t push origin master

Merge branch 'jvhagey-master'
CDCgov · Feb 23, 2022 · b37cbba · b37cbba
2 parents f9289a4 + 32c4cd6
commit b37cbba
Showing 2 changed files with 20 additions and 17 deletions.
diff --git a/datasets/sars-cov-2-nonvoivoc.tsv b/datasets/sars-cov-2-nonvoivoc.tsv
@@ -1,9 +1,9 @@
-dataType	Non_VOI_VOC_Lineages
+source	Norman Hassell and TOAST
+Organism	SARS-CoV-2
 tree	-
+dataType	Non_VOI_VOC_Lineages
 Outbreak	-
-Organism	SARS-CoV-2
 pmid	-
-source	Norman Hassell and TOAST
 
 GISAID_assession	SRArun_acc	biosample_acc	dataSetName	genBankAssembly	lineage_v3.1.3	nucleotide	outbreak	sha256sumAssembly	sha256sumRead1	sha256sumRead2	sha256sumnucleotide	strain	suggestedReference
 -	SRR11915959	SAMN15087311	-	-	B.35	MT641779	-	-	888a4e8a104226e93dfe217915286f3c097c20b0849a2ff46b2c64c9541f35dd	c00a3eb04db8ba34a5e0b97c9c7033a20cfaf462a9a01400b31c0349baf65be7	dd45e46d11424c05e3ffedb49da176c91ef463df4e59e025c160c73c3af3eadc	SARS-CoV-2_human_AUS_TL26_2020	FALSE	
@@ -15,18 +15,18 @@ EPI_ISL_521499	SRR12530461	SAMN15919634	-	-	B.1.1.431	MT972354	-	-	7c614ed2e065f
 EPI_ISL_426665	SRR11577968	SAMN14641063	-	-	B.1.320	MT451248	-	-	9371572d0e792810cc10fd249ee63c10099d03fd8cc76ca27f8245912917d3f7	874f7f794db12efa2b42c483b9b3a399fc327bd57b0806d302181ac5120caf27	408b771d82393526ae3201510dfdcea8d6a88ee3c76a8c41c710ef36aa1ab020	hCoV-19_Australia_VIC357_2020	FALSE	
 EPI_ISL_419780	SRR11494584	SAMN14546879	-	-	B.4.5	MT450980	-	-	fa1c2c95097e76ff6567939e966a520d4a85ba3df8fe2b3bcfcac41ca186e648	147f909823d0828a3f75e9b32e8819c48d40c946f0aea822aef167d355b40e25	97575f940fac1cc04f6e83b0c0dce61558408e7690db81731a3da793c322990c	hCoV-19_Australia_VIC66_2020	FALSE	
 EPI_ISL_571262	SRR13001544	SAMN16689007	-	-	B.1.199	MW064560	-	-	521a5a60c19dc737477ddee995d7b0828c9e8c817de9eed69bdd402b7c191ba3	14d3c6e981294b8976803b3def971d13cc484afccda014d87230428d54411048	eb4d635ba90d58ece0c6b241b19344ea94a6c468e9c010a224b3fb5df177a893	hCoV-19_USA_AR-QDX-537_2020	FALSE	
-EPI_ISL_672188	SRR13195337	SAMN16989742	-	-	B.1.309	MW483225	-	-	c321d1b01fdde58e67f5a135f7fc15a272f290aade633f9f6c758ea455d52f28	a5ff9009124b7f42cfd2207caef0f38343af3313500b645c9cba9eab68ef688a	36819968b4e419947f96518cd503365b581bc14531041a05d4695a785d70db2d	hCoV-19_USA_CA-CZB-10010_2020	FALSE	
-EPI_ISL_672271	SRR13195265	SAMN16989834	-	-	B.1.1.205	MW483314	-	-	23cc2f918832946743dc2f59f75bb04cdba783f437e1d77a42c048d984dca581	d0a97ac4e2f45f8cf0f6be7d4019114b61ea922c77d788aefd77d2f8aa37214d	85b26faa0540ebab69de639d6e01f6c222accd19480293ea39d7a356252e4e71	hCoV-19_USA_CA-CZB-10245_2020	FALSE	
-EPI_ISL_672414	SRR13195052	SAMN16990022	-	-	B.1.1.139	MW483478	-	-	7bd3080759e7325211dd34e28022e45d90397f8e3c294f686cb7b4efb3581ffb	bf441d19e749661e262c279fef25b74f2f35ccdcbcb461b83fd0e82a1e7c87d4	513b8be54c82731416d5dc90b4f09117551d5bee51ae1bda2e11969570dbf1ba	hCoV-19_USA_CA-CZB-13120_2020	FALSE	
-EPI_ISL_739321	SRR13526755	SAMN17570757	-	-	B.1.1.418	MW565773	-	-	053505a894dd4f77b259e0f645cf4c71ad54552c95dca6631360eb398928fe51	5b2e56ae8bd329aa4984cf171cb16c0bee9087e87431a8363a4e5545ec91cd91	31e78ca6db94447d4ea007c97c3ba66d0df16f4f896b1e1c141c681276598a7e	hCoV-19_USA_CA-CZB-13702_2020	FALSE	
-EPI_ISL_738705	SRR13527262	SAMN17571193	-	-	B.1.1.391	MW564975	-	-	801b94f88470ccf9634f80d11fdbb45f0192aa50fa2f42cfcdc643694e99e900	3d93af01ea737f6973367bcf7e3e99d7e527de5baceeacdf8c4ea192f4d95a0b	a8258f42edbae4bc370fb6fc6651d8314f214a7ed704c8fa458cab5378f92d30	hCoV-19_USA_CA-CZB-15265_2020	FALSE	
-EPI_ISL_955570	SRR13689874	SAMN17867197	-	-	B.1.1.512	MW700586	-	-	0b43f14b04d0d6c979d3d5798bd90687106ed2d0ff6174ac9408ba1da1cdb412	d1d7f8a828a2fd2ff5b5358960682b3f934b95c353d5fbd4ba675f1e0f8eb8b9	5f89ba9a19f383d37a7e5751b9c6f8c212d053c920dbc0a6b1cb4a7ab6cf71bd	hCoV-19_USA_CA-CZB-15587_2020	FALSE	
-EPI_ISL_979028	SRR13690340	SAMN17867461	-	-	B.1.232	MW700797	-	-	7e6a845f63c07cf5020e62338b9094c9749975cee7d106a841bd13148335a4d6	e42df988a512793bae441ae5e4f7b9ff8f45533613bbd9e3c941a2efebd63e56	8d4ba0086dc2b83d68ad2dd0cc88aca399e0f05b8a4825ffddb086d25a6230ff	hCoV-19_USA_CA-CZB-16803_2020	FALSE	
-EPI_ISL_955696	SRR13690003	SAMN17867327	-	-	B.1.2	MW700464	-	-	978f9258925092cafcea5360dffb592b3375b92bb175aa005302cc73a7186254	1791cb9cc53b43cb47c888918ea7e465766e02d21783fb389d368a0d2e05e71b	92143cd0273fabf199c754d382c9394ee650b5d49ac1173a9556951d3e023c5d	hCoV-19_USA_CA-CZB-19306_2020	FALSE	
-EPI_ISL_513739	SRR12661075	SAMN16200637	-	-	B.1.452	MW035971	-	-	b8b2ac3b69b0d5730fab33d4678187b84c3f6cf26fb8effbf13cf5d969478019	612058cd3fd6faf7f9cedd9470ad422b0c386ce98a70f6721834a3ddbfc75024	558e96e9a4c0882c652d65bda7863fb61cdbd540e8e2723e14810edecff82520	hCoV-19_USA_CA-CZB-2190_2020	FALSE	
-EPI_ISL_548321	SRR12763543	SAMN16338766	-	-	B.1.1.463	MW134089	-	-	239b7add94ce7571a7c8ad07205eb13028a77dbdbb528d94a91a875fe5a03448	e70f8493612228f044da972b889a307c4fc3e1737df2a0e714221e3c66c3a274	7d71392ea2938dbd7fe8a9991b442b92b762ea1f60bc422809880f019d64df96	hCoV-19_USA_CA-CZB-3273_2020	FALSE	
-EPI_ISL_583189	SRR12833927	SAMN16453974	-	-	B.1.1.514	MW276462	-	-	28ed402343da027dec37b854fc739c1abc240a5aa856f73bbe145695859365e5	e1c611a7a2a0b63c75022c0195c1390176697556d8e89fb87550447626002ba3	1018e1895dfa30ba2846683e90ee2a88ad4249ed670f472c9ee0898667a05403	hCoV-19_USA_CA-CZB-6122_2020	FALSE	
-EPI_ISL_582920	SRR12833718	SAMN16453671	-	-	B.1.1.174	MW276214	-	-	a59d8c5ca92c3a234d6eede33864b3d34b74879375d64c31c7e05f3d02041b36	269db0a1c3425935cd722ace8fcba4ae39ac3e82621d1e8c2d9c6d9b736c513e	1948a5fb718d1e1200b2e075f0f80d791ca23d9aa7ded80f9fc575fd477e8594	hCoV-19_USA_CA-CZB-6993_2020	FALSE	
+EPI_ISL_672188	SRR13195337	SAMN16989742	-	-	B.1.309	MW483225	-	-	41304cff200147da89addd290c2de2a5382ba319055ab8a2a6ee27747a342c90	9a76a23942f6a84430208c7f866816f3ef8ed7854bc0ef236d8f6f6fcd9cc54b	36819968b4e419947f96518cd503365b581bc14531041a05d4695a785d70db2d	hCoV-19_USA_CA-CZB-10010_2020	FALSE	
+EPI_ISL_672271	SRR13195265	SAMN16989834	-	-	B.1.1.205	MW483314	-	-	8818bae3122e1b527c831607bb5e5486f09532717dba46c41b30458b0a668869	d5c288465a8abe7d68630a3f1f613a9dda5640f53f5dc6a6f9c611cb9c06e688	85b26faa0540ebab69de639d6e01f6c222accd19480293ea39d7a356252e4e71	hCoV-19_USA_CA-CZB-10245_2020	FALSE	
+EPI_ISL_672414	SRR13195052	SAMN16990022	-	-	B.1.1.139	MW483478	-	-	82db821f647440426227694934039c70dd6713d75d5128c7e60d13edb9073122	42bc634d1bac5daa6e2809f781d527d176682e87a943693a6e74396eaac2c5a5	513b8be54c82731416d5dc90b4f09117551d5bee51ae1bda2e11969570dbf1ba	hCoV-19_USA_CA-CZB-13120_2020	FALSE	
+EPI_ISL_739321	SRR13526755	SAMN17570757	-	-	B.1.1.418	MW565773	-	-	1e251101eaa3a740f899d6f1489bec588512f56ca946086f9216a9ac72bab5e8	2408bc7fa112dc4ac0281d06917b11db68a1fb32974287e61824cf800770f8ef	31e78ca6db94447d4ea007c97c3ba66d0df16f4f896b1e1c141c681276598a7e	hCoV-19_USA_CA-CZB-13702_2020	FALSE	
+EPI_ISL_738705	SRR13527262	SAMN17571193	-	-	B.1.1.391	MW564975	-	-	68761853878c343fc89b8f4fc0832af7537d52190d1488f3bfb24f7522c6bf68	0f539899f2a4d9d6902fb1c970f0498445f038ecedb301cb6fbaeec785c58ba8	a8258f42edbae4bc370fb6fc6651d8314f214a7ed704c8fa458cab5378f92d30	hCoV-19_USA_CA-CZB-15265_2020	FALSE	
+EPI_ISL_955570	SRR13689874	SAMN17867197	-	-	B.1.1.512	MW700586	-	-	03acf779a61aa979f50c96982fe882a6ff5ca0db48ba7113151d66c31c5f0538	620376b1a241b7e00869807e0b272dae400fcc8a1536c7df66b37cc5306a43f0	5f89ba9a19f383d37a7e5751b9c6f8c212d053c920dbc0a6b1cb4a7ab6cf71bd	hCoV-19_USA_CA-CZB-15587_2020	FALSE	
+EPI_ISL_979028	SRR13690340	SAMN17867461	-	-	B.1.232	MW700797	-	-	a33cc2e83ff4fb93f0b9b243d1f2c08322eb8dc7cb2e6fb1e73eb8b9f5c40e5c	04edf48d78d91cf8e66feb74e165e3e9f38e4871e199366217738ead676140a7	8d4ba0086dc2b83d68ad2dd0cc88aca399e0f05b8a4825ffddb086d25a6230ff	hCoV-19_USA_CA-CZB-16803_2020	FALSE	
+EPI_ISL_955696	SRR13690003	SAMN17867327	-	-	B.1.2	MW700464	-	-	0bc2b4c7d9ae97914f802a760982961c6f28c9e833bc2fa78f8cfa5b01cf45b7	e613be73a131be8b2262f774beb29fc44aa14babec49918e6e0ecb19339244f4	92143cd0273fabf199c754d382c9394ee650b5d49ac1173a9556951d3e023c5d	hCoV-19_USA_CA-CZB-19306_2020	FALSE	
+EPI_ISL_513739	SRR12661075	SAMN16200637	-	-	B.1.452	MW035971	-	-	7a1b3424561c21eb9822464f035bd3b0103355ccc72ba4c8002e5163ec277d99	3aa46b612592d9ba6859c335a9df6f3a36877d00f07f6a2bb35fbf741b2848c3	558e96e9a4c0882c652d65bda7863fb61cdbd540e8e2723e14810edecff82520	hCoV-19_USA_CA-CZB-2190_2020	FALSE	
+EPI_ISL_548321	SRR12763543	SAMN16338766	-	-	B.1.1.463	MW134089	-	-	3fefe9b45d72cea447da44c5039d7d30bb3adddcfef6f5907a11711e40529658	b53d69591abba768e3e277e00de5d2f0f9d646ba54fd9b36f603f6efa266f6a6	7d71392ea2938dbd7fe8a9991b442b92b762ea1f60bc422809880f019d64df96	hCoV-19_USA_CA-CZB-3273_2020	FALSE	
+EPI_ISL_583189	SRR12833927	SAMN16453974	-	-	B.1.1.514	MW276462	-	-	0f9264df4f9a3f28f88dc9924c5814497ef1075297cbd249f628a96367b8e78a	abb4b3610588f2ac1c806ea0ee598d27fe442d15ad0bcc2362a76f3491280548	1018e1895dfa30ba2846683e90ee2a88ad4249ed670f472c9ee0898667a05403	hCoV-19_USA_CA-CZB-6122_2020	FALSE	
+EPI_ISL_582920	SRR12833718	SAMN16453671	-	-	B.1.1.174	MW276214	-	-	410a2f884cf29f1873bfd20103361282110c47d4c1748a345532ba074f1585c8	59f85b57626dffce4a2474b5d54c561cc19f7527f395cca20053c12829f16fe6	1948a5fb718d1e1200b2e075f0f80d791ca23d9aa7ded80f9fc575fd477e8594	hCoV-19_USA_CA-CZB-6993_2020	FALSE	
 EPI_ISL_468562	SRR12192434	SAMN15379415	-	-	B.1.336	MT627409	-	-	aa8d0fb7a0c27112e662a54381d779d73784c408f385854c92e38bac2d953083	01e0e6a0085e9bd0f495949745ff985f5c49e2bdcadaa94829425ed62e08e23c	e25f8e1908fad48223191af383792148e3af54d01fc2eaa1bfdaffafb454d2f1	hCoV-19_USA_CA-QDX-110_2020	FALSE	
 EPI_ISL_604296	SRR13193342	SAMN16988635	-	-	B.1.578	MW190731	-	-	f61e9c26b7b986b88cd3c8926d9e71d05f5ce1d6b5de209a2637f0c7ba7484b9	e21516f2356bda128b18fcedc331695b5b3e7458020e7575aa096538c00a99d4	b21c991cc9f619e4a1e0e23466cb433bc39956febb9b090aa658bbd82db69c52	hCoV-19_USA_CA-QDX-1984_2020	FALSE	
 EPI_ISL_710186	SRR13373851	SAMN17129936	-	-	B.1.492	MW645768	-	-	97e64e28406b32a5c7f17ae6d6f107f148a73767cbe05079ea784c4f29a59598	e358037def23cef58a92cb5b2b0ca536de1c4625b7573c23858e37cea1e79873	c88ff8fa14e0b783c47911398146a42acc9d942ec68b81eb09e3fd1faea73bae	hCoV-19_USA_CO-CDPHE-2004220748_2020	FALSE	

diff --git a/scripts/GenFSGopher.pl b/scripts/GenFSGopher.pl
@@ -28,7 +28,7 @@ sub main{
   GetOptions($settings,qw(tempdir=s help outdir=s compressed|compression format=s shuffled! layout=s numcpus=i run! version citation));
   usage() if($$settings{help});
   $$settings{format}||="tsv"; # by default, input format is tsv
-  $$settings{seqIdTemplate}||='@$ac_$sn[_$rn]/$ri';
+  $$settings{seqIdTemplate}||='@$ac_$sn/$ri';
   $$settings{layout}||="onedir";
   $$settings{layout}=lc($$settings{layout});
   $$settings{numcpus}||=1;
@@ -467,7 +467,10 @@ sub tsvToMakeHash{
 
   # Last of the make target(s)
   if(!$$settings{'calculate-hashsums'}){
-    push(@{ $$make{"sha256sum.log"}{CMD} }, "sha256sum -c $all_targets");
+    push(@{ $$make{"sha256sum.log"}{CMD} }, 
+      "sha256sum -c $all_targets > $make_target",
+      "cat $make_target",
+    );
   }
 
   return $make;