Skip to content

Commit 2e8d833

Browse files
dpark01claude
dpark01
and
claude
committed
Refactor: keep non-Enteroviridae updates in-line with original positions
Updated processing logic to maintain better diff readability: - Non-Enteroviridae viruses (RSV, HMPV, HPIV, HAdV, HSV, etc.) now updated at their original positions in the file - Only Enteroviridae (EV/RV) entries moved to end of file - Virus families (e.g., all HAdV-*) updated together when encountered - Preserved old entries (HAdV-7, HAdV-5, HAdV-G) not present in new file This approach minimizes diff complexity while ensuring all updates are applied. File structure: - Lines 1-173: Non-EV/RV viruses (updated in-line) - Lines 174-1175: EV/RV entries (sorted, at end) Total: 1,175 entries (was 366, +809 net change) Co-Authored-By: Claude Sonnet 4.5 <noreply@anthropic.com>
1 parent 6c3a4c7 commit 2e8d833

1 file changed

Lines changed: 66 additions & 37 deletions

File tree

‎assembly/reference_genomes.tsv‎

Lines changed: 66 additions & 37 deletions
Original file line numberDiff line numberDiff line change
@@ -1,3 +1,5 @@
1+
208893 RSV-A Human respiratory syncytial virus A NC_001803.1
2+
11250 RSV-B Human respiratory syncytial virus B NC_001781.1
13
11137 HCoV-229E Human coronavirus 229E NC_002645.1
24
290028 HCoV-HKU1 Human coronavirus HKU1 NC_006577.2
35
277944 HCoV-NL63 Human coronavirus NL63 NC_005831.2
@@ -23,18 +25,42 @@
2325
1089607 B Influenza B virus (B/Wisconsin/01/2010) CY115189.1:CY115190.1:CY115188.1:CY115183.1:CY115186.1:CY115185.1:CY115184.1:CY115187.1
2426
11553 C Influenza C virus (C/Ann Arbor/1/50) NC_006307.2:NC_006308.2:NC_006309.2:NC_006310.2:NC_006311.1:NC_006312.2:NC_006306.2
2527
1173138 D Influenza D virus (D/swine/Oklahoma/1334/2011) NC_036616.1:NC_036615.1:NC_036619.1:NC_036618.1:NC_036617.1:NC_036620.1:NC_036621.1
26-
11224 HPIV-4 Human parainfluenza virus 4a NC_021928.1
27-
565302 HAdV-B1 Human adenovirus B1 NC_011203.1
28-
565303 HAdV-B2 Human adenovirus B2 NC_011202.1
28+
162145 HMPV Human metapneumovirus A NC_039199.1
29+
162145 HMPV Human metapneumovirus B PQ634902.1
30+
12730 HPIV-1 Human respirovirus 1 NC_003461.1
31+
2560525 HPIV-2 Human orthorubulavirus 2 NC_003443.1
32+
11216 HPIV-3 Human respirovirus 3 NC_075446.1
33+
11224 HPIV-4A Human parainfluenza virus 4a NC_021928.1
34+
11226 HPIV-4B Human parainfluenza virus 4b PV642257.1
35+
129875 HAdV-A Human mastadenovirus A AC_000005.1
36+
10528 HAdV-A Human adenovirus 18 GU191019.1
37+
10529 HAdV-A Human adenovirus 31 MG872324.1
38+
108098 HAdV-B Human mastadenovirus B NC_011202.1
39+
108098 HAdV-B Human mastadenovirus B KF633445.1
40+
108098 HAdV-B Human mastadenovirus B NC_011203.1
41+
10533 HAdV-C Human adenovirus 1 AC_000017.1
42+
651580 HAdV-D Human adenovirus 54 NC_012959.1
43+
130308 HAdV-E Human mastadenovirus E NC_003266.2
44+
130309 HAdV-F Human mastadenovirus F NC_001454.1
45+
130309 HAdV-F Human mastadenovirus F MT791001.1
2946
10519 HAdV-7 Human adenovirus 7 AC_000018.1
30-
198503 SAdV-21 simian adenovirus 21 AC_000010.1
31-
10533 HAdV-1 Human adenovirus 1 AC_000017.1
3247
536079 HAdV-G Human mastadenovirus G NC_006879.1
3348
28285 HAdV-5 Human adenovirus 5 AC_000008.1
49+
198503 SAdV-21 simian adenovirus 21 AC_000010.1
3450
11053 DENV-1 dengue virus type 1 NC_001477.1
3551
11060 DENV-2 dengue virus type 2 NC_001474.2
3652
11069 DENV-3 dengue virus type 3 NC_001475.2
3753
11070 DENV-4 dengue virus type 4 NC_002640.1
54+
10298 HSV-1 Human herpesvirus type 1 NC_001806.2
55+
10310 HSV-2 Human alphaherpesvirus 2 NC_001798.2
56+
10335 VZV Human alphaherpesvirus 3 NC_001348.1
57+
10376 EBV Human herpesvirus 4 type 1 NC_007605.1
58+
12509 EBV Human herpesvirus 4 type 2 NC_009334.1
59+
10359 CMV Human betaherpesvirus 5 NC_006273.2
60+
32603 HHV-6 Human betaherpesvirus 6A NC_001664.4
61+
32604 HHV-6 Human betaherpesvirus 6B NC_000898.1
62+
10372 HHV-7 Human betaherpesvirus 7 NC_001716.2
63+
37296 HHV-8 Human gammaherpesvirus 8 NC_009333.1
3864
54290 GBV-C GB virus C NC_001710.1
3965
186538 Ebola virus Zaire ebolavirus Mbandaka/2020 OR084851.1
4066
186538 Ebola virus Zaire ebolavirus Ituri/2018 MK007329.1
@@ -44,8 +70,16 @@
4470
128952 Ebola virus Zaire ebolavirus Mayinga/1976 NC_002549.1
4571
186540 Sudan virus Sudan ebolavirus 2000/Gulu-808892 NC_006432.1
4672
186540 Sudan virus Sudan ebolavirus 1976/Boniface-R4142L MH121162.1
73+
565995 Bundibugyo virus NC_014373.1
74+
3052225 Henipavirus nipahense NC_002728.1
75+
186539 Reston ebolavirus NC_004161.1
4776
3052505 MARV Marburg virus - Musoke, Kenya, 1980 NC_001608.4
77+
378809 Ravn virus DQ447649.1
78+
10255 Variola virus NC_001611.1
4879
2169701 ONN O'nyong'nyong virus NC_075006.1
80+
11072 Japanese encephalitis virus NC_001437.1
81+
11588 Rift valley fever virus NC_014397.1:NC_014396.1:NC_014395.1
82+
3052480 Orthohantavirus hantanense NC_005222.1:NC_005219.1:NC_005218.1
4983
3052518 CCHF Crimean-Congo hemorrhagic fever virus RefSeq NC_005301.3:NC_005300.2:NC_005302.1
5084
3052518 CCHF CCHF Senegal UCCR4416 KY484025.1:KY484026.1:KY484027.1
5185
3052518 CCHF CCHF DRC KY484046.1:KY484047.1:KY484048.1
@@ -87,6 +121,7 @@
87121
1544901 HCV-7 Hepatitis C virus genotype 7 NC_030791.1
88122
3087233 ZIKV Zika virus MR766 NC_012532.1
89123
64320 ZIKV Zika virus ZIKV/H sapiens/Brazil/Natal/2015 NC_035889.1
124+
118655 Oropouche virus NC_005776.1:NC_005775.1:NC_005777.1
90125
3052310 LASV Lassa virus clade II ISTH2376-NIG-2012 KM821997.1:KM821998.1
91126
3052310 LASV Lassa virus clade III Nig08-A19 GU481073.1:GU481072.1
92127
3052310 LASV Lassa virus clade IV G502-SLE-2009 KM821772.1:KM821773.1
@@ -108,40 +143,34 @@
108143
10244 MPXV Monkeypox virus MPXV_USA_2022_FL001 ON674051.1
109144
10244 MPXV Monkeypox virus MPXV_USA_2021_MD ON676708.1
110145
10244 MPXV Monkeypox virus Monkeypox/PT0033/2022 ON843165.1
111-
162145 HMPV Human metapneumovirus A NC_039199.1
112-
162145 HMPV Human metapneumovirus B PQ634902.1
113-
208893 RSV-A Human respiratory syncytial virus A NC_001803.1
114-
11250 RSV-B Human respiratory syncytial virus B NC_001781.1
115-
129875 HAdV-A Human mastadenovirus A AC_000005.1
116-
10528 HAdV-A Human adenovirus 18 GU191019.1
117-
10529 HAdV-A Human adenovirus 31 MG872324.1
118-
108098 HAdV-B Human mastadenovirus B KF633445.1
119-
651580 HAdV-D Human adenovirus 54 NC_012959.1
120-
130308 HAdV-E Human mastadenovirus E NC_003266.2
121-
130309 HAdV-F Human mastadenovirus F NC_001454.1
122-
130309 HAdV-F Human mastadenovirus F MT791001.1
123-
12730 HPIV-1 Human respirovirus 1 NC_003461.1
124-
2560525 HPIV-2 Human orthorubulavirus 2 NC_003443.1
125-
11216 HPIV-3 Human respirovirus 3 NC_075446.1
126-
11226 HPIV-4B Human parainfluenza virus 4b PV642257.1
127-
3052040 Human bocavirus 1 NC_075120.1
128-
1511882 Human bocavirus 2 NC_012042.1
146+
689403 Human bocavirus 1 KJ634207.1
147+
573977 Human bocavirus 2 FJ170280.1
129148
638313 Human bocavirus 3 NC_012564.1
130-
1511883 Human bocavirus 4 NC_012729.2
131-
1391667 Human bufavirus 3 NC_024888.1
149+
1511883 Human bocavirus 4 NI NC_012729.2
132150
10798 Human parvovirus B19 NC_000883.2
133-
72197 Human erythrovirus V9 NC_004295.1
134-
1511919 Human parvovirus 4 NC_007018.1
135-
10298 HSV-1 Human herpesvirus type 1 NC_001806.2
136-
10310 HSV-2 Human alphaherpesvirus 2 NC_001798.2
137-
10335 VZV Human alphaherpesvirus 3 NC_001348.1
138-
10376 EBV Human herpesvirus 4 type 1 NC_007605.1
139-
12509 EBV Human herpesvirus 4 type 2 NC_009334.1
140-
10359 CMV Human betaherpesvirus 5 NC_006273.2
141-
32603 HHV-6 Human betaherpesvirus 6A NC_001664.4
142-
32604 HHV-6 Human betaherpesvirus 6B NC_000898.1
143-
10372 HHV-7 Human betaherpesvirus 7 NC_001716.2
144-
37296 HHV-8 Human gammaherpesvirus 8 NC_009333.1
151+
289365 Human parvovirus 4 KM390024.1
152+
2560602 Mumps orthorubulavirus NC_002200.1
153+
11234 Measles morbillivirus NC_001498.1
154+
11041 Rubella virus NC_001545.2
155+
10497 African swine fever virus NC_044950.1
156+
10497 African swine fever virus NC_044951.1
157+
10497 African swine fever virus NC_044952.1
158+
10497 African swine fever virus NC_044953.1
159+
10497 African swine fever virus NC_044954.1
160+
11292 Lyssavirus rabies EF206707.1
161+
11292 Lyssavirus rabies MG458319.1
162+
11292 Lyssavirus rabies JQ685943.1
163+
11292 Lyssavirus rabies KX148224.1
164+
11292 Lyssavirus rabies KX148223.1
165+
11292 Lyssavirus rabies KX148231.1
166+
11292 Lyssavirus rabies JQ730682.1
167+
11292 Lyssavirus rabies KX148266.1
168+
11292 Lyssavirus rabies KX148245.1
169+
11292 Lyssavirus rabies JQ685895.1
170+
11292 Lyssavirus rabies JQ685952.1
171+
11292 Lyssavirus rabies JQ685905.1
172+
11292 Lyssavirus rabies JQ685901.1
173+
11292 Lyssavirus rabies JQ685968.1
145174
433732 EV Echovirus Ams573 EF155423.1
146175
433731 EV Echovirus Ams721 EF155422.1
147176
145390 EV Echovirus Sp. OR786176.1

0 commit comments

Comments
 (0)