obitools4/pkg/obiprimer/testdata/ecoprimers_Cyprinidae_I1.pairs.tsv at d7d63f315c23dddd9d954cfdc104f2ba233f2288

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Eric Coissac d7d63f315c Refactor primer logic and enhance taxonomy features

This commit introduces refinements to primer design strategies, species identification rules, and performance analysis. It also updates taxonomy handling by implementing methods for setting and dropping taxonomic paths, along with necessary utility improvements for set handling and comprehensive test coverage.

2026-11-03 22:46:34 +11:00

10 KiB

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1	AGCAATCCAGGTCAGTTT	TGCCACCCCAGTATGTCC	bG	309	454	301	452	197
2	GCAATCCAGGTCAGTTTC	TGCCACCCCAGTATGTCC	bG	309	455	301	453	197
3	AGCAATCCAGGTCAGTTT	CCACCCCAGTATGTCCTT	bG	311	484	302	482	197
4	CCACCCCAGTATGTCCTT	GCAATCCAGGTCAGTTTC	Gb	311	485	302	483	197
5	AGCAATCCAGGTCAGTTT	GCCACCCCAGTATGTCCT	bG	308	445	300	444	196
6	GCAATCCAGGTCAGTTTC	GCCACCCCAGTATGTCCT	bG	308	446	300	445	196
7	ACCGGAGCAATCCAGGTC	TGCCACCCCAGTATGTCC	bG	308	453	300	451	196
8	GAGCAATCCAGGTCAGTT	TGCCACCCCAGTATGTCC	bG	308	453	300	451	196
9	AGACCGGAGCAATCCAGG	CCACCCCAGTATGTCCTT	bG	310	483	301	481	196
10	CCACCCCAGTATGTCCTT	GAGCAATCCAGGTCAGTT	Gb	310	483	301	481	196
11	ACCGGAGCAATCCAGGTC	CCACCCCAGTATGTCCTT	bG	310	484	301	482	196
12	CCACCCCAGTATGTCCTT	GACCGGAGCAATCCAGGT	Gb	310	484	301	482	196
13	CCACCCCAGTATGTCCTT	GGTCAGTTTCTATCTGTA	Gb	309	460	300	459	195
14	AGGTCAGTTTCTATCTGT	TGCCACCCCAGTATGTCC	bG	307	438	299	437	195
15	CAGGTCAGTTTCTATCTG	TGCCACCCCAGTATGTCC	bG	307	440	299	439	195
16	GGTCAGTTTCTATCTGTA	TGCCACCCCAGTATGTCC	bG	307	441	299	440	195
17	GAGCAATCCAGGTCAGTT	GCCACCCCAGTATGTCCT	bG	307	444	299	443	195
18	ACCGGAGCAATCCAGGTC	GCCACCCCAGTATGTCCT	bG	307	445	299	444	195
19	GACCGGAGCAATCCAGGT	GCCACCCCAGTATGTCCT	bG	307	445	299	444	195
20	AGGTCAGTTTCTATCTGT	CCACCCCAGTATGTCCTT	bG	309	469	300	467	195
21	CAGGTCAGTTTCTATCTG	CCACCCCAGTATGTCCTT	bG	309	470	300	468	195
22	GGAGCAATCCAGGTCAGT	TGCCACCCCAGTATGTCC	bG	307	454	299	452	195
23	CCAGGTCAGTTTCTATCT	TGCCACCCCAGTATGTCC	bG	307	455	299	453	195
24	AATCCAGGTCAGTTTCTA	TGCCACCCCAGTATGTCC	bG	307	455	299	453	195
25	CAATCCAGGTCAGTTTCT	TGCCACCCCAGTATGTCC	bG	307	455	299	453	195
26	ATCCAGGTCAGTTTCTAT	TGCCACCCCAGTATGTCC	bG	307	455	299	453	195
27	TCCAGGTCAGTTTCTATC	TGCCACCCCAGTATGTCC	bG	307	455	299	453	195
28	CCACCCCAGTATGTCCTT	GGAGCAATCCAGGTCAGT	Gb	309	484	300	482	195
29	CAATCCAGGTCAGTTTCT	CCACCCCAGTATGTCCTT	bG	309	485	300	483	195
30	AATCCAGGTCAGTTTCTA	CCACCCCAGTATGTCCTT	bG	309	485	300	483	195
31	ATCCAGGTCAGTTTCTAT	CCACCCCAGTATGTCCTT	bG	309	485	300	483	195
32	CCACCCCAGTATGTCCTT	TCCAGGTCAGTTTCTATC	Gb	309	485	300	483	195
33	CCACCCCAGTATGTCCTT	CCAGGTCAGTTTCTATCT	Gb	309	485	300	483	195
34	GCCACCCCAGTATGTCCT	GGTCAGTTTCTATCTGTA	Gb	306	437	298	437	194
35	AGGTCAGTTTCTATCTGT	GCCACCCCAGTATGTCCT	bG	306	440	298	439	194
36	CAGGTCAGTTTCTATCTG	GCCACCCCAGTATGTCCT	bG	306	442	298	441	194
37	GCCACCCCAGTATGTCCT	GGAGCAATCCAGGTCAGT	Gb	306	445	298	444	194
38	GCCACCCCAGTATGTCCT	TCCAGGTCAGTTTCTATC	Gb	306	446	298	445	194
39	CCAGGTCAGTTTCTATCT	GCCACCCCAGTATGTCCT	bG	306	446	298	445	194
40	CAATCCAGGTCAGTTTCT	GCCACCCCAGTATGTCCT	bG	306	446	298	445	194
41	AATCCAGGTCAGTTTCTA	GCCACCCCAGTATGTCCT	bG	306	446	298	445	194
42	ATCCAGGTCAGTTTCTAT	GCCACCCCAGTATGTCCT	bG	306	446	298	445	194
43	CGGAGCAATCCAGGTCAG	TGCCACCCCAGTATGTCC	bG	304	445	296	444	192
44	CCGGAGCAATCCAGGTCA	TGCCACCCCAGTATGTCC	bG	304	445	296	444	192
45	TGCCACCCCAGTATGTCC	TTTTCCTAGTACGAAAGG	Gb	308	453	300	452	192
46	CCACCCCAGTATGTCCTT	CCGGAGCAATCCAGGTCA	Gb	306	476	297	474	192
47	CCACCCCAGTATGTCCTT	CGGAGCAATCCAGGTCAG	Gb	306	476	297	474	192
48	GACCGGAGCAATCCAGGT	TGCCACCCCAGTATGTCC	bG	304	453	296	451	192
49	CCACCCCAGTATGTCCTT	GTCAGTTTCTATCTGTAA	Gb	304	408	295	407	190
50	CCACCCCAGTATGTCCTT	TTTTCCTAGTACGAAAGG	Gb	310	484	301	482	192
51	CAGACCGGAGCAATCCAG	CCACCCCAGTATGTCCTT	bG	306	484	297	482	192
52	GTCAGTTTCTATCTGTAA	TGCCACCCCAGTATGTCC	bG	302	390	294	390	190
53	AGCAATCCAGGTCAGTTT	CCCAGTATGTCCTTATTT	bG	301	310	292	309	187
54	CCCAGTATGTCCTTATTT	GCAATCCAGGTCAGTTTC	Gb	301	311	292	310	187
55	ACTTTTCCTAGTACGAAA	TGCCACCCCAGTATGTCC	bG	307	443	299	442	191
56	GCCACCCCAGTATGTCCT	TTTTCCTAGTACGAAAGG	Gb	307	445	299	444	191
57	CGGAGCAATCCAGGTCAG	GCCACCCCAGTATGTCCT	bG	303	443	295	442	191
58	CCGGAGCAATCCAGGTCA	GCCACCCCAGTATGTCCT	bG	303	443	295	442	191
59	CTTTTCCTAGTACGAAAG	TGCCACCCCAGTATGTCC	bG	307	448	299	447	191
60	AGACCGGAGCAATCCAGG	GCCACCCCAGTATGTCCT	bG	303	445	295	444	191
61	ACTTTTCCTAGTACGAAA	CCACCCCAGTATGTCCTT	bG	309	478	300	476	191
62	CCACCCCAGTATGTCCTT	CTTTTCCTAGTACGAAAG	Gb	309	482	300	480	191
63	GCCACCCCAGTATGTCCT	GTCAGTTTCTATCTGTAA	Gb	301	390	293	390	189
64	AGACCGGAGCAATCCAGG	CCCAGTATGTCCTTATTT	bG	300	310	291	309	186
65	CAGACCGGAGCAATCCAG	CCCAGTATGTCCTTATTT	bG	300	310	291	309	186
66	CCCAGTATGTCCTTATTT	GAGCAATCCAGGTCAGTT	Gb	300	310	291	309	186
67	ACCGGAGCAATCCAGGTC	CCCAGTATGTCCTTATTT	bG	300	311	291	310	186
68	CCCAGTATGTCCTTATTT	GACCGGAGCAATCCAGGT	Gb	300	311	291	310	186
69	CCCAGTATGTCCTTATTT	TCAGACCGGAGCAATCCA	Gb	300	311	291	310	186
70	CCCAGTATGTCCTTATTT	TTCAGACCGGAGCAATCC	Gb	300	311	291	310	186
71	CCCAGTATGTCCTTATTT	GTTCAGACCGGAGCAATC	Gb	300	311	291	310	186
72	CTTTTCCTAGTACGAAAG	GCCACCCCAGTATGTCCT	bG	306	443	298	442	190
73	ACTTTTCCTAGTACGAAA	GCCACCCCAGTATGTCCT	bG	306	443	298	442	190
74	AGACCGGAGCAATCCAGG	TGCCACCCCAGTATGTCC	bG	302	453	294	451	190
75	CCACCCCAGTATGTCCTT	TCAGACCGGAGCAATCCA	Gb	304	485	295	483	190
76	AGGTCAGTTTCTATCTGT	CCCAGTATGTCCTTATTT	bG	299	309	290	308	185
77	CAGGTCAGTTTCTATCTG	CCCAGTATGTCCTTATTT	bG	299	309	290	308	185
78	CCCAGTATGTCCTTATTT	GGTCAGTTTCTATCTGTA	Gb	299	309	290	308	185
79	ATCCAGGTCAGTTTCTAT	CCCAGTATGTCCTTATTT	bG	299	311	290	310	185
80	CCAGGTCAGTTTCTATCT	CCCAGTATGTCCTTATTT	bG	299	311	290	310	185
81	CCCAGTATGTCCTTATTT	GGAGCAATCCAGGTCAGT	Gb	299	311	290	310	185
82	CCCAGTATGTCCTTATTT	TCCAGGTCAGTTTCTATC	Gb	299	311	290	310	185
83	CAATCCAGGTCAGTTTCT	CCCAGTATGTCCTTATTT	bG	299	311	290	310	185
84	AATCCAGGTCAGTTTCTA	CCCAGTATGTCCTTATTT	bG	299	311	290	310	185
85	TGCCACCCCAGTATGTCC	TTTCCTAGTACGAAAGGA	Gb	305	449	297	447	189
86	CAGACCGGAGCAATCCAG	GCCACCCCAGTATGTCCT	bG	301	446	293	445	189
87	CCACCCCAGTATGTCCTT	TTTCCTAGTACGAAAGGA	Gb	307	479	298	477	189
88	CCACCCCAGTATGTCCTT	TACGAAAGGATCGGAAAA	Gb	307	453	298	452	188
89	CCCAGTATGTCCTTATTT	CCGGAGCAATCCAGGTCA	Gb	298	309	289	308	184
90	CCCAGTATGTCCTTATTT	CGGAGCAATCCAGGTCAG	Gb	298	309	289	308	184
91	GCCACCCCAGTATGTCCT	TTTCCTAGTACGAAAGGA	Gb	304	440	296	439	188
92	GCAATTTACCATGCTCTG	TTTTCCTAGTACGAAAGG	Gb	308	505	299	501	189
93	ACTTTTCCTAGTACGAAA	GCAATTTACCATGCTCTG	bG	307	478	298	474	188
94	CAGACCGGAGCAATCCAG	TGCCACCCCAGTATGTCC	bG	300	454	292	452	188
95	CCTAGTACGAAAGGATCG	TGCCACCCCAGTATGTCC	bG	303	427	295	425	187
96	CCACCCCAGTATGTCCTT	TTCAGACCGGAGCAATCC	Gb	302	485	293	483	188
97	TACGAAAGGATCGGAAAA	TGCCACCCCAGTATGTCC	bG	304	430	296	430	187
98	GCCACCCCAGTATGTCCT	TACGAAAGGATCGGAAAA	Gb	304	430	296	430	187
99	CCACCCCAGTATGTCCTT	CCTAGTACGAAAGGATCG	Gb	305	459	296	457	187
100	CTTTTCCTAGTACGAAAG	GCAATTTACCATGCTCTG	bG	307	498	298	494	188
101	CGCAATTTACCATGCTCT	TTTTCCTAGTACGAAAGG	Gb	306	463	297	459	187
102	GCAATTTACCATGCTCTG	TTTCCTAGTACGAAAGGA	Gb	307	506	298	502	188
103	GCAATTTACCATGCTCTG	GGTCAGTTTCTATCTGTA	Gb	301	433	292	429	186
104	GCCACCCCAGTATGTCCT	TCAGACCGGAGCAATCCA	Gb	299	446	291	445	187
105	CCTAGTACGAAAGGATCG	GCCACCCCAGTATGTCCT	bG	302	419	294	418	186
106	CCCAGTATGTCCTTATTT	GTCAGTTTCTATCTGTAA	Gb	295	264	286	263	181
107	ACTTTTCCTAGTACGAAA	CGCAATTTACCATGCTCT	bG	305	449	296	445	186
108	TCGCAATTTACCATGCTC	TTTTCCTAGTACGAAAGG	Gb	305	456	296	452	186
109	TTCGCAATTTACCATGCT	TTTTCCTAGTACGAAAGG	Gb	305	456	296	452	186
110	AGTTCAGACCGGAGCAAT	CCCAGTATGTCCTTATTT	bG	296	310	287	309	182
111	CGCAATTTACCATGCTCT	CTTTTCCTAGTACGAAAG	Gb	305	460	296	456	186
112	CGCAATTTACCATGCTCT	TTTCCTAGTACGAAAGGA	Gb	305	463	296	459	186
113	CCTAGTACGAAAGGATCG	GCAATTTACCATGCTCTG	bG	305	472	296	468	186
114	TCAGACCGGAGCAATCCA	TGCCACCCCAGTATGTCC	bG	298	454	290	452	186
115	ACTTTTCCTAGTACGAAA	TCGCAATTTACCATGCTC	bG	304	447	295	443	185
116	ACTTTTCCTAGTACGAAA	TTCGCAATTTACCATGCT	bG	304	447	295	443	185
117	CTTTTCCTAGTACGAAAG	TCGCAATTTACCATGCTC	bG	304	453	295	449	185
118	CTTTTCCTAGTACGAAAG	TTCGCAATTTACCATGCT	bG	304	453	295	449	185
119	CCACCCCAGTATGTCCTT	GTTCAGACCGGAGCAATC	Gb	300	485	291	483	186
120	TCGCAATTTACCATGCTC	TTTCCTAGTACGAAAGGA	Gb	304	456	295	452	185
121	TTTCGCAATTTACCATGC	TTTTCCTAGTACGAAAGG	Gb	304	456	295	452	185
122	TTCGCAATTTACCATGCT	TTTCCTAGTACGAAAGGA	Gb	304	456	295	452	185
123	GCAATTTACCATGCTCTG	TACGAAAGGATCGGAAAA	Gb	304	427	295	425	184
124	CCTAGTACGAAAGGATCG	CGCAATTTACCATGCTCT	bG	303	433	294	429	184
125	AGGTCAGTTTCTATCTGT	GCAATTTACCATGCTCTG	bG	299	431	290	427	184
126	GCCACCCCAGTATGTCCT	TTCAGACCGGAGCAATCC	Gb	297	446	289	445	185
127	ACTTTTCCTAGTACGAAA	TTTCGCAATTTACCATGC	bG	303	447	294	443	184
128	GCAATTTACCATGCTCTG	GTCAGTTTCTATCTGTAA	Gb	295	375	286	373	182
129	CTTTTCCTAGTACGAAAG	TTTCGCAATTTACCATGC	bG	303	453	294	449	184
130	TTTCCTAGTACGAAAGGA	TTTCGCAATTTACCATGC	bG	303	456	294	452	184
131	CCCAGTATGTCCTTATTT	TTTTCCTAGTACGAAAGG	Gb	300	311	291	310	180
132	CCCAGTATGTCCTTATTT	GAGTTCAGACCGGAGCAA	Gb	294	310	285	309	180
133	CCTAGTACGAAAGGATCG	TCGCAATTTACCATGCTC	bG	302	430	293	426	183
134	CCTAGTACGAAAGGATCG	TTCGCAATTTACCATGCT	bG	302	430	293	426	183
135	CGCAATTTACCATGCTCT	TACGAAAGGATCGGAAAA	Gb	302	420	293	418	182
136	ACTTTTCCTAGTACGAAA	CCCAGTATGTCCTTATTT	bG	299	311	290	310	179
137	CCCAGTATGTCCTTATTT	CTTTTCCTAGTACGAAAG	Gb	299	311	290	310	179
138	CGCAATTTACCATGCTCT	GGTCAGTTTCTATCTGTA	Gb	297	426	288	422	182
139	CCTAGTACGAAAGGATCG	TTTCGCAATTTACCATGC	bG	301	430	292	426	182
140	CAGGTCAGTTTCTATCTG	GCAATTTACCATGCTCTG	bG	297	431	288	427	182
141	TACGAAAGGATCGGAAAA	TTCGCAATTTACCATGCT	bG	301	418	292	416	181
142	TACGAAAGGATCGGAAAA	TCGCAATTTACCATGCTC	bG	301	418	292	416	181
143	GGCCTTTCGCAATTTACC	TTTTCCTAGTACGAAAGG	Gb	302	510	293	506	183
144	ACTTTTCCTAGTACGAAA	GGCCTTTCGCAATTTACC	bG	301	479	292	475	182
145	TACGAAAGGATCGGAAAA	TTTCGCAATTTACCATGC	bG	300	418	291	416	180
146	CCCAGTATGTCCTTATTT	TTTCCTAGTACGAAAGGA	Gb	297	310	288	309	177
147	CTTTTCCTAGTACGAAAG	GGCCTTTCGCAATTTACC	bG	301	500	292	496	182
148	AGGTCAGTTTCTATCTGT	CGCAATTTACCATGCTCT	bG	295	428	286	424	180
149	GGCCTTTCGCAATTTACC	TTTCCTAGTACGAAAGGA	Gb	301	511	292	507	182
150	GCCTTTCGCAATTTACCA	TTTTCCTAGTACGAAAGG	Gb	299	440	290	436	180
151	CTTTCGCAATTTACCATG	TTTTCCTAGTACGAAAGG	Gb	298	412	289	408	179
152	CCCAGTATGTCCTTATTT	CCTAGTACGAAAGGATCG	Gb	296	305	287	304	176
153	CCCAGTATGTCCTTATTT	TACGAAAGGATCGGAAAA	Gb	297	307	288	306	176
154	GGTCAGTTTCTATCTGTA	TCGCAATTTACCATGCTC	bG	294	425	285	421	179
155	ACTTTTCCTAGTACGAAA	GCCTTTCGCAATTTACCA	bG	298	436	289	432	179
156	CTTTTCCTAGTACGAAAG	GCCTTTCGCAATTTACCA	bG	298	438	289	434	179
157	GCCTTTCGCAATTTACCA	TTTCCTAGTACGAAAGGA	Gb	298	440	289	436	179
158	CCTAGTACGAAAGGATCG	GGCCTTTCGCAATTTACC	bG	299	484	290	480	180
159	ACTTTTCCTAGTACGAAA	CTTTCGCAATTTACCATG	bG	297	411	288	407	178
160	CTTTCGCAATTTACCATG	CTTTTCCTAGTACGAAAG	Gb	297	411	288	407	178
161	CTTTCGCAATTTACCATG	TTTCCTAGTACGAAAGGA	Gb	297	412	288	408	178
162	GGCCTTTCGCAATTTACC	TACGAAAGGATCGGAAAA	Gb	298	425	289	423	178
163	AGTTCAGACCGGAGCAAT	CCACCCCAGTATGTCCTT	bG	293	484	284	482	179
164	CCTAGTACGAAAGGATCG	GCCTTTCGCAATTTACCA	bG	296	416	287	412	177
165	CCTAGTACGAAAGGATCG	CTTTCGCAATTTACCATG	bG	295	390	286	386	176
166	CCAGGTCAGTTTCTATCT	GCAATTTACCATGCTCTG	bG	294	513	285	509	179
167	CCTTTCGCAATTTACCAT	TTTTCCTAGTACGAAAGG	Gb	295	411	286	407	176
168	GCAATTTACCATGCTCTG	TTCCTAGTACGAAAGGAT	Gb	293	423	284	419	176
169	CTTTCGCAATTTACCATG	TACGAAAGGATCGGAAAA	Gb	295	398	286	396	175
170	ACTTTTCCTAGTACGAAA	CCTTTCGCAATTTACCAT	bG	294	409	285	405	175
171	CCTTTCGCAATTTACCAT	CTTTTCCTAGTACGAAAG	Gb	294	409	285	405	175
172	CCTTTCGCAATTTACCAT	TTTCCTAGTACGAAAGGA	Gb	294	410	285	406	175
173	GCCTTTCGCAATTTACCA	TACGAAAGGATCGGAAAA	Gb	295	413	286	411	175

10 KiB Raw Blame History

10 KiB

Raw Blame History