_cannot_fix_new.tsv', sep='\t', na_filter=False),

manual_fixes_pombase/manual_cannot_fix_new.tsv

@@ -157,3 +157,28 @@ SPNCRNA.899	SPNCRNA.899-G754C	G754C	nucleotide_mutation	PMID:32142608	C754G	SPNC
 SPBC31F10.14c	hip3-Q808-stop	Q808stop	amino_acid_mutation	PMID:34580178	C808*	hip3-C808*		typo in pombase
 SPAC6B12.07c	pqr1-I84S	I87S	amino_acid_mutation	PMID:35012333	I84S			typo in pombase
 SPCC16C4.11	pef1-N146S	N146S	amino_acid_mutation	PMID:31895039	N131S	pef1-N131S		
+SPBC28F2.12	rpb1-CTD-S2A	(CTD)S2A	amino_acid_mutation	PMID:20605454,PMID:34389684,PMID:34967420	CTD-S2A			
+SPAC2G11.12	rqh1-h2	ntC28520T	amino_acid_mutation	PMID:10497270,PMID:11864600				
+SPAC22F3.09c	res2-G1	ntG16590A	amino_acid_mutation	PMID:11864600				
+SPAC22F3.09c	res2-J3	ntG16597A	amino_acid_mutation	PMID:11864600				
+SPAC22G7.06c	ura1-61	ntG16857A	amino_acid_mutation	PMID:11864600				
+SPAC821.11	pro1-1	ntG30304A	amino_acid_mutation	PMID:11864600				
+SPACUNK4.07c	sev4-L5	ntG1844A	amino_acid_mutation	PMID:16394583				
+SPBC649.05	cut12.PDswap	GILKTPTQIKKTVNF-71-ILGHKLEYNYNSHMVYI	amino_acid_mutation	PMID:23333317				
+SPBC215.05	gpd1-G4BS	TTACGTCA-329CGGAAGACTCTCCTCCG	nucleotide_mutation	PMID:25122751				
+SPCC757.07c	ctt1-G4BS	ATGACGT-435CGGAAGACTCTCCTCCG	nucleotide_mutation	PMID:25122751	
+SPAC26F1.06	gpm1-R120,121Q	R120,121Q	amino_acid_mutation	PMID:11106417				
+SPBC4F6.09	str1-promoter-mut-CYC1-lacZ	-870AGATAA-865 ->GCCGTC	nucleotide_mutation	PMID:12888492				
+SPBC1734.02c	cdc27-R5	1101-CATAAAGAAAAGGAGCCTCTCTTGCCAAAGGAGGAGAAGTTGTCTGAGCAAGCAAAGAGAGAGCGCGATGATCTGAAAAATATTATGCAGCTAGAAGATGAATCAGTATCTACCACTAGCGTTCACGATTCTGAAGATGATAATTTAGATTCTAATAATTTCCAATTGGAAAT	nucleotide_insertion	PMID:15576681,PMID:15576681				
+SPBC23E6.07c	rfc1-47	676-HLGAP	amino_acid_insertion	PMID:16040599				
+SPBC23E6.07c	rfc1-50	871-VGVPH	amino_acid_insertion	PMID:16040599				
+SPACUNK4.07c	sev4-L5	ntG1844A	amino_acid_mutation	PMID:16394583				
+SPAC1D4.12	rad15-P	G45D	nucleotide_mutation	PMID:166019,PMID:7254221,PMID:9658208				
+SPBC17A3.07	pgr1-M1V	M1V	amino_acid_mutation	PMID:16950927				
+SPBC14C8.07c	cdc18-T6A-TAP	T10A,T46A,T60A,T104A,T134A,T374A-TAP	amino_acid_mutation	PMID:17690116				
+SPAC5D6.08c	mes1-K1	K16R,K46R,K54R,K86R,K90RK55R,K57R,K58R,	amino_acid_mutation	PMID:18331722				
+SPAC5D6.08c	mes1-K0	K7R,K16R,K46R,K54R,K86R,K90RK55R,K57R,K58R,	amino_acid_mutation	PMID:18331722,PMID:21389117				
+SPBC342.05	crb2-(1-520)LZ	521-778 replaced by leucine zipper	amino_acid_deletion_and_mutation	PMID:20679485				
+SPCC285.09c	cgs2-2	1366-T	nucleotide_insertion	PMID:21118717				
+SPCC285.11	dsc5-1	Q111X	amino_acid_mutation	PMID:22086920				
+SPCC285.11	dsc5-3	T126X	amino_acid_mutation	PMID:22086920				

results/allele_cannot_fix_other_errors.tsv

@@ -7,7 +7,6 @@ SPAC140.02	gar2::ura4+	Gar2 aa 1-163, Ura4 aa 1-39	pattern_error	Gar2 aa 1-163,
 SPAC140.02	gar2::ura4+	Gar2 aa 1-163,Ura4 aa 1-39	pattern_error	Gar2 aa 1-163,Ura4 aa 1-39
 SPAC1610.03c	meu5-E33	T386G-primary_transcript	pattern_error	-primary_transcript
 SPAC17H9.04c	dri1-W46X	aa46->stop	pattern_error	a
-SPAC18G6.02c	chp1-alpha-mut1	KKRKK-71-NEHG	invalid_error	lengths don't match: KKRKK-NEHG
 SPAC19G12.02c	pms1-16	insertion of marker at HindIII site 1517bp downstream of start codon	pattern_error	insertion of marker at HindIII site 1517bp downstream of start codon
 SPAC1D4.12	rad15-P	G45D	pattern_error	G4,D
 SPAC1D4.12	rad15delta::LEU2	rad15delta::LEU2(nt483-1668)	pattern_error	rad15delta::LEU2(nt483-1668)
@@ -24,9 +23,6 @@ SPAC20G8.05c	cdc15-27A	non-phosphorylatable	pattern_error	non-phosphorylatable
 SPAC20G8.05c	cdc15-27D	phospho-mimetic	pattern_error	phospho-mimetic
 SPAC22A12.08c	crd1delta41-372	41-372	invalid_error	Peptide sequence of SPAC22A12.08c missing (perhaps multiple transcripts)
 SPAC22A12.08c	crd1deltaRGFH	369-372	invalid_error	Peptide sequence of SPAC22A12.08c missing (perhaps multiple transcripts)
-SPAC22F3.09c	res2-G1	ntG16590A	invalid_error	lengths don't match: ntG-A
-SPAC22F3.09c	res2-J3	ntG16597A	invalid_error	lengths don't match: ntG-A
-SPAC22G7.06c	ura1-61	ntG16857A	invalid_error	lengths don't match: ntG-A
 SPAC23C4.19	spt5-(CTD)T1A(7)	(CTD)T1A(7)	pattern_error	(CTD)
 SPAC23C4.19	spt5-(T1A)7	CTD-T1A	pattern_error	CTD-
 SPAC23C4.19	spt5-(T1A)7	CTR-T1A	pattern_error	CTR-
@@ -38,7 +34,6 @@ SPAC25G10.04c	rec10-155::LEU2	deletes aa 691-791 and adds IVVIMGGMLE at C-termin
 SPAC26F1.06	gpm1-R120,121Q	R120,121Q	pattern_error	R1,1Q
 SPAC27F1.09c	prp10-LLLFSLFQ-ins	LLLFSLFQ	pattern_error	LLLFSLFQ
 SPAC2G11.12	rad12-hd	helicase domain::ura4	pattern_error	helicase domain::ura4
-SPAC2G11.12	rqh1-h2	ntC28520T	invalid_error	lengths don't match: ntC-T
 SPAC343.13	gta2-T-intron	212-T-primary_transcript	pattern_error	-T-primary_transcript
 SPAC3G9.04	ssu72-Gln57Stop	aa57->stop	pattern_error	a
 SPAC56E4.04c	Pcut6MUT	disrupted Cbf11 binding site in promoter (GTGGGA to cTcGag)	pattern_error	disrupted Cbf, binding site in promoter (GTGGGA to cTcGag)
@@ -51,10 +46,7 @@ SPAC6F12.03c	stx8(A+G)	152-224 substituted by a hinge of A+G	pattern_error	 subs
 SPAC6F6.17	rif1::ura4+	ura4+ @ 5' HindIII site	pattern_error	ura4+ @ 5' HindIII site
 SPAC7D4.04	atg11(522-583)F526AY527A	522-583, F526AY527A	pattern_error	, F5,6AY5,7A
 SPAC7D4.04	atg11(522-583)F526AY527A	522-583,F526AY527A	pattern_error	,F5,6AY5,7A
-SPAC821.11	pro1-1	ntG30304A	invalid_error	lengths don't match: ntG-A
 SPAC890.02c	alp7-5A(K341,Y344,R346,K347,Y348)	K341,Y344,R346,K347,Y348	pattern_error	K3,,Y3,,R3,,K3,,Y3
-SPAC977.10	nhe1-REL6	EIEKSIYE-390-QSSGNSHIKE	invalid_error	lengths don't match: EIEKSIYE-QSSGNSHIKE
-SPACUNK4.07c	sev4-L5	ntG1844A	invalid_error	lengths don't match: ntG-A
 SPAPB2B4.03	Pcig2-96--12-LacZ	cig2-96---12-LacZ fusion	pattern_error	cig2,-LacZ fusion
 SPAPB2B4.03	Pcig2-mut1	cig2 promoter region -64--44-LacZ fusion	pattern_error	cig2 promoter region ,-LacZ fusion
 SPAPB2B4.03	Pcig2delta-147--40-LacZ	cig2-170--148, -39-+1-LacZ fusion	pattern_error	cig2,-LacZ fusion
@@ -104,12 +96,12 @@ SPBC1A4.03c	top2-12KR	K1228,K1254,K1255,K1269,K1280,K1284,K1292,K1309,K1376,K139
 SPBC1A4.03c	top2-26-40/SV	amino acids 26-40 replaced by SV40 NLS sequence PKKKRKV	pattern_error	amino acids , replaced by SV, NLS sequence PKKKRKV
 SPBC1A4.03c	top2-26-40/SV-delta-Sph	amino acids 26-40 replaced by SV40 NLS sequence PKKKRKV,and amino acids 1200-1485 deleted	pattern_error	amino acids , replaced by SV, NLS sequence PKKKRKV,and amino acids , deleted
 SPBC1A4.03c	top2-26-40/SV-delta-Xba	amino acids 26-40 replaced by SV40 NLS sequence PKKKRKV,and amino acids 1221-1485 deleted	pattern_error	amino acids , replaced by SV, NLS sequence PKKKRKV,and amino acids , deleted
-SPBC215.05	gpd1-G4BS	TTACGTCA-329CGGAAGACTCTCCTCCG	invalid_error	lengths don't match: TTACGTCA-CGGAAGACTCTCCTCCG
 SPBC216.07c	tor2-ts10	asked	pattern_error	asked
 SPBC216.07c	tor2-ts6	asked	pattern_error	asked
 SPBC23E6.07c	rfc1-47	676-HLGAP	pattern_error	-HLGAP
 SPBC23E6.07c	rfc1-50	871-VGVPH	pattern_error	-VGVPH
 SPBC28F2.12	rpb1-CTD-(S2A-S7A)	CTD-S2A,S7A	pattern_error	CTD-
+SPBC28F2.12	rpb1-CTD-P3.P3A	(CTD)P3A(alternating)	pattern_error	(CTD),(alternating)
 SPBC28F2.12	rpb1-CTD-P3.P3A	CTD-P3.P3A(alternating)	pattern_error	CTD-P3.,(alternating)
 SPBC28F2.12	rpb1-CTD-P6.P6A	(CTD)P6A(alternating)	pattern_error	(CTD),(alternating)
 SPBC28F2.12	rpb1-CTD-P6.P6A	CTD-P6.P6A(alternating)	pattern_error	CTD-P6.,(alternating)
@@ -162,9 +154,7 @@ SPBC2F12.13	klp5-del	short deletion with a frameshift at codon 772,resulting in
 SPBC342.05	crb2-(1-520)LZ	521-778 replaced by leucine zipper	pattern_error	 replaced by leucine zipper
 SPBC3B9.11c	ctf1 Tyr260Stop	aa260stop	pattern_error	a
 SPBC3D6.10	apn2::ura4+	nt56-1496	pattern_error	nt56-1496
-SPBC428.08c	clr4-alpha-mut	KRRKR-58-NEHG	invalid_error	lengths don't match: KRRKR-NEHG
 SPBC4F6.09	str1-promoter-mut-CYC1-lacZ	-870AGATAA-865 ->GCCGTC	pattern_error	0AGATAA-, ->GCCGTC
-SPBC649.05	cut12.PDswap	GILKTPTQIKKTVNF-71-ILGHKLEYNYNSHMVYI	invalid_error	lengths don't match: GILKTPTQIKKTVNF-ILGHKLEYNYNSHMVYI
 SPBC725.06c	ppk31--579-T (5'-UTR-uORF)	-579-T	pattern_error	-T
 SPCC11E10.07c	tif221-2	frameshift at L43	pattern_error	frameshift at L43
 SPCC1259.03	pa12delta::ura4+	ura4+@AA39	pattern_error	ura4+@AA39
@@ -185,7 +175,6 @@ SPCC285.11	dsc5-3	T126X	pattern_error	T1,X
 SPCC330.05c	ura4-D18	unknown	pattern_error	unknown
 SPCC338.08	ctp1-30	I110N with frameshift at T197 truncating at position 208	pattern_error	I110N with frameshift at T197 truncating at position 208
 SPCC613.04c	rng3::ura4+	lacking AA330-655	pattern_error	lacking AA330-655
-SPCC757.07c	ctt1-G4BS	ATGACGT-435CGGAAGACTCTCCTCCG	invalid_error	lengths don't match: ATGACGT-CGGAAGACTCTCCTCCG
 SPCC970.01	swi9-136	E659K	pattern_error	E,K
 SPCC970.09	sec8-1	unknown	pattern_error	unknown
 SPNCRNA.103	sme2-3'	1-507	invalid_error	Nucleotide sequence of SPNCRNA.103 missing

results/allele_cannot_fix_sequence_errors.tsv

@@ -9,6 +9,9 @@ SPAC19E9.02	fin1-KD	K63R,N165A	K63|N165
 SPAC222.14c	sey1-K53A	K53A	K53
 SPAC22A12.15c	bip1-G373C	G373C	G373
 SPAC22A12.15c	bip1-G373U	G373U	G373
+SPAC22F3.09c	res2-G1	ntG16590A	n16590/t16591/G16592
+SPAC22F3.09c	res2-J3	ntG16597A	n16597/t16598/G16599
+SPAC22G7.06c	ura1-61	ntG16857A	n16857/t16858/G16859
 SPAC22G7.08	ppk8'-1	G474C	G474
 SPAC22G7.08	ppk8'-4	T471A,C472T,A476T	T471||
 SPAC22G7.08	ppk8'-5	T471A,G473C	T471|G473
@@ -21,6 +24,7 @@ SPAC27D7.03c	mei2--G1512T	-G1512T	G1512
 SPAC27D7.03c	mei2--G1512T,-G1692T	-G1512T,-G1692T	G1512|G1692
 SPAC27F1.09c	prp10-1	A1089V,S1097F	A1089|S1097
 SPAC29A4.08c	prp19-W88P	W88P	W88
+SPAC2G11.12	rqh1-h2	ntC28520T	n28520/t28521/C28522
 SPAC3H5.06c	pol1-L471A	L471A	L471
 SPAC3H5.06c	pol1-S470A	S470A	S470
 SPAC3H5.06c	pol1-ts11	C2519T	C2519
@@ -32,8 +36,10 @@ SPAC644.14c	rad51-AT2CG	GGT-237TTC,GGT-188TTC	G(-237)/G(-236)/T(-235)|G(-187)/T(
 SPAC644.14c	rad51-ATGTG	G-188T,G-237T	|G(-237)
 SPAC644.14c	rad51-CT2CA	AGGTG-236CTTCA,AGGTA187CTTCG	A(-236)/G(-235)/G(-232)|G188/G189/T190
 SPAC6B12.07c	pqr1-I84S	I87S	I87
+SPAC821.11	pro1-1	ntG30304A	n30304/t30305/G30306
 SPAC926.04c	hsp90-EATA	E34A,T179A	|T179
 SPAC926.04c	hsp90-EATK	E34A,E384K	|E384
+SPACUNK4.07c	sev4-L5	ntG1844A	n1844/t1845/G1846
 SPAPB1E7.02c	cos1-17	T698A	T698
 SPAPB1E7.02c	cos1-38	G1865A	G1865
 SPAPB1E7.02c	cos1-7	G724A	G724
@@ -62,6 +68,7 @@ SPBC16D10.09	pcn1-20	E232A	E232
 SPBC1718.07c	zfs1-S164A,T1645A	S164A,T164A	|T164
 SPBC1734.02c	cdc27-R39	A837-TCGACAATCGATAAGACTGACA	A837
 SPBC19C2.09	sre1-MP	C-4865A, A-484T, C-483A, C-480A, A-479T, T-478A, C-528A, A-527T, G-526A, C-523A, A-522T, C-521A	C(-4865)||C(-483)|||T(-478)|||G(-526)|||C(-521)
+SPBC215.05	gpd1-G4BS	TTACGTCA-329CGGAAGACTCTCCTCCG	T(-328)/A(-327)/C(-326)/G(-325)/C(-323)
 SPBC23G7.11	mag2-A56S	A56S	A56
 SPBC26H8.07c	nda3noD	U1347A, U1349C	T1347|T1349
 SPBC26H8.07c	nda3noD	U1347A,U1349C	T1347|T1349
@@ -85,6 +92,7 @@ SPBC36B7.09	gcn2-Y1119L,R1120L	Y1119L,R1120L	Y1119|R1120
 SPBC3B9.21	dcp1-P69S	C205T	C205
 SPBC428.16c	rhb1-RD24-1	D111G,E168G,K120R	D111||
 SPBC428.16c	rhb1-RD72-1	P72S,I76V,I98K,N153S	P72|||
+SPBC649.05	cut12.PDswap	GILKTPTQIKKTVNF-71-ILGHKLEYNYNSHMVYI	T77/Q78/I79/K80/K81/T82/V83/N84/F85
 SPBC685.09	orc2-T159A,S162A,T196A,T209A,T214A,T217A	T159A,S162A,T196A,T209A,T214A,T217A	T159|S162||T209|T214|T217
 SPBC6B1.09c	nbs1-s10	G308A	G308
 SPBC725.16	res1'-10	G973C,T976A,T977A	|T976|
@@ -129,6 +137,7 @@ SPCC645.03c	isa1-C72A	C72A	C72
 SPCC645.05c	snipID	G1000A	G1000
 SPCC645.07	rgf1-Nes1*	L865A,L866A,I867A	L865|L866|I867
 SPCC736.14	dis1-203	Q265*	Q265
+SPCC757.07c	ctt1-G4BS	ATGACGT-435CGGAAGACTCTCCTCCG	A(-435)/T(-434)/G(-433)/C(-431)/G(-430)
 SPCC777.09c	arg1-1	E136K,S187N	E136|
 SPCC825.02	gbs1-W409A	W409A	W409
 SPCC825.02	gbs1-W409F	W409F	W409

results/protein_modification_cannot_fix_sequence_errors.tsv

@@ -150,8 +150,8 @@ SPCC162.07	ent1	MOD:00047	tryptic phosphopeptide mapping assay evidence used in
 SPCC162.07	ent1	MOD:00047	tryptic phosphopeptide mapping assay evidence used in automatic assertion	T647		PMID:30726745	4896	2019-02-05	T647
 SPCC16C4.17	mug123	MOD:00046	tryptic phosphopeptide mapping assay evidence used in automatic assertion	S228,S101		PMID:30726745	4896	2019-02-05	S228|
 SPCC1739.11c	cdc11	MOD:00046	Inferred from Direct Assay	S12		PMID:22419817	4896	2013-08-22	S12
-SPCC1795.06	map2	MOD:01641	Inferred from Direct Assay	L23	removed_by(PomBase:SPAC1296.03c)	PMID:9191272	4896	2011-10-10	L23
 SPCC1795.06	map2	MOD:01641	Inferred from Direct Assay	L23	removed_by(PomBase:SPAC1296.03c)	PMID:8861202	4896	2011-10-19	L23
+SPCC1795.06	map2	MOD:01641	Inferred from Direct Assay	L23	removed_by(PomBase:SPAC1296.03c)	PMID:9191272	4896	2011-10-10	L23
 SPCC1795.06	map2	MOD:01641	Inferred from Direct Assay	L23	removed_by(PomBase:SPAC1296.03c)	PMID:8654750	4896	2011-10-10	L23
 SPCC1795.06	map2	MOD:01641	Inferred from Direct Assay	L23	removed_by(PomBase:SPAC1296.03c)	PMID:8654750	4896	2011-10-10	L23
 SPCC1795.06	map2	MOD:01641	Inferred from Direct Assay	L23	removed_by(PomBase:SPAC1296.03c)	PMID:8654750	4896	2011-10-10	L23

test_data/aminoacid_alleles_fixable.tsv

@@ -15,10 +15,10 @@ amino_acid_mutation	AA-23VV	AA-23-VV
 amino_acid_mutation	AA23-VV	AA-23-VV
 
 # error is returned when there are syntax inconsistencies as well
-amino_acid_mutation	AA-23-VVV			lengths don't match: AA-VVV
-amino_acid_mutation	AA23VVV			lengths don't match: AA-VVV
-amino_acid_mutation	AAA-23-VV			lengths don't match: AAA-VV
-amino_acid_mutation	AAA23VV			lengths don't match: AAA-VV
+amino_acid_mutation	AA-23-VVV
+amino_acid_mutation	AA23VVV	AA-23-VVV
+amino_acid_mutation	AAA-23-VV
+amino_acid_mutation	AAA23VV	AAA-23-VV
 
 # It can fix both the syntax and the type
 partial_amino_acid_deletion	AA23VV	AA-23-VV	amino_acid_mutation