Mercurial > repos > iuc > gffcompare

diff test-data/gffcompare_out3.gtf @ 5:f99dd58de04f draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
author iuc
date Fri, 03 Feb 2023 10:57:30 +0000
parents 2bb86e2c417f
children
line wrap: on
line diff
--- a/test-data/gffcompare_out3.gtf	Thu Oct 17 03:01:26 2019 -0400
+++ b/test-data/gffcompare_out3.gtf	Fri Feb 03 10:57:30 2023 +0000
@@ -1,8 +1,8 @@
-chr1	StringTie	transcript	160930303	160940234	.	+	.	transcript_id "MSTRG.3.1"; gene_id "MSTRG.3"; gene_name "uc007del.2"; xloc "XLOC_000001"; cmp_ref "uc007del.2"; class_code "c"; tss_id "TSS1";
+chr1	StringTie	transcript	160930303	160940234	.	+	.	transcript_id "MSTRG.3.1"; gene_id "MSTRG.3"; gene_name "MSTRG.3"; xloc "XLOC_000001"; cmp_ref "MSTRG.3.1"; class_code "="; tss_id "TSS1";
 chr1	StringTie	exon	160930303	160930344	.	+	.	transcript_id "MSTRG.3.1"; gene_id "MSTRG.3"; exon_number "1";
 chr1	StringTie	exon	160938112	160938232	.	+	.	transcript_id "MSTRG.3.1"; gene_id "MSTRG.3"; exon_number "2";
 chr1	StringTie	exon	160939995	160940234	.	+	.	transcript_id "MSTRG.3.1"; gene_id "MSTRG.3"; exon_number "3";
-chr1	StringTie	transcript	160940817	160967997	.	+	.	transcript_id "MSTRG.4.1"; gene_id "MSTRG.4"; gene_name "uc007del.2"; xloc "XLOC_000001"; cmp_ref "uc007del.2"; class_code "c"; tss_id "TSS2";
+chr1	StringTie	transcript	160940817	160967997	.	+	.	transcript_id "MSTRG.4.1"; gene_id "MSTRG.4"; gene_name "MSTRG.4"; xloc "XLOC_000002"; cmp_ref "MSTRG.4.1"; class_code "="; tss_id "TSS2";
 chr1	StringTie	exon	160940817	160940994	.	+	.	transcript_id "MSTRG.4.1"; gene_id "MSTRG.4"; exon_number "1";
 chr1	StringTie	exon	160942528	160942728	.	+	.	transcript_id "MSTRG.4.1"; gene_id "MSTRG.4"; exon_number "2";
 chr1	StringTie	exon	160946534	160946666	.	+	.	transcript_id "MSTRG.4.1"; gene_id "MSTRG.4"; exon_number "3";
@@ -19,21 +19,21 @@
 chr1	StringTie	exon	160964950	160965120	.	+	.	transcript_id "MSTRG.4.1"; gene_id "MSTRG.4"; exon_number "14";
 chr1	StringTie	exon	160965673	160965788	.	+	.	transcript_id "MSTRG.4.1"; gene_id "MSTRG.4"; exon_number "15";
 chr1	StringTie	exon	160967647	160967997	.	+	.	transcript_id "MSTRG.4.1"; gene_id "MSTRG.4"; exon_number "16";
-chr1	StringTie	transcript	160968644	160972020	.	+	.	transcript_id "MSTRG.5.1"; gene_id "MSTRG.5"; gene_name "uc007del.2"; xloc "XLOC_000001"; cmp_ref "uc007del.2"; class_code "c"; tss_id "TSS3";
+chr1	StringTie	transcript	160968644	160972020	.	+	.	transcript_id "MSTRG.5.1"; gene_id "MSTRG.5"; gene_name "MSTRG.5"; xloc "XLOC_000003"; cmp_ref "MSTRG.5.1"; class_code "="; tss_id "TSS3";
 chr1	StringTie	exon	160968644	160972020	.	+	.	transcript_id "MSTRG.5.1"; gene_id "MSTRG.5"; exon_number "1";
-chr1	StringTie	transcript	160972938	160974977	.	+	.	transcript_id "MSTRG.6.1"; gene_id "MSTRG.6"; gene_name "uc007del.2"; xloc "XLOC_000001"; cmp_ref "uc007del.2"; class_code "c"; tss_id "TSS4";
+chr1	StringTie	transcript	160972938	160974977	.	+	.	transcript_id "MSTRG.6.1"; gene_id "MSTRG.6"; gene_name "MSTRG.6"; xloc "XLOC_000004"; cmp_ref "MSTRG.6.1"; class_code "="; tss_id "TSS4";
 chr1	StringTie	exon	160972938	160974977	.	+	.	transcript_id "MSTRG.6.1"; gene_id "MSTRG.6"; exon_number "1";
-chr1	StringTie	transcript	161003085	161003516	.	+	.	transcript_id "MSTRG.7.1"; gene_id "MSTRG.7"; xloc "XLOC_000002"; class_code "u"; tss_id "TSS5";
+chr1	StringTie	transcript	161003085	161003516	.	+	.	transcript_id "MSTRG.7.1"; gene_id "MSTRG.7"; gene_name "MSTRG.7"; xloc "XLOC_000005"; cmp_ref "MSTRG.7.1"; class_code "="; tss_id "TSS5";
 chr1	StringTie	exon	161003085	161003516	.	+	.	transcript_id "MSTRG.7.1"; gene_id "MSTRG.7"; exon_number "1";
-chr1	StringTie	transcript	161006151	161006466	.	+	.	transcript_id "MSTRG.10.1"; gene_id "MSTRG.10"; xloc "XLOC_000003"; class_code "u"; tss_id "TSS6";
+chr1	StringTie	transcript	161006151	161006466	.	+	.	transcript_id "MSTRG.10.1"; gene_id "MSTRG.10"; gene_name "MSTRG.10"; xloc "XLOC_000006"; cmp_ref "MSTRG.10.1"; class_code "="; tss_id "TSS6";
 chr1	StringTie	exon	161006151	161006466	.	+	.	transcript_id "MSTRG.10.1"; gene_id "MSTRG.10"; exon_number "1";
-chr1	StringTie	transcript	161008375	161008625	.	+	.	transcript_id "MSTRG.12.1"; gene_id "MSTRG.12"; xloc "XLOC_000004"; class_code "u"; tss_id "TSS7";
+chr1	StringTie	transcript	161008375	161008625	.	+	.	transcript_id "MSTRG.12.1"; gene_id "MSTRG.12"; gene_name "MSTRG.12"; xloc "XLOC_000007"; cmp_ref "MSTRG.12.1"; class_code "="; tss_id "TSS7";
 chr1	StringTie	exon	161008375	161008625	.	+	.	transcript_id "MSTRG.12.1"; gene_id "MSTRG.12"; exon_number "1";
-chr1	StringTie	transcript	161009768	161010195	.	+	.	transcript_id "MSTRG.13.1"; gene_id "MSTRG.13"; xloc "XLOC_000005"; class_code "u"; tss_id "TSS8";
+chr1	StringTie	transcript	161009768	161010195	.	+	.	transcript_id "MSTRG.13.1"; gene_id "MSTRG.13"; gene_name "MSTRG.13"; xloc "XLOC_000008"; cmp_ref "MSTRG.13.1"; class_code "="; tss_id "TSS8";
 chr1	StringTie	exon	161009768	161010195	.	+	.	transcript_id "MSTRG.13.1"; gene_id "MSTRG.13"; exon_number "1";
-chr1	StringTie	transcript	161019713	161019962	.	+	.	transcript_id "MSTRG.14.1"; gene_id "MSTRG.14"; gene_name "uc007der.1"; xloc "XLOC_000006"; cmp_ref "uc007der.1"; class_code "x"; tss_id "TSS9";
+chr1	StringTie	transcript	161019713	161019962	.	+	.	transcript_id "MSTRG.14.1"; gene_id "MSTRG.14"; gene_name "MSTRG.14"; xloc "XLOC_000009"; cmp_ref "MSTRG.14.1"; class_code "="; tss_id "TSS9";
 chr1	StringTie	exon	161019713	161019962	.	+	.	transcript_id "MSTRG.14.1"; gene_id "MSTRG.14"; exon_number "1";
-chr1	StringTie	transcript	161034351	161038539	.	+	.	transcript_id "MSTRG.16.1"; gene_id "MSTRG.16"; gene_name "uc007dev.1"; xloc "XLOC_000007"; cmp_ref "uc007dev.1"; class_code "j"; tss_id "TSS10";
+chr1	StringTie	transcript	161034351	161038539	.	+	.	transcript_id "MSTRG.16.1"; gene_id "MSTRG.16"; gene_name "MSTRG.16"; xloc "XLOC_000010"; cmp_ref "MSTRG.16.1"; class_code "="; tss_id "TSS10";
 chr1	StringTie	exon	161034351	161034719	.	+	.	transcript_id "MSTRG.16.1"; gene_id "MSTRG.16"; exon_number "1";
 chr1	StringTie	exon	161035752	161035804	.	+	.	transcript_id "MSTRG.16.1"; gene_id "MSTRG.16"; exon_number "2";
 chr1	StringTie	exon	161035983	161036014	.	+	.	transcript_id "MSTRG.16.1"; gene_id "MSTRG.16"; exon_number "3";
@@ -45,7 +45,7 @@
 chr1	StringTie	exon	161037995	161038037	.	+	.	transcript_id "MSTRG.16.1"; gene_id "MSTRG.16"; exon_number "9";
 chr1	StringTie	exon	161038225	161038272	.	+	.	transcript_id "MSTRG.16.1"; gene_id "MSTRG.16"; exon_number "10";
 chr1	StringTie	exon	161038457	161038539	.	+	.	transcript_id "MSTRG.16.1"; gene_id "MSTRG.16"; exon_number "11";
-chr1	StringTie	transcript	161034584	161038539	.	+	.	transcript_id "MSTRG.16.2"; gene_id "MSTRG.16"; gene_name "uc007dev.1"; xloc "XLOC_000007"; cmp_ref "uc007dev.1"; class_code "j"; tss_id "TSS11";
+chr1	StringTie	transcript	161034584	161038539	.	+	.	transcript_id "MSTRG.16.2"; gene_id "MSTRG.16"; gene_name "MSTRG.16"; xloc "XLOC_000010"; cmp_ref "MSTRG.16.2"; class_code "="; tss_id "TSS11";
 chr1	StringTie	exon	161034584	161034719	.	+	.	transcript_id "MSTRG.16.2"; gene_id "MSTRG.16"; exon_number "1";
 chr1	StringTie	exon	161035752	161035804	.	+	.	transcript_id "MSTRG.16.2"; gene_id "MSTRG.16"; exon_number "2";
 chr1	StringTie	exon	161035983	161036014	.	+	.	transcript_id "MSTRG.16.2"; gene_id "MSTRG.16"; exon_number "3";
@@ -58,7 +58,7 @@
 chr1	StringTie	exon	161037995	161038037	.	+	.	transcript_id "MSTRG.16.2"; gene_id "MSTRG.16"; exon_number "10";
 chr1	StringTie	exon	161038225	161038272	.	+	.	transcript_id "MSTRG.16.2"; gene_id "MSTRG.16"; exon_number "11";
 chr1	StringTie	exon	161038457	161038539	.	+	.	transcript_id "MSTRG.16.2"; gene_id "MSTRG.16"; exon_number "12";
-chr1	StringTie	transcript	161034642	161038338	.	+	.	transcript_id "MSTRG.16.3"; gene_id "MSTRG.16"; gene_name "uc007dev.1"; xloc "XLOC_000007"; cmp_ref "uc007dev.1"; class_code "j"; tss_id "TSS11";
+chr1	StringTie	transcript	161034642	161038338	.	+	.	transcript_id "MSTRG.16.3"; gene_id "MSTRG.16"; gene_name "MSTRG.16"; xloc "XLOC_000010"; cmp_ref "MSTRG.16.3"; class_code "="; tss_id "TSS11";
 chr1	StringTie	exon	161034642	161035194	.	+	.	transcript_id "MSTRG.16.3"; gene_id "MSTRG.16"; exon_number "1";
 chr1	StringTie	exon	161035752	161035804	.	+	.	transcript_id "MSTRG.16.3"; gene_id "MSTRG.16"; exon_number "2";
 chr1	StringTie	exon	161035983	161036014	.	+	.	transcript_id "MSTRG.16.3"; gene_id "MSTRG.16"; exon_number "3";
@@ -70,7 +70,7 @@
 chr1	StringTie	exon	161037505	161037547	.	+	.	transcript_id "MSTRG.16.3"; gene_id "MSTRG.16"; exon_number "9";
 chr1	StringTie	exon	161037995	161038037	.	+	.	transcript_id "MSTRG.16.3"; gene_id "MSTRG.16"; exon_number "10";
 chr1	StringTie	exon	161038225	161038338	.	+	.	transcript_id "MSTRG.16.3"; gene_id "MSTRG.16"; exon_number "11";
-chr1	StringTie	transcript	161035095	161038539	.	+	.	transcript_id "MSTRG.16.4"; gene_id "MSTRG.16"; gene_name "uc007dev.1"; xloc "XLOC_000007"; cmp_ref "uc007dev.1"; class_code "j"; tss_id "TSS12";
+chr1	StringTie	transcript	161035095	161038539	.	+	.	transcript_id "MSTRG.16.4"; gene_id "MSTRG.16"; gene_name "MSTRG.16"; xloc "XLOC_000010"; cmp_ref "MSTRG.16.4"; class_code "="; tss_id "TSS12";
 chr1	StringTie	exon	161035095	161035194	.	+	.	transcript_id "MSTRG.16.4"; gene_id "MSTRG.16"; exon_number "1";
 chr1	StringTie	exon	161035752	161035804	.	+	.	transcript_id "MSTRG.16.4"; gene_id "MSTRG.16"; exon_number "2";
 chr1	StringTie	exon	161035983	161036014	.	+	.	transcript_id "MSTRG.16.4"; gene_id "MSTRG.16"; exon_number "3";
@@ -82,7 +82,7 @@
 chr1	StringTie	exon	161037995	161038037	.	+	.	transcript_id "MSTRG.16.4"; gene_id "MSTRG.16"; exon_number "9";
 chr1	StringTie	exon	161038225	161038272	.	+	.	transcript_id "MSTRG.16.4"; gene_id "MSTRG.16"; exon_number "10";
 chr1	StringTie	exon	161038457	161038539	.	+	.	transcript_id "MSTRG.16.4"; gene_id "MSTRG.16"; exon_number "11";
-chr1	StringTie	transcript	161035164	161038539	.	+	.	transcript_id "MSTRG.16.5"; gene_id "MSTRG.16"; gene_name "uc007dev.1"; xloc "XLOC_000007"; cmp_ref "uc007dev.1"; class_code "="; tss_id "TSS12";
+chr1	StringTie	transcript	161035164	161038539	.	+	.	transcript_id "MSTRG.16.5"; gene_id "MSTRG.16"; gene_name "MSTRG.16"; xloc "XLOC_000010"; cmp_ref "MSTRG.16.5"; class_code "="; tss_id "TSS12";
 chr1	StringTie	exon	161035164	161035194	.	+	.	transcript_id "MSTRG.16.5"; gene_id "MSTRG.16"; exon_number "1";
 chr1	StringTie	exon	161035752	161035804	.	+	.	transcript_id "MSTRG.16.5"; gene_id "MSTRG.16"; exon_number "2";
 chr1	StringTie	exon	161035983	161036014	.	+	.	transcript_id "MSTRG.16.5"; gene_id "MSTRG.16"; exon_number "3";
@@ -94,7 +94,7 @@
 chr1	StringTie	exon	161037995	161038037	.	+	.	transcript_id "MSTRG.16.5"; gene_id "MSTRG.16"; exon_number "9";
 chr1	StringTie	exon	161038225	161038272	.	+	.	transcript_id "MSTRG.16.5"; gene_id "MSTRG.16"; exon_number "10";
 chr1	StringTie	exon	161038457	161038539	.	+	.	transcript_id "MSTRG.16.5"; gene_id "MSTRG.16"; exon_number "11";
-chr1	StringTie	transcript	161041562	161070639	.	+	.	transcript_id "MSTRG.18.1"; gene_id "MSTRG.18"; gene_name "uc007dey.2"; xloc "XLOC_000008"; cmp_ref "uc007dey.2"; class_code "s"; tss_id "TSS13";
+chr1	StringTie	transcript	161041562	161070639	.	+	.	transcript_id "MSTRG.18.1"; gene_id "MSTRG.18"; gene_name "MSTRG.18"; xloc "XLOC_000011"; cmp_ref "MSTRG.18.1"; class_code "="; tss_id "TSS13";
 chr1	StringTie	exon	161041562	161041930	.	+	.	transcript_id "MSTRG.18.1"; gene_id "MSTRG.18"; exon_number "1";
 chr1	StringTie	exon	161043613	161043688	.	+	.	transcript_id "MSTRG.18.1"; gene_id "MSTRG.18"; exon_number "2";
 chr1	StringTie	exon	161044959	161045069	.	+	.	transcript_id "MSTRG.18.1"; gene_id "MSTRG.18"; exon_number "3";
@@ -111,26 +111,26 @@
 chr1	StringTie	exon	161065225	161065291	.	+	.	transcript_id "MSTRG.18.1"; gene_id "MSTRG.18"; exon_number "14";
 chr1	StringTie	exon	161069080	161069179	.	+	.	transcript_id "MSTRG.18.1"; gene_id "MSTRG.18"; exon_number "15";
 chr1	StringTie	exon	161069993	161070639	.	+	.	transcript_id "MSTRG.18.1"; gene_id "MSTRG.18"; exon_number "16";
-chr1	StringTie	transcript	161045151	161056533	.	+	.	transcript_id "MSTRG.18.2"; gene_id "MSTRG.18"; gene_name "uc007dey.2"; xloc "XLOC_000008"; cmp_ref "uc007dey.2"; class_code "s"; tss_id "TSS14";
+chr1	StringTie	transcript	161045151	161056533	.	+	.	transcript_id "MSTRG.18.2"; gene_id "MSTRG.18"; gene_name "MSTRG.18"; xloc "XLOC_000011"; cmp_ref "MSTRG.18.2"; class_code "="; tss_id "TSS14";
 chr1	StringTie	exon	161045151	161045476	.	+	.	transcript_id "MSTRG.18.2"; gene_id "MSTRG.18"; exon_number "1";
 chr1	StringTie	exon	161046777	161046929	.	+	.	transcript_id "MSTRG.18.2"; gene_id "MSTRG.18"; exon_number "2";
 chr1	StringTie	exon	161049938	161050000	.	+	.	transcript_id "MSTRG.18.2"; gene_id "MSTRG.18"; exon_number "3";
 chr1	StringTie	exon	161051331	161051438	.	+	.	transcript_id "MSTRG.18.2"; gene_id "MSTRG.18"; exon_number "4";
 chr1	StringTie	exon	161053941	161054120	.	+	.	transcript_id "MSTRG.18.2"; gene_id "MSTRG.18"; exon_number "5";
 chr1	StringTie	exon	161056461	161056533	.	+	.	transcript_id "MSTRG.18.2"; gene_id "MSTRG.18"; exon_number "6";
-chr1	StringTie	transcript	161070945	161078458	.	+	.	transcript_id "MSTRG.20.1"; gene_id "MSTRG.20"; gene_name "uc007dfd.3"; xloc "XLOC_000009"; cmp_ref "uc007dfd.3"; class_code "c"; tss_id "TSS15";
+chr1	StringTie	transcript	161070945	161078458	.	+	.	transcript_id "MSTRG.20.1"; gene_id "MSTRG.20"; gene_name "MSTRG.20"; xloc "XLOC_000012"; cmp_ref "MSTRG.20.1"; class_code "="; tss_id "TSS15";
 chr1	StringTie	exon	161070945	161071356	.	+	.	transcript_id "MSTRG.20.1"; gene_id "MSTRG.20"; exon_number "1";
 chr1	StringTie	exon	161074757	161074930	.	+	.	transcript_id "MSTRG.20.1"; gene_id "MSTRG.20"; exon_number "2";
 chr1	StringTie	exon	161078329	161078458	.	+	.	transcript_id "MSTRG.20.1"; gene_id "MSTRG.20"; exon_number "3";
-chr1	StringTie	transcript	161082956	161083421	.	+	.	transcript_id "MSTRG.21.1"; gene_id "MSTRG.21"; gene_name "uc007dfe.4"; xloc "XLOC_000009"; cmp_ref "uc007dfe.4"; class_code "c"; tss_id "TSS16";
+chr1	StringTie	transcript	161082956	161083421	.	+	.	transcript_id "MSTRG.21.1"; gene_id "MSTRG.21"; gene_name "MSTRG.21"; xloc "XLOC_000013"; cmp_ref "MSTRG.21.1"; class_code "="; tss_id "TSS16";
 chr1	StringTie	exon	161082956	161083421	.	+	.	transcript_id "MSTRG.21.1"; gene_id "MSTRG.21"; exon_number "1";
-chr1	StringTie	transcript	161084121	161084344	.	+	.	transcript_id "MSTRG.22.1"; gene_id "MSTRG.22"; gene_name "uc007dfe.4"; xloc "XLOC_000009"; cmp_ref "uc007dfe.4"; class_code "c"; tss_id "TSS17";
+chr1	StringTie	transcript	161084121	161084344	.	+	.	transcript_id "MSTRG.22.1"; gene_id "MSTRG.22"; gene_name "MSTRG.22"; xloc "XLOC_000014"; cmp_ref "MSTRG.22.1"; class_code "="; tss_id "TSS17";
 chr1	StringTie	exon	161084121	161084344	.	+	.	transcript_id "MSTRG.22.1"; gene_id "MSTRG.22"; exon_number "1";
-chr1	StringTie	transcript	161085014	161086329	.	+	.	transcript_id "MSTRG.23.1"; gene_id "MSTRG.23"; gene_name "uc056yep.1"; xloc "XLOC_000009"; cmp_ref "uc056yep.1"; class_code "c"; tss_id "TSS18";
+chr1	StringTie	transcript	161085014	161086329	.	+	.	transcript_id "MSTRG.23.1"; gene_id "MSTRG.23"; gene_name "MSTRG.23"; xloc "XLOC_000015"; cmp_ref "MSTRG.23.1"; class_code "="; tss_id "TSS18";
 chr1	StringTie	exon	161085014	161086329	.	+	.	transcript_id "MSTRG.23.1"; gene_id "MSTRG.23"; exon_number "1";
-chr1	StringTie	transcript	161088497	161088913	.	+	.	transcript_id "MSTRG.24.1"; gene_id "MSTRG.24"; gene_name "uc007dff.1"; xloc "XLOC_000010"; cmp_ref "uc007dff.1"; class_code "x"; tss_id "TSS19";
+chr1	StringTie	transcript	161088497	161088913	.	+	.	transcript_id "MSTRG.24.1"; gene_id "MSTRG.24"; gene_name "MSTRG.24"; xloc "XLOC_000016"; cmp_ref "MSTRG.24.1"; class_code "="; tss_id "TSS19";
 chr1	StringTie	exon	161088497	161088913	.	+	.	transcript_id "MSTRG.24.1"; gene_id "MSTRG.24"; exon_number "1";
-chr1	StringTie	transcript	161089415	161131512	.	+	.	transcript_id "MSTRG.26.1"; gene_id "MSTRG.26"; gene_name "uc007dff.1"; xloc "XLOC_000011"; cmp_ref "uc007dff.1"; class_code "s"; tss_id "TSS20";
+chr1	StringTie	transcript	161089415	161131512	.	+	.	transcript_id "MSTRG.26.1"; gene_id "MSTRG.26"; gene_name "MSTRG.26"; xloc "XLOC_000017"; cmp_ref "MSTRG.26.1"; class_code "="; tss_id "TSS20";
 chr1	StringTie	exon	161089415	161090511	.	+	.	transcript_id "MSTRG.26.1"; gene_id "MSTRG.26"; exon_number "1";
 chr1	StringTie	exon	161093681	161093787	.	+	.	transcript_id "MSTRG.26.1"; gene_id "MSTRG.26"; exon_number "2";
 chr1	StringTie	exon	161095529	161095737	.	+	.	transcript_id "MSTRG.26.1"; gene_id "MSTRG.26"; exon_number "3";
@@ -143,28 +143,28 @@
 chr1	StringTie	exon	161109222	161109795	.	+	.	transcript_id "MSTRG.26.1"; gene_id "MSTRG.26"; exon_number "10";
 chr1	StringTie	exon	161130389	161130452	.	+	.	transcript_id "MSTRG.26.1"; gene_id "MSTRG.26"; exon_number "11";
 chr1	StringTie	exon	161131363	161131512	.	+	.	transcript_id "MSTRG.26.1"; gene_id "MSTRG.26"; exon_number "12";
-chr1	StringTie	transcript	161123665	161123877	.	+	.	transcript_id "MSTRG.28.1"; gene_id "MSTRG.28"; gene_name "uc007dff.1"; xloc "XLOC_000012"; cmp_ref "uc007dff.1"; class_code "i"; tss_id "TSS21";
+chr1	StringTie	transcript	161123665	161123877	.	+	.	transcript_id "MSTRG.28.1"; gene_id "MSTRG.28"; gene_name "MSTRG.28"; xloc "XLOC_000018"; cmp_ref "MSTRG.28.1"; class_code "="; tss_id "TSS21";
 chr1	StringTie	exon	161123665	161123877	.	+	.	transcript_id "MSTRG.28.1"; gene_id "MSTRG.28"; exon_number "1";
-chr1	StringTie	transcript	29485012	29485458	.	-	.	transcript_id "MSTRG.1.1"; gene_id "MSTRG.1"; xloc "XLOC_000013"; class_code "u"; tss_id "TSS22";
+chr1	StringTie	transcript	29485012	29485458	.	-	.	transcript_id "MSTRG.1.1"; gene_id "MSTRG.1"; gene_name "MSTRG.1"; xloc "XLOC_000019"; cmp_ref "MSTRG.1.1"; class_code "="; tss_id "TSS22";
 chr1	StringTie	exon	29485012	29485458	.	-	.	transcript_id "MSTRG.1.1"; gene_id "MSTRG.1"; exon_number "1";
-chr1	StringTie	transcript	86909344	86909692	.	-	.	transcript_id "MSTRG.2.1"; gene_id "MSTRG.2"; xloc "XLOC_000014"; class_code "u"; tss_id "TSS23";
+chr1	StringTie	transcript	86909344	86909692	.	-	.	transcript_id "MSTRG.2.1"; gene_id "MSTRG.2"; gene_name "MSTRG.2"; xloc "XLOC_000020"; cmp_ref "MSTRG.2.1"; class_code "="; tss_id "TSS23";
 chr1	StringTie	exon	86909344	86909692	.	-	.	transcript_id "MSTRG.2.1"; gene_id "MSTRG.2"; exon_number "1";
-chr1	StringTie	transcript	161003658	161004769	.	-	.	transcript_id "MSTRG.8.1"; gene_id "MSTRG.8"; xloc "XLOC_000015"; class_code "u"; tss_id "TSS24";
+chr1	StringTie	transcript	161003658	161004769	.	-	.	transcript_id "MSTRG.8.1"; gene_id "MSTRG.8"; gene_name "MSTRG.8"; xloc "XLOC_000021"; cmp_ref "MSTRG.8.1"; class_code "="; tss_id "TSS24";
 chr1	StringTie	exon	161003658	161004769	.	-	.	transcript_id "MSTRG.8.1"; gene_id "MSTRG.8"; exon_number "1";
-chr1	StringTie	transcript	161005030	161005802	.	-	.	transcript_id "MSTRG.9.1"; gene_id "MSTRG.9"; xloc "XLOC_000016"; class_code "u"; tss_id "TSS25";
+chr1	StringTie	transcript	161005030	161005802	.	-	.	transcript_id "MSTRG.9.1"; gene_id "MSTRG.9"; gene_name "MSTRG.9"; xloc "XLOC_000022"; cmp_ref "MSTRG.9.1"; class_code "="; tss_id "TSS25";
 chr1	StringTie	exon	161005030	161005802	.	-	.	transcript_id "MSTRG.9.1"; gene_id "MSTRG.9"; exon_number "1";
-chr1	StringTie	transcript	161007444	161007700	.	-	.	transcript_id "MSTRG.11.1"; gene_id "MSTRG.11"; xloc "XLOC_000017"; class_code "u"; tss_id "TSS26";
+chr1	StringTie	transcript	161007444	161007700	.	-	.	transcript_id "MSTRG.11.1"; gene_id "MSTRG.11"; gene_name "MSTRG.11"; xloc "XLOC_000023"; cmp_ref "MSTRG.11.1"; class_code "="; tss_id "TSS26";
 chr1	StringTie	exon	161007444	161007700	.	-	.	transcript_id "MSTRG.11.1"; gene_id "MSTRG.11"; exon_number "1";
-chr1	StringTie	transcript	161032044	161032396	.	-	.	transcript_id "MSTRG.15.1"; gene_id "MSTRG.15"; gene_name "uc007des.1"; xloc "XLOC_000018"; cmp_ref "uc007des.1"; class_code "c"; tss_id "TSS27";
+chr1	StringTie	transcript	161032044	161032396	.	-	.	transcript_id "MSTRG.15.1"; gene_id "MSTRG.15"; gene_name "MSTRG.15"; xloc "XLOC_000024"; cmp_ref "MSTRG.15.1"; class_code "="; tss_id "TSS27";
 chr1	StringTie	exon	161032044	161032396	.	-	.	transcript_id "MSTRG.15.1"; gene_id "MSTRG.15"; exon_number "1";
-chr1	StringTie	transcript	161041525	161050001	.	-	.	transcript_id "MSTRG.17.1"; gene_id "MSTRG.17"; gene_name "uc007dey.2"; xloc "XLOC_000019"; cmp_ref "uc007dey.2"; class_code "c"; tss_id "TSS28";
+chr1	StringTie	transcript	161041525	161050001	.	-	.	transcript_id "MSTRG.17.1"; gene_id "MSTRG.17"; gene_name "MSTRG.17"; xloc "XLOC_000025"; cmp_ref "MSTRG.17.1"; class_code "="; tss_id "TSS28";
 chr1	StringTie	exon	161041525	161041930	.	-	.	transcript_id "MSTRG.17.1"; gene_id "MSTRG.17"; exon_number "1";
 chr1	StringTie	exon	161043613	161043688	.	-	.	transcript_id "MSTRG.17.1"; gene_id "MSTRG.17"; exon_number "2";
 chr1	StringTie	exon	161044959	161045069	.	-	.	transcript_id "MSTRG.17.1"; gene_id "MSTRG.17"; exon_number "3";
 chr1	StringTie	exon	161045258	161045476	.	-	.	transcript_id "MSTRG.17.1"; gene_id "MSTRG.17"; exon_number "4";
 chr1	StringTie	exon	161046777	161046929	.	-	.	transcript_id "MSTRG.17.1"; gene_id "MSTRG.17"; exon_number "5";
 chr1	StringTie	exon	161049938	161050001	.	-	.	transcript_id "MSTRG.17.1"; gene_id "MSTRG.17"; exon_number "6";
-chr1	StringTie	transcript	161051330	161070504	.	-	.	transcript_id "MSTRG.19.1"; gene_id "MSTRG.19"; gene_name "uc007dey.2"; xloc "XLOC_000019"; cmp_ref "uc007dey.2"; class_code "c"; tss_id "TSS29";
+chr1	StringTie	transcript	161051330	161070504	.	-	.	transcript_id "MSTRG.19.1"; gene_id "MSTRG.19"; gene_name "MSTRG.19"; xloc "XLOC_000026"; cmp_ref "MSTRG.19.1"; class_code "="; tss_id "TSS29";
 chr1	StringTie	exon	161051330	161051438	.	-	.	transcript_id "MSTRG.19.1"; gene_id "MSTRG.19"; exon_number "1";
 chr1	StringTie	exon	161053941	161054120	.	-	.	transcript_id "MSTRG.19.1"; gene_id "MSTRG.19"; exon_number "2";
 chr1	StringTie	exon	161056461	161056530	.	-	.	transcript_id "MSTRG.19.1"; gene_id "MSTRG.19"; exon_number "3";
@@ -176,7 +176,7 @@
 chr1	StringTie	exon	161065225	161065291	.	-	.	transcript_id "MSTRG.19.1"; gene_id "MSTRG.19"; exon_number "9";
 chr1	StringTie	exon	161069080	161069179	.	-	.	transcript_id "MSTRG.19.1"; gene_id "MSTRG.19"; exon_number "10";
 chr1	StringTie	exon	161069993	161070504	.	-	.	transcript_id "MSTRG.19.1"; gene_id "MSTRG.19"; exon_number "11";
-chr1	StringTie	transcript	161051331	161070649	.	-	.	transcript_id "MSTRG.19.2"; gene_id "MSTRG.19"; gene_name "uc007dey.2"; xloc "XLOC_000019"; cmp_ref "uc007dey.2"; class_code "j"; tss_id "TSS30";
+chr1	StringTie	transcript	161051331	161070649	.	-	.	transcript_id "MSTRG.19.2"; gene_id "MSTRG.19"; gene_name "MSTRG.19"; xloc "XLOC_000026"; cmp_ref "MSTRG.19.2"; class_code "="; tss_id "TSS30";
 chr1	StringTie	exon	161051331	161051438	.	-	.	transcript_id "MSTRG.19.2"; gene_id "MSTRG.19"; exon_number "1";
 chr1	StringTie	exon	161056461	161056530	.	-	.	transcript_id "MSTRG.19.2"; gene_id "MSTRG.19"; exon_number "2";
 chr1	StringTie	exon	161057447	161057553	.	-	.	transcript_id "MSTRG.19.2"; gene_id "MSTRG.19"; exon_number "3";
@@ -187,9 +187,9 @@
 chr1	StringTie	exon	161065225	161065291	.	-	.	transcript_id "MSTRG.19.2"; gene_id "MSTRG.19"; exon_number "8";
 chr1	StringTie	exon	161069080	161069179	.	-	.	transcript_id "MSTRG.19.2"; gene_id "MSTRG.19"; exon_number "9";
 chr1	StringTie	exon	161069993	161070649	.	-	.	transcript_id "MSTRG.19.2"; gene_id "MSTRG.19"; exon_number "10";
-chr1	StringTie	transcript	161088915	161090275	.	-	.	transcript_id "MSTRG.25.1"; gene_id "MSTRG.25"; gene_name "uc007dff.1"; xloc "XLOC_000020"; cmp_ref "uc007dff.1"; class_code "c"; tss_id "TSS31";
+chr1	StringTie	transcript	161088915	161090275	.	-	.	transcript_id "MSTRG.25.1"; gene_id "MSTRG.25"; gene_name "MSTRG.25"; xloc "XLOC_000027"; cmp_ref "MSTRG.25.1"; class_code "="; tss_id "TSS31";
 chr1	StringTie	exon	161088915	161090275	.	-	.	transcript_id "MSTRG.25.1"; gene_id "MSTRG.25"; exon_number "1";
-chr1	StringTie	transcript	161090412	161131492	.	-	.	transcript_id "MSTRG.27.1"; gene_id "MSTRG.27"; gene_name "uc007dff.1"; xloc "XLOC_000020"; cmp_ref "uc007dff.1"; class_code "="; tss_id "TSS32";
+chr1	StringTie	transcript	161090412	161131492	.	-	.	transcript_id "MSTRG.27.1"; gene_id "MSTRG.27"; gene_name "MSTRG.27"; xloc "XLOC_000028"; cmp_ref "MSTRG.27.1"; class_code "="; tss_id "TSS32";
 chr1	StringTie	exon	161090412	161090511	.	-	.	transcript_id "MSTRG.27.1"; gene_id "MSTRG.27"; exon_number "1";
 chr1	StringTie	exon	161093681	161093787	.	-	.	transcript_id "MSTRG.27.1"; gene_id "MSTRG.27"; exon_number "2";
 chr1	StringTie	exon	161095529	161095737	.	-	.	transcript_id "MSTRG.27.1"; gene_id "MSTRG.27"; exon_number "3";
@@ -202,5 +202,5 @@
 chr1	StringTie	exon	161109222	161109795	.	-	.	transcript_id "MSTRG.27.1"; gene_id "MSTRG.27"; exon_number "10";
 chr1	StringTie	exon	161130389	161130452	.	-	.	transcript_id "MSTRG.27.1"; gene_id "MSTRG.27"; exon_number "11";
 chr1	StringTie	exon	161131363	161131492	.	-	.	transcript_id "MSTRG.27.1"; gene_id "MSTRG.27"; exon_number "12";
-chr1	StringTie	transcript	192074156	192074378	.	-	.	transcript_id "MSTRG.29.1"; gene_id "MSTRG.29"; xloc "XLOC_000021"; class_code "u"; tss_id "TSS33";
+chr1	StringTie	transcript	192074156	192074378	.	-	.	transcript_id "MSTRG.29.1"; gene_id "MSTRG.29"; gene_name "MSTRG.29"; xloc "XLOC_000029"; cmp_ref "MSTRG.29.1"; class_code "="; tss_id "TSS33";
 chr1	StringTie	exon	192074156	192074378	.	-	.	transcript_id "MSTRG.29.1"; gene_id "MSTRG.29"; exon_number "1";