Repository 'jbrowse2'
hg clone https://toolshed.g2.bx.psu.edu/repos/fubar/jbrowse2

Changeset 123:160f33c6ba85 (2024-10-04)
Previous changeset 122:ae07c55ab96b (2024-10-04) Next changeset 124:137e08517410 (2024-10-04)
Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit a9124072bc71dd670ee58ff8e4846e14d6d603ec-dirty
modified:
__pycache__/jbrowse2.cpython-312.pyc
jbrowse2.py
removed:
3.gff
foo
foo.tbi
mvdb1.gff
mvdb2.gff
mvdb3.gff
mvdb4.gff
b
diff -r ae07c55ab96b -r 160f33c6ba85 3.gff
--- a/3.gff Fri Oct 04 04:07:03 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
b
b'@@ -1,53 +0,0 @@\n-##gff-version 3\n-##sequence-region Merlin 1 172788\n-Merlin\tGeneMark.hmm\tgene\t10\t30\t.\t+\t.\tID=Merlin_1;seqid=Merlin\n-Merlin\tGeneMark.hmm\tmRNA\t14\t30\t.\t+\t.\tID=Merlin_1_mRNA;Parent=Merlin_1\n-Merlin\tGeneMark.hmm\tCDS\t14\t20\t1000\t+\t0\tID=Merlin_1_CDS ;Parent=Merlin_1_mRNA\n-Merlin\tGeneMark.hmm\tCDS\t24\t30\t500\t+\t2\tID=Merlin_1_CDS ;Parent=Merlin_1_mRNA\n-Scaffold2\tWebApollo\texon\t1254745\t1254849\t.\t+\t.\tID=401F7E03FCBD10CD78911C045ACBF057;Name=401F7E03FCBD10CD78911C045ACBF057;Parent=41832FDEEC226086FDE25CFA1AADAE2D;date_last_modified=2014-08-24;date_creation=2014-08-24;owner=kpanfilio\n-Scaffold2\tWebApollo\texon\t1247878\t1248122\t.\t+\t.\tID=F2FD3567BB92973E7CC0D266CD9C3002;Name=F2FD3567BB92973E7CC0D266CD9C3002;Parent=41832FDEEC226086FDE25CFA1AADAE2D;date_last_modified=2014-08-24;date_creation=2014-08-24;owner=kpanfilio\n-Scaffold2\tWebApollo\texon\t1183361\t1183513\t.\t+\t.\tID=C602B0741979CD5F41F7092A1E68C46C;Name=C602B0741979CD5F41F7092A1E68C46C;Parent=41832FDEEC226086FDE25CFA1AADAE2D;date_last_modified=2014-08-24;date_creation=2014-08-24;owner=kpanfilio\n-Scaffold2\tWebApollo\texon\t1190237\t1190428\t.\t+\t.\tID=F204CCA66BFB64505E989AB0113F80E0;Name=F204CCA66BFB64505E989AB0113F80E0;Parent=41832FDEEC226086FDE25CFA1AADAE2D;date_last_modified=2014-08-24;date_creation=2014-08-24;owner=kpanfilio\n-Scaffold2\tWebApollo\texon\t1257900\t1257970\t.\t+\t.\tID=8D10D6C74AEB731074328D6231C3711E;Name=8D10D6C74AEB731074328D6231C3711E;Parent=41832FDEEC226086FDE25CFA1AADAE2D;date_last_modified=2014-08-24;date_creation=2014-08-24;owner=kpanfilio\n-Scaffold2\tWebApollo\texon\t1177308\t1177459\t.\t+\t.\tID=FAF84802E1B3BCBF1B34304A8C17E687;Name=FAF84802E1B3BCBF1B34304A8C17E687;Parent=41832FDEEC226086FDE25CFA1AADAE2D;date_last_modified=2014-08-24;date_creation=2014-08-24;owner=kpanfilio\n-Scaffold2\tWebApollo\texon\t1251226\t1251384\t.\t+\t.\tID=AA6625EFFFC93760257BA2AEBD9084F7;Name=AA6625EFFFC93760257BA2AEBD9084F7;Parent=41832FDEEC226086FDE25CFA1AADAE2D;date_last_modified=2014-08-24;date_creation=2014-08-24;owner=kpanfilio\n-Scaffold2\tWebApollo\texon\t1244244\t1244423\t.\t+\t.\tID=A1BAF5141ED123FAF0B13695C3399F67;Name=A1BAF5141ED123FAF0B13695C3399F67;Parent=41832FDEEC226086FDE25CFA1AADAE2D;date_last_modified=2014-08-24;date_creation=2014-08-24;owner=kpanfilio\n-Scaffold2\tWebApollo\tnon_canonical_five_prime_splice_site\t1285352\t1285352\t.\t+\t.\tID=41832FDEEC226086FDE25CFA1AADAE2D-non_canonical_five_prive_splice_site-1285351;Name=41832FDEEC226086FDE25CFA1AADAE2D-non_canonical_five_prive_splice_site-1285351;Parent=41832FDEEC226086FDE25CFA1AADAE2D;date_last_modified=2014-08-24;date_creation=2014-08-24;owner=kpanfilio\n-Scaffold2\tWebApollo\texon\t1199147\t1199311\t.\t+\t.\tID=7DCC704132150E28FB9A07E1718D77AC;Name=7DCC704132150E28FB9A07E1718D77AC;Parent=41832FDEEC226086FDE25CFA1AADAE2D;date_last_modified=2014-08-24;date_creation=2014-08-24;owner=kpanfilio\n-Scaffold2\tWebApollo\texon\t1192019\t1192263\t.\t+\t.\tID=5DC0DFF1BACA4A435123BD574A158DC3;Name=5DC0DFF1BACA4A435123BD574A158DC3;Parent=41832FDEEC226086FDE25CFA1AADAE2D;date_last_modified=2014-08-24;date_creation=2014-08-24;owner=kpanfilio\n-Scaffold2\tWebApollo\texon\t1195224\t1195412\t.\t+\t.\tID=C36A537054A80DEE326018CEB3968517;Name=C36A537054A80DEE326018CEB3968517;Parent=41832FDEEC226086FDE25CFA1AADAE2D;date_last_modified=2014-08-24;date_creation=2014-08-24;owner=kpanfilio\n-Scaffold2\tWebApollo\texon\t1242059\t1242253\t.\t+\t.\tID=7C8270DCD43F93327251E91EAADA08DC;Name=7C8270DCD43F93327251E91EAADA08DC;Parent=41832FDEEC226086FDE25CFA1AADAE2D;date_last_modified=2014-08-24;date_creation=2014-08-24;owner=kpanfilio\n-Scaffold2\tWebApollo\texon\t1285496\t1286136\t.\t+\t.\tID=7ECCDA418811FA633C27E1F67B725F2A;Name=7ECCDA418811FA633C27E1F67B725F2A;Parent=41832FDEEC226086FDE25CFA1AADAE2D;date_last_modified=2014-08-24;date_creation=2014-08-24;owner=kpanfilio\n-Scaffold2\tWebApollo\texon\t1182200\t1182500\t.\t+\t.\tID=F01FA790A090E8B667281A115E1C718C;Name=F01FA790A090E8B667281A115E1C718C;Parent=41832FDEEC226086FDE25CFA1AADAE2D;date_last_modified=2014-08-24;date_creation=2014-08-24;owner=kpanfilio\n-Scaffold2\tWebApollo\texo'..b"43AA3956E107;Name=4573453BC6A42F32CCDB43AA3956E107;Parent=41832FDEEC226086FDE25CFA1AADAE2D;date_last_modified=2014-08-24;date_creation=2014-08-24;owner=kpanfilio\n-Scaffold2\tWebApollo\tnon_canonical_three_prime_splice_site\t1285496\t1285496\t.\t+\t.\tID=41832FDEEC226086FDE25CFA1AADAE2D-non_canonical_three_prive_splice_site-1285495;Name=41832FDEEC226086FDE25CFA1AADAE2D-non_canonical_three_prive_splice_site-1285495;Parent=41832FDEEC226086FDE25CFA1AADAE2D;date_last_modified=2014-08-24;date_creation=2014-08-24;owner=kpanfilio\n-Scaffold2\tWebApollo\texon\t1159199\t1160031\t.\t+\t.\tID=B547501074442430E7FAF89065AF9AF5;Name=B547501074442430E7FAF89065AF9AF5;Parent=41832FDEEC226086FDE25CFA1AADAE2D;date_last_modified=2014-08-24;date_creation=2014-08-24;owner=kpanfilio\n-Scaffold2\tWebApollo\texon\t1221344\t1221502\t.\t+\t.\tID=165AA5F27B3323F4A45CE39064B070E5;Name=165AA5F27B3323F4A45CE39064B070E5;Parent=41832FDEEC226086FDE25CFA1AADAE2D;date_last_modified=2014-08-24;date_creation=2014-08-24;owner=kpanfilio\n-Scaffold2\tWebApollo\texon\t1230949\t1231157\t.\t+\t.\tID=A83A793CF6675C0372DBDECA8C7332C0;Name=A83A793CF6675C0372DBDECA8C7332C0;Parent=41832FDEEC226086FDE25CFA1AADAE2D;date_last_modified=2014-08-24;date_creation=2014-08-24;owner=kpanfilio\n-Scaffold2\tWebApollo\texon\t1184667\t1184790\t.\t+\t.\tID=32B79C620D7009F3DCC8E946BFB4558A;Name=32B79C620D7009F3DCC8E946BFB4558A;Parent=41832FDEEC226086FDE25CFA1AADAE2D;date_last_modified=2014-08-24;date_creation=2014-08-24;owner=kpanfilio\n-Scaffold2\tWebApollo\texon\t1187866\t1188029\t.\t+\t.\tID=38FD66EE4EC19C037466B82FDA8E9FAD;Name=38FD66EE4EC19C037466B82FDA8E9FAD;Parent=41832FDEEC226086FDE25CFA1AADAE2D;date_last_modified=2014-08-24;date_creation=2014-08-24;owner=kpanfilio\n-Scaffold2\tWebApollo\texon\t1174871\t1175000\t.\t+\t.\tID=F3D5FFA0634EE4DD40C3FB31887BCD57;Name=F3D5FFA0634EE4DD40C3FB31887BCD57;Parent=41832FDEEC226086FDE25CFA1AADAE2D;date_last_modified=2014-08-24;date_creation=2014-08-24;owner=kpanfilio\n-Scaffold2\tWebApollo\texon\t1270962\t1271143\t.\t+\t.\tID=FC53825CEB9A78AA28A8BD7ED2661697;Name=FC53825CEB9A78AA28A8BD7ED2661697;Parent=41832FDEEC226086FDE25CFA1AADAE2D;date_last_modified=2014-08-24;date_creation=2014-08-24;owner=kpanfilio\n-Scaffold2\tWebApollo\tCDS\t1174871\t1175000\t.\t+\t0\tID=43F646FAA11B5075698A73959D6FB383;Name=43F646FAA11B5075698A73959D6FB383;Parent=41832FDEEC226086FDE25CFA1AADAE2D;date_last_modified=2014-08-24;date_creation=2014-08-24;owner=kpanfilio\n-Scaffold2\tWebApollo\tgene\t1159199\t1286136\t.\t+\t.\tID=52F3AF8B2DC566ADAB6A63D796BC8C96;Name=52F3AF8B2DC566ADAB6A63D796BC8C96;owner=kpanfilio;date_last_modified=2014-08-24;date_creation=2014-08-24\n-Scaffold2\tWebApollo\tmRNA\t1159199\t1286136\t.\t+\t.\tID=41832FDEEC226086FDE25CFA1AADAE2D;Name=spectrin beta chain;Parent=52F3AF8B2DC566ADAB6A63D796BC8C96;Note=Annotation type: Modify an existing gene model,Result of: Merging of two or more gene models.,Result of: Adding an exon to the gene model,Result of: Removing an exon from the gene model,Note to curator: final exon (3' UTR only) interrupted by gap in assembly: rendered as two separate exons with non-canonical splice sites to exclude gap nucleotide positions in excess of the length of the mapped isotig.,Added 5'UTR;Dbxref=GenBank Zootermopsis nevadensis:KDR16227.1;status=Approved;symbol=\xc2\xa3]-Spec;owner=kpanfilio;date_creation=2014-08-24;date_last_modified=2014-08-24\n-Scaffold2\tWebApollo\texon\t1250986\t1251124\t.\t+\t.\tID=196B75DC18386FCD03A46B68FDACA807;Name=196B75DC18386FCD03A46B68FDACA807;Parent=41832FDEEC226086FDE25CFA1AADAE2D;date_last_modified=2014-08-24;date_creation=2014-08-24;owner=kpanfilio\n-Scaffold2\tWebApollo\texon\t1200664\t1200876\t.\t+\t.\tID=74F95DCA5FF13BA5D9099FC9EDC65062;Name=74F95DCA5FF13BA5D9099FC9EDC65062;Parent=41832FDEEC226086FDE25CFA1AADAE2D;date_last_modified=2014-08-24;date_creation=2014-08-24;owner=kpanfilio\n-Scaffold2\tWebApollo\texon\t1199927\t1200166\t.\t+\t.\tID=07C567475620CB6A0116E49AD995A468;Name=07C567475620CB6A0116E49AD995A468;Parent=41832FDEEC226086FDE25CFA1AADAE2D;date_last_modified=2014-08-24;date_creation=2014-08-24;owner=kpanfilio\n"
b
diff -r ae07c55ab96b -r 160f33c6ba85 __pycache__/jbrowse2.cpython-312.pyc
b
Binary file __pycache__/jbrowse2.cpython-312.pyc has changed
b
diff -r ae07c55ab96b -r 160f33c6ba85 foo
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Binary file foo has changed
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diff -r ae07c55ab96b -r 160f33c6ba85 foo.tbi
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Binary file foo.tbi has changed
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diff -r ae07c55ab96b -r 160f33c6ba85 jbrowse2.py
--- a/jbrowse2.py Fri Oct 04 04:07:03 2024 +0000
+++ b/jbrowse2.py Fri Oct 04 04:20:38 2024 +0000
b
@@ -420,7 +420,7 @@
         self.tracksToAdd = {}
         self.config_json = {}
         self.config_json_file = os.path.join(outdir, "config.json")
-        self.clone_jbrowse()
+        self.clone_jbrowse(realclone=False)
 
     def get_cwd(self, cwd):
         if cwd:
b
diff -r ae07c55ab96b -r 160f33c6ba85 mvdb1.gff
--- a/mvdb1.gff Fri Oct 04 04:07:03 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
b
b"@@ -1,49 +0,0 @@\n-##gff-version 3\n-##sequence-region Scaffold2 1 2247300\n-Scaffold2\tWebApollo\tgene\t1159199\t1286136\t.\t+\t.\tID=52F3AF8B2DC566ADAB6A63D796BC8C96;Name=52F3AF8B2DC566ADAB6A63D796BC8C96;owner=kpanfilio;date_last_modified=2014-08-24;date_creation=2014-08-24\n-Scaffold2\tWebApollo\tmRNA\t1159199\t1286136\t.\t+\t.\tID=41832FDEEC226086FDE25CFA1AADAE2D;Name=spectrin beta chain;Parent=52F3AF8B2DC566ADAB6A63D796BC8C96;Note=Annotation type: Modify an existing gene model,Result of: Merging of two or more gene models.,Result of: Adding an exon to the gene model,Result of: Removing an exon from the gene model,Note to curator: final exon (3' UTR only) interrupted by gap in assembly: rendered as two separate exons with non-canonical splice sites to exclude gap nucleotide positions in excess of the length of the mapped isotig.,Added 5'UTR;Dbxref=GenBank Zootermopsis nevadensis:KDR16227.1;status=Approved;symbol=\xc2\xa3]-Spec;owner=kpanfilio;date_creation=2014-08-24;date_last_modified=2014-08-24\n-Scaffold2\tWebApollo\texon\t1250986\t1251124\t.\t+\t.\tID=196B75DC18386FCD03A46B68FDACA807;Name=196B75DC18386FCD03A46B68FDACA807;Parent=41832FDEEC226086FDE25CFA1AADAE2D;date_last_modified=2014-08-24;date_creation=2014-08-24;owner=kpanfilio\n-Scaffold2\tWebApollo\texon\t1200664\t1200876\t.\t+\t.\tID=74F95DCA5FF13BA5D9099FC9EDC65062;Name=74F95DCA5FF13BA5D9099FC9EDC65062;Parent=41832FDEEC226086FDE25CFA1AADAE2D;date_last_modified=2014-08-24;date_creation=2014-08-24;owner=kpanfilio\n-Scaffold2\tWebApollo\texon\t1199927\t1200166\t.\t+\t.\tID=07C567475620CB6A0116E49AD995A468;Name=07C567475620CB6A0116E49AD995A468;Parent=41832FDEEC226086FDE25CFA1AADAE2D;date_last_modified=2014-08-24;date_creation=2014-08-24;owner=kpanfilio\n-Scaffold2\tWebApollo\texon\t1254745\t1254849\t.\t+\t.\tID=401F7E03FCBD10CD78911C045ACBF057;Name=401F7E03FCBD10CD78911C045ACBF057;Parent=41832FDEEC226086FDE25CFA1AADAE2D;date_last_modified=2014-08-24;date_creation=2014-08-24;owner=kpanfilio\n-Scaffold2\tWebApollo\texon\t1247878\t1248122\t.\t+\t.\tID=F2FD3567BB92973E7CC0D266CD9C3002;Name=F2FD3567BB92973E7CC0D266CD9C3002;Parent=41832FDEEC226086FDE25CFA1AADAE2D;date_last_modified=2014-08-24;date_creation=2014-08-24;owner=kpanfilio\n-Scaffold2\tWebApollo\texon\t1183361\t1183513\t.\t+\t.\tID=C602B0741979CD5F41F7092A1E68C46C;Name=C602B0741979CD5F41F7092A1E68C46C;Parent=41832FDEEC226086FDE25CFA1AADAE2D;date_last_modified=2014-08-24;date_creation=2014-08-24;owner=kpanfilio\n-Scaffold2\tWebApollo\texon\t1190237\t1190428\t.\t+\t.\tID=F204CCA66BFB64505E989AB0113F80E0;Name=F204CCA66BFB64505E989AB0113F80E0;Parent=41832FDEEC226086FDE25CFA1AADAE2D;date_last_modified=2014-08-24;date_creation=2014-08-24;owner=kpanfilio\n-Scaffold2\tWebApollo\texon\t1257900\t1257970\t.\t+\t.\tID=8D10D6C74AEB731074328D6231C3711E;Name=8D10D6C74AEB731074328D6231C3711E;Parent=41832FDEEC226086FDE25CFA1AADAE2D;date_last_modified=2014-08-24;date_creation=2014-08-24;owner=kpanfilio\n-Scaffold2\tWebApollo\texon\t1177308\t1177459\t.\t+\t.\tID=FAF84802E1B3BCBF1B34304A8C17E687;Name=FAF84802E1B3BCBF1B34304A8C17E687;Parent=41832FDEEC226086FDE25CFA1AADAE2D;date_last_modified=2014-08-24;date_creation=2014-08-24;owner=kpanfilio\n-Scaffold2\tWebApollo\texon\t1251226\t1251384\t.\t+\t.\tID=AA6625EFFFC93760257BA2AEBD9084F7;Name=AA6625EFFFC93760257BA2AEBD9084F7;Parent=41832FDEEC226086FDE25CFA1AADAE2D;date_last_modified=2014-08-24;date_creation=2014-08-24;owner=kpanfilio\n-Scaffold2\tWebApollo\texon\t1244244\t1244423\t.\t+\t.\tID=A1BAF5141ED123FAF0B13695C3399F67;Name=A1BAF5141ED123FAF0B13695C3399F67;Parent=41832FDEEC226086FDE25CFA1AADAE2D;date_last_modified=2014-08-24;date_creation=2014-08-24;owner=kpanfilio\n-Scaffold2\tWebApollo\tnon_canonical_five_prime_splice_site\t1285352\t1285352\t.\t+\t.\tID=41832FDEEC226086FDE25CFA1AADAE2D-non_canonical_five_prive_splice_site-1285351;Name=41832FDEEC226086FDE25CFA1AADAE2D-non_canonical_five_prive_splice_site-1285351;Parent=41832FDEEC226086FDE25CFA1AADAE2D;date_last_modified=2014-08-24;date_creation=2014-08-24;owner=kpanfilio\n-Scaffold2\tWebApollo\texon\t1199147\t1199311\t.\t+\t.\tID=7DCC704132150E28FB9A07E1718D77AC;Name=7D"..b'me=C21B321082955BEEF756B7C2C6A5D096;Parent=41832FDEEC226086FDE25CFA1AADAE2D;date_last_modified=2014-08-24;date_creation=2014-08-24;owner=kpanfilio\n-Scaffold2\tWebApollo\texon\t1189584\t1189771\t.\t+\t.\tID=0C78D78BD6ACF31510F655DE39B71480;Name=0C78D78BD6ACF31510F655DE39B71480;Parent=41832FDEEC226086FDE25CFA1AADAE2D;date_last_modified=2014-08-24;date_creation=2014-08-24;owner=kpanfilio\n-Scaffold2\tWebApollo\texon\t1218961\t1219161\t.\t+\t.\tID=066A45C91A12DACCC0C5EB5B1E4CA123;Name=066A45C91A12DACCC0C5EB5B1E4CA123;Parent=41832FDEEC226086FDE25CFA1AADAE2D;date_last_modified=2014-08-24;date_creation=2014-08-24;owner=kpanfilio\n-Scaffold2\tWebApollo\texon\t1177543\t1177716\t.\t+\t.\tID=F033CCC56F48E2B806E46447EA267060;Name=F033CCC56F48E2B806E46447EA267060;Parent=41832FDEEC226086FDE25CFA1AADAE2D;date_last_modified=2014-08-24;date_creation=2014-08-24;owner=kpanfilio\n-Scaffold2\tWebApollo\texon\t1266960\t1267088\t.\t+\t.\tID=1E54500A43F613F837285D030B0F54C4;Name=1E54500A43F613F837285D030B0F54C4;Parent=41832FDEEC226086FDE25CFA1AADAE2D;date_last_modified=2014-08-24;date_creation=2014-08-24;owner=kpanfilio\n-Scaffold2\tWebApollo\texon\t1278339\t1278592\t.\t+\t.\tID=78EB00577011260745429FB168F0D9C4;Name=78EB00577011260745429FB168F0D9C4;Parent=41832FDEEC226086FDE25CFA1AADAE2D;date_last_modified=2014-08-24;date_creation=2014-08-24;owner=kpanfilio\n-Scaffold2\tWebApollo\texon\t1193579\t1193770\t.\t+\t.\tID=9F48014565E36955074793258E678A51;Name=9F48014565E36955074793258E678A51;Parent=41832FDEEC226086FDE25CFA1AADAE2D;date_last_modified=2014-08-24;date_creation=2014-08-24;owner=kpanfilio\n-Scaffold2\tWebApollo\texon\t1282265\t1282453\t.\t+\t.\tID=4573453BC6A42F32CCDB43AA3956E107;Name=4573453BC6A42F32CCDB43AA3956E107;Parent=41832FDEEC226086FDE25CFA1AADAE2D;date_last_modified=2014-08-24;date_creation=2014-08-24;owner=kpanfilio\n-Scaffold2\tWebApollo\tnon_canonical_three_prime_splice_site\t1285496\t1285496\t.\t+\t.\tID=41832FDEEC226086FDE25CFA1AADAE2D-non_canonical_three_prive_splice_site-1285495;Name=41832FDEEC226086FDE25CFA1AADAE2D-non_canonical_three_prive_splice_site-1285495;Parent=41832FDEEC226086FDE25CFA1AADAE2D;date_last_modified=2014-08-24;date_creation=2014-08-24;owner=kpanfilio\n-Scaffold2\tWebApollo\texon\t1159199\t1160031\t.\t+\t.\tID=B547501074442430E7FAF89065AF9AF5;Name=B547501074442430E7FAF89065AF9AF5;Parent=41832FDEEC226086FDE25CFA1AADAE2D;date_last_modified=2014-08-24;date_creation=2014-08-24;owner=kpanfilio\n-Scaffold2\tWebApollo\texon\t1221344\t1221502\t.\t+\t.\tID=165AA5F27B3323F4A45CE39064B070E5;Name=165AA5F27B3323F4A45CE39064B070E5;Parent=41832FDEEC226086FDE25CFA1AADAE2D;date_last_modified=2014-08-24;date_creation=2014-08-24;owner=kpanfilio\n-Scaffold2\tWebApollo\texon\t1230949\t1231157\t.\t+\t.\tID=A83A793CF6675C0372DBDECA8C7332C0;Name=A83A793CF6675C0372DBDECA8C7332C0;Parent=41832FDEEC226086FDE25CFA1AADAE2D;date_last_modified=2014-08-24;date_creation=2014-08-24;owner=kpanfilio\n-Scaffold2\tWebApollo\texon\t1184667\t1184790\t.\t+\t.\tID=32B79C620D7009F3DCC8E946BFB4558A;Name=32B79C620D7009F3DCC8E946BFB4558A;Parent=41832FDEEC226086FDE25CFA1AADAE2D;date_last_modified=2014-08-24;date_creation=2014-08-24;owner=kpanfilio\n-Scaffold2\tWebApollo\texon\t1187866\t1188029\t.\t+\t.\tID=38FD66EE4EC19C037466B82FDA8E9FAD;Name=38FD66EE4EC19C037466B82FDA8E9FAD;Parent=41832FDEEC226086FDE25CFA1AADAE2D;date_last_modified=2014-08-24;date_creation=2014-08-24;owner=kpanfilio\n-Scaffold2\tWebApollo\texon\t1174871\t1175000\t.\t+\t.\tID=F3D5FFA0634EE4DD40C3FB31887BCD57;Name=F3D5FFA0634EE4DD40C3FB31887BCD57;Parent=41832FDEEC226086FDE25CFA1AADAE2D;date_last_modified=2014-08-24;date_creation=2014-08-24;owner=kpanfilio\n-Scaffold2\tWebApollo\texon\t1270962\t1271143\t.\t+\t.\tID=FC53825CEB9A78AA28A8BD7ED2661697;Name=FC53825CEB9A78AA28A8BD7ED2661697;Parent=41832FDEEC226086FDE25CFA1AADAE2D;date_last_modified=2014-08-24;date_creation=2014-08-24;owner=kpanfilio\n-Scaffold2\tWebApollo\tCDS\t1174871\t1175000\t.\t+\t0\tID=43F646FAA11B5075698A73959D6FB383;Name=43F646FAA11B5075698A73959D6FB383;Parent=41832FDEEC226086FDE25CFA1AADAE2D;date_last_modified=2014-08-24;date_creation=2014-08-24;owner=kpanfilio\n'
b
diff -r ae07c55ab96b -r 160f33c6ba85 mvdb2.gff
--- a/mvdb2.gff Fri Oct 04 04:07:03 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
b
@@ -1,6 +0,0 @@
-##gff-version 3
-##sequence-region Merlin 1 172788
-Merlin GeneMark.hmm gene 10 30 . + . ID=Merlin_1;seqid=Merlin
-Merlin GeneMark.hmm mRNA 14 30 . + . ID=Merlin_1_mRNA;Parent=Merlin_1
-Merlin GeneMark.hmm CDS 14 20 1000 + 0 ID=Merlin_1_CDS ;Parent=Merlin_1_mRNA
-Merlin GeneMark.hmm CDS 24 30 500 + 2 ID=Merlin_1_CDS ;Parent=Merlin_1_mRNA
b
diff -r ae07c55ab96b -r 160f33c6ba85 mvdb3.gff
--- a/mvdb3.gff Fri Oct 04 04:07:03 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
b
b'@@ -1,44 +0,0 @@\n-##gff-version 3\n-##sequence-region Scaffold2 1 2247300\n-Scaffold2\tWebApollo\texon\t1254745\t1254849\t.\t+\t.\tID=401F7E03FCBD10CD78911C045ACBF057;Name=401F7E03FCBD10CD78911C045ACBF057;Parent=41832FDEEC226086FDE25CFA1AADAE2D;date_last_modified=2014-08-24;date_creation=2014-08-24;owner=kpanfilio\n-Scaffold2\tWebApollo\texon\t1247878\t1248122\t.\t+\t.\tID=F2FD3567BB92973E7CC0D266CD9C3002;Name=F2FD3567BB92973E7CC0D266CD9C3002;Parent=41832FDEEC226086FDE25CFA1AADAE2D;date_last_modified=2014-08-24;date_creation=2014-08-24;owner=kpanfilio\n-Scaffold2\tWebApollo\texon\t1183361\t1183513\t.\t+\t.\tID=C602B0741979CD5F41F7092A1E68C46C;Name=C602B0741979CD5F41F7092A1E68C46C;Parent=41832FDEEC226086FDE25CFA1AADAE2D;date_last_modified=2014-08-24;date_creation=2014-08-24;owner=kpanfilio\n-Scaffold2\tWebApollo\texon\t1190237\t1190428\t.\t+\t.\tID=F204CCA66BFB64505E989AB0113F80E0;Name=F204CCA66BFB64505E989AB0113F80E0;Parent=41832FDEEC226086FDE25CFA1AADAE2D;date_last_modified=2014-08-24;date_creation=2014-08-24;owner=kpanfilio\n-Scaffold2\tWebApollo\texon\t1257900\t1257970\t.\t+\t.\tID=8D10D6C74AEB731074328D6231C3711E;Name=8D10D6C74AEB731074328D6231C3711E;Parent=41832FDEEC226086FDE25CFA1AADAE2D;date_last_modified=2014-08-24;date_creation=2014-08-24;owner=kpanfilio\n-Scaffold2\tWebApollo\texon\t1177308\t1177459\t.\t+\t.\tID=FAF84802E1B3BCBF1B34304A8C17E687;Name=FAF84802E1B3BCBF1B34304A8C17E687;Parent=41832FDEEC226086FDE25CFA1AADAE2D;date_last_modified=2014-08-24;date_creation=2014-08-24;owner=kpanfilio\n-Scaffold2\tWebApollo\texon\t1251226\t1251384\t.\t+\t.\tID=AA6625EFFFC93760257BA2AEBD9084F7;Name=AA6625EFFFC93760257BA2AEBD9084F7;Parent=41832FDEEC226086FDE25CFA1AADAE2D;date_last_modified=2014-08-24;date_creation=2014-08-24;owner=kpanfilio\n-Scaffold2\tWebApollo\texon\t1244244\t1244423\t.\t+\t.\tID=A1BAF5141ED123FAF0B13695C3399F67;Name=A1BAF5141ED123FAF0B13695C3399F67;Parent=41832FDEEC226086FDE25CFA1AADAE2D;date_last_modified=2014-08-24;date_creation=2014-08-24;owner=kpanfilio\n-Scaffold2\tWebApollo\tnon_canonical_five_prime_splice_site\t1285352\t1285352\t.\t+\t.\tID=41832FDEEC226086FDE25CFA1AADAE2D-non_canonical_five_prive_splice_site-1285351;Name=41832FDEEC226086FDE25CFA1AADAE2D-non_canonical_five_prive_splice_site-1285351;Parent=41832FDEEC226086FDE25CFA1AADAE2D;date_last_modified=2014-08-24;date_creation=2014-08-24;owner=kpanfilio\n-Scaffold2\tWebApollo\texon\t1199147\t1199311\t.\t+\t.\tID=7DCC704132150E28FB9A07E1718D77AC;Name=7DCC704132150E28FB9A07E1718D77AC;Parent=41832FDEEC226086FDE25CFA1AADAE2D;date_last_modified=2014-08-24;date_creation=2014-08-24;owner=kpanfilio\n-Scaffold2\tWebApollo\texon\t1192019\t1192263\t.\t+\t.\tID=5DC0DFF1BACA4A435123BD574A158DC3;Name=5DC0DFF1BACA4A435123BD574A158DC3;Parent=41832FDEEC226086FDE25CFA1AADAE2D;date_last_modified=2014-08-24;date_creation=2014-08-24;owner=kpanfilio\n-Scaffold2\tWebApollo\texon\t1195224\t1195412\t.\t+\t.\tID=C36A537054A80DEE326018CEB3968517;Name=C36A537054A80DEE326018CEB3968517;Parent=41832FDEEC226086FDE25CFA1AADAE2D;date_last_modified=2014-08-24;date_creation=2014-08-24;owner=kpanfilio\n-Scaffold2\tWebApollo\texon\t1242059\t1242253\t.\t+\t.\tID=7C8270DCD43F93327251E91EAADA08DC;Name=7C8270DCD43F93327251E91EAADA08DC;Parent=41832FDEEC226086FDE25CFA1AADAE2D;date_last_modified=2014-08-24;date_creation=2014-08-24;owner=kpanfilio\n-Scaffold2\tWebApollo\texon\t1285496\t1286136\t.\t+\t.\tID=7ECCDA418811FA633C27E1F67B725F2A;Name=7ECCDA418811FA633C27E1F67B725F2A;Parent=41832FDEEC226086FDE25CFA1AADAE2D;date_last_modified=2014-08-24;date_creation=2014-08-24;owner=kpanfilio\n-Scaffold2\tWebApollo\texon\t1182200\t1182500\t.\t+\t.\tID=F01FA790A090E8B667281A115E1C718C;Name=F01FA790A090E8B667281A115E1C718C;Parent=41832FDEEC226086FDE25CFA1AADAE2D;date_last_modified=2014-08-24;date_creation=2014-08-24;owner=kpanfilio\n-Scaffold2\tWebApollo\texon\t1222068\t1222331\t.\t+\t.\tID=DBF6032F0157E014674EB52BB48272DC;Name=DBF6032F0157E014674EB52BB48272DC;Parent=41832FDEEC226086FDE25CFA1AADAE2D;date_last_modified=2014-08-24;date_creation=2014-08-24;owner=kpanfilio\n-Scaffold2\tWebApollo\texon\t1190549\t1190749\t.\t+\t.\tID=AE143CA0766310EB3A1E6BD23'..b'me=C21B321082955BEEF756B7C2C6A5D096;Parent=41832FDEEC226086FDE25CFA1AADAE2D;date_last_modified=2014-08-24;date_creation=2014-08-24;owner=kpanfilio\n-Scaffold2\tWebApollo\texon\t1189584\t1189771\t.\t+\t.\tID=0C78D78BD6ACF31510F655DE39B71480;Name=0C78D78BD6ACF31510F655DE39B71480;Parent=41832FDEEC226086FDE25CFA1AADAE2D;date_last_modified=2014-08-24;date_creation=2014-08-24;owner=kpanfilio\n-Scaffold2\tWebApollo\texon\t1218961\t1219161\t.\t+\t.\tID=066A45C91A12DACCC0C5EB5B1E4CA123;Name=066A45C91A12DACCC0C5EB5B1E4CA123;Parent=41832FDEEC226086FDE25CFA1AADAE2D;date_last_modified=2014-08-24;date_creation=2014-08-24;owner=kpanfilio\n-Scaffold2\tWebApollo\texon\t1177543\t1177716\t.\t+\t.\tID=F033CCC56F48E2B806E46447EA267060;Name=F033CCC56F48E2B806E46447EA267060;Parent=41832FDEEC226086FDE25CFA1AADAE2D;date_last_modified=2014-08-24;date_creation=2014-08-24;owner=kpanfilio\n-Scaffold2\tWebApollo\texon\t1266960\t1267088\t.\t+\t.\tID=1E54500A43F613F837285D030B0F54C4;Name=1E54500A43F613F837285D030B0F54C4;Parent=41832FDEEC226086FDE25CFA1AADAE2D;date_last_modified=2014-08-24;date_creation=2014-08-24;owner=kpanfilio\n-Scaffold2\tWebApollo\texon\t1278339\t1278592\t.\t+\t.\tID=78EB00577011260745429FB168F0D9C4;Name=78EB00577011260745429FB168F0D9C4;Parent=41832FDEEC226086FDE25CFA1AADAE2D;date_last_modified=2014-08-24;date_creation=2014-08-24;owner=kpanfilio\n-Scaffold2\tWebApollo\texon\t1193579\t1193770\t.\t+\t.\tID=9F48014565E36955074793258E678A51;Name=9F48014565E36955074793258E678A51;Parent=41832FDEEC226086FDE25CFA1AADAE2D;date_last_modified=2014-08-24;date_creation=2014-08-24;owner=kpanfilio\n-Scaffold2\tWebApollo\texon\t1282265\t1282453\t.\t+\t.\tID=4573453BC6A42F32CCDB43AA3956E107;Name=4573453BC6A42F32CCDB43AA3956E107;Parent=41832FDEEC226086FDE25CFA1AADAE2D;date_last_modified=2014-08-24;date_creation=2014-08-24;owner=kpanfilio\n-Scaffold2\tWebApollo\tnon_canonical_three_prime_splice_site\t1285496\t1285496\t.\t+\t.\tID=41832FDEEC226086FDE25CFA1AADAE2D-non_canonical_three_prive_splice_site-1285495;Name=41832FDEEC226086FDE25CFA1AADAE2D-non_canonical_three_prive_splice_site-1285495;Parent=41832FDEEC226086FDE25CFA1AADAE2D;date_last_modified=2014-08-24;date_creation=2014-08-24;owner=kpanfilio\n-Scaffold2\tWebApollo\texon\t1159199\t1160031\t.\t+\t.\tID=B547501074442430E7FAF89065AF9AF5;Name=B547501074442430E7FAF89065AF9AF5;Parent=41832FDEEC226086FDE25CFA1AADAE2D;date_last_modified=2014-08-24;date_creation=2014-08-24;owner=kpanfilio\n-Scaffold2\tWebApollo\texon\t1221344\t1221502\t.\t+\t.\tID=165AA5F27B3323F4A45CE39064B070E5;Name=165AA5F27B3323F4A45CE39064B070E5;Parent=41832FDEEC226086FDE25CFA1AADAE2D;date_last_modified=2014-08-24;date_creation=2014-08-24;owner=kpanfilio\n-Scaffold2\tWebApollo\texon\t1230949\t1231157\t.\t+\t.\tID=A83A793CF6675C0372DBDECA8C7332C0;Name=A83A793CF6675C0372DBDECA8C7332C0;Parent=41832FDEEC226086FDE25CFA1AADAE2D;date_last_modified=2014-08-24;date_creation=2014-08-24;owner=kpanfilio\n-Scaffold2\tWebApollo\texon\t1184667\t1184790\t.\t+\t.\tID=32B79C620D7009F3DCC8E946BFB4558A;Name=32B79C620D7009F3DCC8E946BFB4558A;Parent=41832FDEEC226086FDE25CFA1AADAE2D;date_last_modified=2014-08-24;date_creation=2014-08-24;owner=kpanfilio\n-Scaffold2\tWebApollo\texon\t1187866\t1188029\t.\t+\t.\tID=38FD66EE4EC19C037466B82FDA8E9FAD;Name=38FD66EE4EC19C037466B82FDA8E9FAD;Parent=41832FDEEC226086FDE25CFA1AADAE2D;date_last_modified=2014-08-24;date_creation=2014-08-24;owner=kpanfilio\n-Scaffold2\tWebApollo\texon\t1174871\t1175000\t.\t+\t.\tID=F3D5FFA0634EE4DD40C3FB31887BCD57;Name=F3D5FFA0634EE4DD40C3FB31887BCD57;Parent=41832FDEEC226086FDE25CFA1AADAE2D;date_last_modified=2014-08-24;date_creation=2014-08-24;owner=kpanfilio\n-Scaffold2\tWebApollo\texon\t1270962\t1271143\t.\t+\t.\tID=FC53825CEB9A78AA28A8BD7ED2661697;Name=FC53825CEB9A78AA28A8BD7ED2661697;Parent=41832FDEEC226086FDE25CFA1AADAE2D;date_last_modified=2014-08-24;date_creation=2014-08-24;owner=kpanfilio\n-Scaffold2\tWebApollo\tCDS\t1174871\t1175000\t.\t+\t0\tID=43F646FAA11B5075698A73959D6FB383;Name=43F646FAA11B5075698A73959D6FB383;Parent=41832FDEEC226086FDE25CFA1AADAE2D;date_last_modified=2014-08-24;date_creation=2014-08-24;owner=kpanfilio\n'
b
diff -r ae07c55ab96b -r 160f33c6ba85 mvdb4.gff
--- a/mvdb4.gff Fri Oct 04 04:07:03 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
b
@@ -1,7 +0,0 @@
-##gff-version 3
-##sequence-region Scaffold2 1 2247300
-Scaffold2 WebApollo gene 1159199 1286136 . + . ID=52F3AF8B2DC566ADAB6A63D796BC8C96;Name=52F3AF8B2DC566ADAB6A63D796BC8C96;owner=kpanfilio;date_last_modified=2014-08-24;date_creation=2014-08-24
-Scaffold2 WebApollo mRNA 1159199 1286136 . + . ID=41832FDEEC226086FDE25CFA1AADAE2D;Name=spectrin beta chain;Parent=52F3AF8B2DC566ADAB6A63D796BC8C96;Note=Annotation type: Modify an existing gene model,Result of: Merging of two or more gene models.,Result of: Adding an exon to the gene model,Result of: Removing an exon from the gene model,Note to curator: final exon (3' UTR only) interrupted by gap in assembly: rendered as two separate exons with non-canonical splice sites to exclude gap nucleotide positions in excess of the length of the mapped isotig.,Added 5'UTR;Dbxref=GenBank Zootermopsis nevadensis:KDR16227.1;status=Approved;symbol=£]-Spec;owner=kpanfilio;date_creation=2014-08-24;date_last_modified=2014-08-24
-Scaffold2 WebApollo exon 1250986 1251124 . + . ID=196B75DC18386FCD03A46B68FDACA807;Name=196B75DC18386FCD03A46B68FDACA807;Parent=41832FDEEC226086FDE25CFA1AADAE2D;date_last_modified=2014-08-24;date_creation=2014-08-24;owner=kpanfilio
-Scaffold2 WebApollo exon 1200664 1200876 . + . ID=74F95DCA5FF13BA5D9099FC9EDC65062;Name=74F95DCA5FF13BA5D9099FC9EDC65062;Parent=41832FDEEC226086FDE25CFA1AADAE2D;date_last_modified=2014-08-24;date_creation=2014-08-24;owner=kpanfilio
-Scaffold2 WebApollo exon 1199927 1200166 . + . ID=07C567475620CB6A0116E49AD995A468;Name=07C567475620CB6A0116E49AD995A468;Parent=41832FDEEC226086FDE25CFA1AADAE2D;date_last_modified=2014-08-24;date_creation=2014-08-24;owner=kpanfilio