scout-browser 4.88.1__py3-none-any.whl → 4.89__py3-none-any.whl

scout/demo/resources/ensembl_exons_38_reduced.txt

@@ -15662,6 +15662,172 @@ Chromosome/scaffold name	Gene stable ID	Transcript stable ID	Exon stable ID	Exon
 5	ENSG00000170458	ENST00000401743	ENSE00001862834	140011313	140012565			140011313	140011440	-1	3
 5	ENSG00000170458	ENST00000401743	ENSE00001429397	140012654	140012877	140012657	140012877			-1	2
 5	ENSG00000170458	ENST00000401743	ENSE00001554029	140013116	140013286	140013116	140013286			-1	1
+5	ENSG00000205571	ENST00000511812	ENSE00002054021	70049638	70049766	70049638	70049685			1	1
+5	ENSG00000205571	ENST00000511812	ENSE00001725187	70063415	70063486					1	2
+5	ENSG00000205571	ENST00000511812	ENSE00003668426	70065965	70066084					1	3
+5	ENSG00000205571	ENST00000511812	ENSE00003698225	70067294	70067446					1	4
+5	ENSG00000205571	ENST00000511812	ENSE00003550962	70069235	70069330					1	5
+5	ENSG00000205571	ENST00000511812	ENSE00003620900	70070641	70070751					1	6
+5	ENSG00000205571	ENST00000511812	ENSE00002055618	70076521	70076706			70076572	70076706	1	7
+5	ENSG00000205571	ENST00000626847	ENSE00001725187	70063415	70063486					1	2
+5	ENSG00000205571	ENST00000626847	ENSE00003668426	70065965	70066084					1	3
+5	ENSG00000205571	ENST00000626847	ENSE00003698225	70067294	70067446					1	5
+5	ENSG00000205571	ENST00000626847	ENSE00003550962	70069235	70069330					1	6
+5	ENSG00000205571	ENST00000626847	ENSE00003620900	70070641	70070751					1	7
+5	ENSG00000205571	ENST00000626847	ENSE00003762300	70049654	70049766	70049654	70049685			1	1
+5	ENSG00000205571	ENST00000626847	ENSE00003579743	70066934	70067134					1	4
+5	ENSG00000205571	ENST00000626847	ENSE00003765895	70077019	70077592			70077034	70077592	1	8
+5	ENSG00000205571	ENST00000506734	ENSE00001725187	70063415	70063486					1	2
+5	ENSG00000205571	ENST00000506734	ENSE00003668426	70065965	70066084					1	3
+5	ENSG00000205571	ENST00000506734	ENSE00003698225	70067294	70067446					1	5
+5	ENSG00000205571	ENST00000506734	ENSE00003550962	70069235	70069330					1	6
+5	ENSG00000205571	ENST00000506734	ENSE00003620900	70070641	70070751					1	7
+5	ENSG00000205571	ENST00000506734	ENSE00003579743	70066934	70067134					1	4
+5	ENSG00000205571	ENST00000506734	ENSE00002041070	70049657	70049766	70049657	70049685			1	1
+5	ENSG00000205571	ENST00000506734	ENSE00002038304	70071282	70071390			70071333	70071390	1	8
+5	ENSG00000205571	ENST00000506734	ENSE00002033350	70077019	70077596			70077019	70077596	1	9
+5	ENSG00000205571	ENST00000380742	ENSE00001725187	70063415	70063486					1	2
+5	ENSG00000205571	ENST00000380742	ENSE00003668426	70065965	70066084					1	3
+5	ENSG00000205571	ENST00000380742	ENSE00003698225	70067294	70067446					1	5
+5	ENSG00000205571	ENST00000380742	ENSE00003620900	70070641	70070751					1	6
+5	ENSG00000205571	ENST00000380742	ENSE00003579743	70066934	70067134					1	4
+5	ENSG00000205571	ENST00000380742	ENSE00001897950	70049664	70049766	70049664	70049685			1	1
+5	ENSG00000205571	ENST00000380742	ENSE00003698693	70076521	70076574			70076572	70076574	1	7
+5	ENSG00000205571	ENST00000380742	ENSE00001812360	70077019	70077592			70077019	70077592	1	8
+5	ENSG00000205571	ENST00000380743	ENSE00001725187	70063415	70063486					1	2
+5	ENSG00000205571	ENST00000380743	ENSE00003668426	70065965	70066084					1	3
+5	ENSG00000205571	ENST00000380743	ENSE00003698225	70067294	70067446					1	5
+5	ENSG00000205571	ENST00000380743	ENSE00003550962	70069235	70069330					1	6
+5	ENSG00000205571	ENST00000380743	ENSE00003620900	70070641	70070751					1	7
+5	ENSG00000205571	ENST00000380743	ENSE00003579743	70066934	70067134					1	4
+5	ENSG00000205571	ENST00000380743	ENSE00003698693	70076521	70076574			70076572	70076574	1	8
+5	ENSG00000205571	ENST00000380743	ENSE00001904512	70049669	70049766	70049669	70049685			1	1
+5	ENSG00000205571	ENST00000380743	ENSE00003898412	70077019	70077595			70077019	70077595	1	9
+5	ENSG00000205571	ENST00000628696	ENSE00001725187	70063415	70063486					1	2
+5	ENSG00000205571	ENST00000628696	ENSE00003668426	70065965	70066084					1	3
+5	ENSG00000205571	ENST00000628696	ENSE00003698225	70067294	70067446					1	5
+5	ENSG00000205571	ENST00000628696	ENSE00003550962	70069235	70069330					1	6
+5	ENSG00000205571	ENST00000628696	ENSE00003620900	70070641	70070751					1	7
+5	ENSG00000205571	ENST00000628696	ENSE00003579743	70066934	70067134					1	4
+5	ENSG00000205571	ENST00000628696	ENSE00001792916	70049686	70049766					1	1
+5	ENSG00000205571	ENST00000628696	ENSE00003762314	70071282	70071332					1	8
+5	ENSG00000205571	ENST00000380741	ENSE00001725187	70063415	70063486					1	2
+5	ENSG00000205571	ENST00000380741	ENSE00003668426	70065965	70066084					1	3
+5	ENSG00000205571	ENST00000380741	ENSE00003698225	70067294	70067446					1	5
+5	ENSG00000205571	ENST00000380741	ENSE00003550962	70069235	70069330					1	6
+5	ENSG00000205571	ENST00000380741	ENSE00003620900	70070641	70070751					1	7
+5	ENSG00000205571	ENST00000380741	ENSE00003579743	70066934	70067134					1	4
+5	ENSG00000205571	ENST00000380741	ENSE00001792916	70049686	70049766					1	1
+5	ENSG00000205571	ENST00000380741	ENSE00003723821	70076521	70076586			70076572	70076586	1	8
+5	ENSG00000205571	ENST00000614240	ENSE00001725187	70063415	70063486					1	2
+5	ENSG00000205571	ENST00000614240	ENSE00003668426	70065965	70066084					1	3
+5	ENSG00000205571	ENST00000614240	ENSE00003698225	70067294	70067446					1	5
+5	ENSG00000205571	ENST00000614240	ENSE00003620900	70070641	70070751					1	6
+5	ENSG00000205571	ENST00000614240	ENSE00003579743	70066934	70067134					1	4
+5	ENSG00000205571	ENST00000614240	ENSE00001792916	70049686	70049766					1	1
+5	ENSG00000205571	ENST00000614240	ENSE00003723821	70076521	70076586			70076572	70076586	1	7
+5	ENSG00000205571	ENST00000503678	ENSE00002056052	70063411	70063486					1	1
+5	ENSG00000205571	ENST00000503678	ENSE00003685383	70065965	70066084					1	2
+5	ENSG00000205571	ENST00000503678	ENSE00003650356	70066934	70067134					1	3
+5	ENSG00000205571	ENST00000503678	ENSE00003700892	70067294	70067446					1	4
+5	ENSG00000205571	ENST00000503678	ENSE00003668557	70069235	70069330					1	5
+5	ENSG00000205571	ENST00000503678	ENSE00002064131	70070641	70070755					1	6
+5	ENSG00000205571	ENST00000511873	ENSE00003698225	70067294	70067446					1	2
+5	ENSG00000205571	ENST00000511873	ENSE00003668557	70069235	70069330			70069235	70069330	1	4
+5	ENSG00000205571	ENST00000511873	ENSE00002038537	70067084	70067134					1	1
+5	ENSG00000205571	ENST00000511873	ENSE00002050020	70069026	70069142			70069062	70069142	1	3
+5	ENSG00000205571	ENST00000511873	ENSE00003697649	70070641	70070654			70070641	70070654	1	5
+5	ENSG00000205571	ENST00000509805	ENSE00003700892	70067294	70067446					1	2
+5	ENSG00000205571	ENST00000509805	ENSE00003668557	70069235	70069330					1	3
+5	ENSG00000205571	ENST00000509805	ENSE00002036057	70067094	70067134					1	1
+5	ENSG00000205571	ENST00000509805	ENSE00002062850	70070641	70070849					1	4
+5	ENSG00000205571	ENST00000505346	ENSE00003700892	70067294	70067446					1	2
+5	ENSG00000205571	ENST00000505346	ENSE00002067458	70067099	70067134					1	1
+5	ENSG00000205571	ENST00000505346	ENSE00003529016	70070641	70070751					1	3
+5	ENSG00000205571	ENST00000505346	ENSE00002073006	70076521	70076927					1	4
+5	ENSG00000205571	ENST00000514914	ENSE00003668557	70069235	70069330					1	2
+5	ENSG00000205571	ENST00000514914	ENSE00003529016	70070641	70070751					1	3
+5	ENSG00000205571	ENST00000514914	ENSE00002051731	70067279	70067446					1	1
+5	ENSG00000205571	ENST00000514914	ENSE00003696722	70076521	70076574					1	4
+5	ENSG00000205571	ENST00000514914	ENSE00002023398	70077019	70077251					1	5
+5	ENSG00000205571	ENST00000508258	ENSE00002032527	70069233	70069330					1	1
+5	ENSG00000205571	ENST00000508258	ENSE00002041684	70070641	70070753					1	2
+5	ENSG00000205571	ENST00000507458	ENSE00003698693	70076521	70076574			70076572	70076574	1	2
+5	ENSG00000205571	ENST00000507458	ENSE00002036578	70070664	70070751					1	1
+5	ENSG00000205571	ENST00000507458	ENSE00002067548	70077019	70077160			70077019	70077160	1	3
+5	ENSG00000205571	ENST00000507458	ENSE00002085226	70077762	70078522			70077762	70078522	1	4
+5	ENSG00000172062	ENST00000503079	ENSE00001922009	70925030	70925184	70925030	70925103			1	1
+5	ENSG00000172062	ENST00000503079	ENSE00001688516	70938839	70938910					1	2
+5	ENSG00000172062	ENST00000503079	ENSE00001638255	70941389	70941508					1	3
+5	ENSG00000172062	ENST00000503079	ENSE00001766361	70942358	70942558					1	4
+5	ENSG00000172062	ENST00000503079	ENSE00003576392	70942718	70942870					1	5
+5	ENSG00000172062	ENST00000503079	ENSE00001593733	70946066	70946176					1	6
+5	ENSG00000172062	ENST00000503079	ENSE00002062475	70951941	70952347			70951992	70952347	1	7
+5	ENSG00000172062	ENST00000514951	ENSE00001688516	70938839	70938910					1	2
+5	ENSG00000172062	ENST00000514951	ENSE00001638255	70941389	70941508					1	3
+5	ENSG00000172062	ENST00000514951	ENSE00003576392	70942718	70942870					1	4
+5	ENSG00000172062	ENST00000514951	ENSE00001593733	70946066	70946176					1	6
+5	ENSG00000172062	ENST00000514951	ENSE00002034950	70925056	70925184	70925056	70925103			1	1
+5	ENSG00000172062	ENST00000514951	ENSE00003611930	70944658	70944753					1	5
+5	ENSG00000172062	ENST00000514951	ENSE00002045198	70951941	70952567			70951992	70952567	1	7
+5	ENSG00000172062	ENST00000506239	ENSE00001688516	70938839	70938910					1	2
+5	ENSG00000172062	ENST00000506239	ENSE00001638255	70941389	70941508					1	3
+5	ENSG00000172062	ENST00000506239	ENSE00001766361	70942358	70942558					1	4
+5	ENSG00000172062	ENST00000506239	ENSE00003576392	70942718	70942870					1	5
+5	ENSG00000172062	ENST00000506239	ENSE00001593733	70946066	70946176					1	7
+5	ENSG00000172062	ENST00000506239	ENSE00003611930	70944658	70944753					1	6
+5	ENSG00000172062	ENST00000506239	ENSE00002073998	70925075	70925184	70925075	70925103			1	1
+5	ENSG00000172062	ENST00000506239	ENSE00002042046	70946707	70946815			70946758	70946815	1	8
+5	ENSG00000172062	ENST00000506239	ENSE00002052357	70952439	70953016			70952439	70953016	1	9
+5	ENSG00000172062	ENST00000380707	ENSE00001688516	70938839	70938910					1	2
+5	ENSG00000172062	ENST00000380707	ENSE00001638255	70941389	70941508					1	3
+5	ENSG00000172062	ENST00000380707	ENSE00001766361	70942358	70942558					1	4
+5	ENSG00000172062	ENST00000380707	ENSE00003576392	70942718	70942870					1	5
+5	ENSG00000172062	ENST00000380707	ENSE00001593733	70946066	70946176					1	7
+5	ENSG00000172062	ENST00000380707	ENSE00003611930	70944658	70944753					1	6
+5	ENSG00000172062	ENST00000380707	ENSE00003899118	70925087	70925184	70925087	70925103			1	1
+5	ENSG00000172062	ENST00000380707	ENSE00003693452	70951941	70951994			70951992	70951994	1	8
+5	ENSG00000172062	ENST00000380707	ENSE00001885073	70952439	70953015			70952439	70953015	1	9
+5	ENSG00000172062	ENST00000506163	ENSE00001688516	70938839	70938910					1	2
+5	ENSG00000172062	ENST00000506163	ENSE00001638255	70941389	70941508					1	3
+5	ENSG00000172062	ENST00000506163	ENSE00001766361	70942358	70942558					1	4
+5	ENSG00000172062	ENST00000506163	ENSE00003576392	70942718	70942870					1	5
+5	ENSG00000172062	ENST00000506163	ENSE00001593733	70946066	70946176					1	7
+5	ENSG00000172062	ENST00000506163	ENSE00003611930	70944658	70944753					1	6
+5	ENSG00000172062	ENST00000506163	ENSE00002033586	70925095	70925184	70925095	70925103			1	1
+5	ENSG00000172062	ENST00000506163	ENSE00002025434	70952439	70953040			70952454	70953040	1	8
+5	ENSG00000172062	ENST00000625245	ENSE00001688516	70938839	70938910					1	2
+5	ENSG00000172062	ENST00000625245	ENSE00001638255	70941389	70941508					1	3
+5	ENSG00000172062	ENST00000625245	ENSE00001766361	70942358	70942558					1	4
+5	ENSG00000172062	ENST00000625245	ENSE00003576392	70942718	70942870					1	5
+5	ENSG00000172062	ENST00000625245	ENSE00001593733	70946066	70946176					1	7
+5	ENSG00000172062	ENST00000625245	ENSE00003611930	70944658	70944753					1	6
+5	ENSG00000172062	ENST00000625245	ENSE00001695536	70925104	70925184					1	1
+5	ENSG00000172062	ENST00000625245	ENSE00003771397	70946707	70946757					1	8
+5	ENSG00000172062	ENST00000351205	ENSE00001688516	70938839	70938910					1	2
+5	ENSG00000172062	ENST00000351205	ENSE00001638255	70941389	70941508					1	3
+5	ENSG00000172062	ENST00000351205	ENSE00001766361	70942358	70942558					1	4
+5	ENSG00000172062	ENST00000351205	ENSE00003576392	70942718	70942870					1	5
+5	ENSG00000172062	ENST00000351205	ENSE00001593733	70946066	70946176					1	7
+5	ENSG00000172062	ENST00000351205	ENSE00003611930	70944658	70944753					1	6
+5	ENSG00000172062	ENST00000351205	ENSE00001695536	70925104	70925184					1	1
+5	ENSG00000172062	ENST00000351205	ENSE00003727855	70951941	70952006			70951992	70952006	1	8
+5	ENSG00000172062	ENST00000518504	ENSE00002115234	70942472	70942558					1	1
+5	ENSG00000172062	ENST00000518504	ENSE00003586477	70942718	70942870					1	2
+5	ENSG00000172062	ENST00000518504	ENSE00002067240	70946066	70946278					1	3
+5	ENSG00000172062	ENST00000507905	ENSE00003576392	70942718	70942870					1	2
+5	ENSG00000172062	ENST00000507905	ENSE00002065935	70942508	70942558					1	1
+5	ENSG00000172062	ENST00000507905	ENSE00002019326	70944449	70944565			70944485	70944565	1	3
+5	ENSG00000172062	ENST00000507905	ENSE00003477349	70944658	70944753			70944658	70944753	1	4
+5	ENSG00000172062	ENST00000507905	ENSE00002110817	70946066	70946079			70946066	70946079	1	5
+5	ENSG00000172062	ENST00000513228	ENSE00003586477	70942718	70942870					1	2
+5	ENSG00000172062	ENST00000513228	ENSE00003477349	70944658	70944753					1	3
+5	ENSG00000172062	ENST00000513228	ENSE00002053468	70942518	70942558					1	1
+5	ENSG00000172062	ENST00000513228	ENSE00002065580	70946066	70946274					1	4
+5	ENSG00000172062	ENST00000510679	ENSE00002063740	70946089	70946176					1	1
+5	ENSG00000172062	ENST00000510679	ENSE00003581587	70951941	70951994					1	2
+5	ENSG00000172062	ENST00000510679	ENSE00002068209	70952439	70952580					1	3
+5	ENSG00000172062	ENST00000510679	ENSE00002084907	70953182	70953942					1	4
 6	ENSG00000118503	ENST00000421450	ENSE00001636894	138188351	138188679	138188351	138188679			1	1
 6	ENSG00000118503	ENST00000421450	ENSE00001724607	138192350	138192441	138192350	138192364			1	2
 6	ENSG00000118503	ENST00000420009	ENSE00001680250	138188459	138188655	138188459	138188655			1	1

scout/demo/resources/ensembl_genes_37_reduced.txt

@@ -194,6 +194,8 @@ Chromosome/scaffold name	Gene start (bp)	Gene end (bp)	Gene stable ID	HGNC symbo
 5	1392909	1445545	ENSG00000142319	SLC6A3	11049
 5	174151536	174157896	ENSG00000120149	MSX2	7392
 5	140011313	140013286	ENSG00000170458	CD14	1628
+5	70220768	70249769	ENSG00000172062	SMN1	11117
+5	69345350	69374349	ENSG00000205571	SMN2	11118
 6	138188351	138204449	ENSG00000118503	TNFAIP3	11896
 6	157099063	157531913	ENSG00000049618	ARID1B	18040
 6	7727030	7881655	ENSG00000153162	BMP6	1073

scout/demo/resources/ensembl_genes_38_reduced.txt

@@ -194,6 +194,8 @@ Chromosome/scaffold name	Gene start (bp)	Gene end (bp)	Gene stable ID	HGNC symbo
 5	140631728	140633701	ENSG00000170458	CD14	1628
 5	95751319	95823005	ENSG00000173221	GLRX	4330
 5	174724533	174730893	ENSG00000120149	MSX2	7392
+5	70925030	70953942	ENSG00000172062	SMN1	11117
+5	70049638	70078522	ENSG00000205571	SMN2	11118
 6	139371807	139374620	ENSG00000164442	CITED2	1987
 6	137867188	137883312	ENSG00000118503	TNFAIP3	11896
 6	156777374	157210779	ENSG00000049618	ARID1B	18040

scout/demo/resources/ensembl_transcripts_37_reduced.txt

@@ -1996,6 +1996,33 @@ Chromosome/scaffold name	Gene stable ID	Transcript stable ID	Transcript start (b
 5	ENSG00000170458	ENST00000401743	140011313	140013286	NM_001174105
 5	ENSG00000170458	ENST00000401743	140011313	140013286	NM_001040021
 5	ENSG00000170458	ENST00000401743	140011313	140013286	NM_001174104
+5	ENSG00000205571	ENST00000380743	69345439	69373419	NM_017411		
+5	ENSG00000205571	ENST00000511812	69345465	69372533			
+5	ENSG00000205571	ENST00000506734	69345484	69373423			
+5	ENSG00000205571	ENST00000380742	69345491	69373419	NM_022876		
+5	ENSG00000205571	ENST00000503678	69359238	69366582			
+5	ENSG00000205571	ENST00000511873	69362911	69366481			
+5	ENSG00000205571	ENST00000509805	69362921	69366676			
+5	ENSG00000205571	ENST00000505346	69362926	69372754			
+5	ENSG00000205571	ENST00000514914	69363106	69373078			
+5	ENSG00000205571	ENST00000508258	69365060	69366580			
+5	ENSG00000205571	ENST00000507458	69366491	69374349			
+5	ENSG00000205571	ENST00000380741	69345350	69373421	NM_022875	XM_005276775	
+5	ENSG00000205571	ENST00000380741	69345350	69373421	NM_022875	XM_005248575	
+5	ENSG00000205571	ENST00000380741	69345350	69373421	NM_022877	XM_005276775	
+5	ENSG00000205571	ENST00000380741	69345350	69373421	NM_022877	XM_005248575	
+5	ENSG00000172062	ENST00000503079	70220857	70248174			
+5	ENSG00000172062	ENST00000380707	70220857	70248839	NM_000344		
+5	ENSG00000172062	ENST00000514951	70220883	70248394		XM_005276777	
+5	ENSG00000172062	ENST00000514951	70220883	70248394		XM_005248578	
+5	ENSG00000172062	ENST00000514951	70220883	70248394		XM_005248577	
+5	ENSG00000172062	ENST00000506239	70220902	70248843			
+5	ENSG00000172062	ENST00000506163	70220922	70248867			
+5	ENSG00000172062	ENST00000518504	70238299	70242105			
+5	ENSG00000172062	ENST00000507905	70238335	70241906			
+5	ENSG00000172062	ENST00000513228	70238345	70242101			
+5	ENSG00000172062	ENST00000510679	70241916	70249769			
+5	ENSG00000172062	ENST00000351205	70220768	70248841	NM_022874		
 6	ENSG00000118503	ENST00000421450	138188351	138192441
 6	ENSG00000118503	ENST00000420009	138188459	138196172
 6	ENSG00000118503	ENST00000237289	138188581	138204449	NM_001270507	XM_005267119

scout/demo/resources/ensembl_transcripts_38_reduced.txt

@@ -3013,6 +3013,42 @@ Chromosome/scaffold name	Gene stable ID	Transcript stable ID	Transcript start (b
 5	ENSG00000173221	ENST00000512469	95816410	95822711
 5	ENSG00000120149	ENST00000239243	174724533	174730893	NM_002449
 5	ENSG00000120149	ENST00000507785	174724602	174729880		XM_017009489
+5	ENSG00000172062	ENST00000503079	70925030	70952347	NM_022874	XM_047417616			
+5	ENSG00000172062	ENST00000514951	70925056	70952567		XM_011543597			
+5	ENSG00000172062	ENST00000506239	70925075	70953016					
+5	ENSG00000172062	ENST00000380707	70925087	70953015	NM_000344			NM_000344.4	
+5	ENSG00000172062	ENST00000506163	70925095	70953040	NM_001297715	XM_047417615			
+5	ENSG00000172062	ENST00000506163	70925095	70953040	NM_001297715	XM_017009786			
+5	ENSG00000172062	ENST00000506163	70925095	70953040	NM_001297715	XM_047417618			
+5	ENSG00000172062	ENST00000625245	70925104	70946757		XM_011543596			
+5	ENSG00000172062	ENST00000351205	70925104	70952006					
+5	ENSG00000172062	ENST00000518504	70942472	70946278					
+5	ENSG00000172062	ENST00000507905	70942508	70946079					
+5	ENSG00000172062	ENST00000513228	70942518	70946274					
+5	ENSG00000172062	ENST00000510679	70946089	70953942					
+5	ENSG00000205571	ENST00000511812	70049638	70076706		XM_047417621			
+5	ENSG00000205571	ENST00000511812	70049638	70076706		XM_047417622			
+5	ENSG00000205571	ENST00000511812	70049638	70076706		XM_011543600			
+5	ENSG00000205571	ENST00000626847	70049654	70077592	NM_022877	XM_047417619			
+5	ENSG00000205571	ENST00000626847	70049654	70077592	NM_022877	XM_011543601			
+5	ENSG00000205571	ENST00000626847	70049654	70077592	NM_022877	XM_011543603			
+5	ENSG00000205571	ENST00000626847	70049654	70077592	NM_022875	XM_047417619			
+5	ENSG00000205571	ENST00000626847	70049654	70077592	NM_022875	XM_011543601			
+5	ENSG00000205571	ENST00000626847	70049654	70077592	NM_022875	XM_011543603			
+5	ENSG00000205571	ENST00000506734	70049657	70077596					
+5	ENSG00000205571	ENST00000380742	70049664	70077592	NM_022876	XM_011543602			
+5	ENSG00000205571	ENST00000380743	70049669	70077595	NM_017411			NM_017411.4	
+5	ENSG00000205571	ENST00000628696	70049686	70071332		XM_011543599			
+5	ENSG00000205571	ENST00000628696	70049686	70071332		XM_017009787			
+5	ENSG00000205571	ENST00000380741	70049686	70076586					
+5	ENSG00000205571	ENST00000614240	70049686	70076586		XM_047417620			
+5	ENSG00000205571	ENST00000503678	70063411	70070755					
+5	ENSG00000205571	ENST00000511873	70067084	70070654					
+5	ENSG00000205571	ENST00000509805	70067094	70070849					
+5	ENSG00000205571	ENST00000505346	70067099	70076927					
+5	ENSG00000205571	ENST00000514914	70067279	70077251					
+5	ENSG00000205571	ENST00000508258	70069233	70070753					
+5	ENSG00000205571	ENST00000507458	70070664	70078522					
 6	ENSG00000164442	ENST00000367651	139371807	139374620	NM_006079
 6	ENSG00000164442	ENST00000537332	139372255	139374213	NM_001168389
 6	ENSG00000164442	ENST00000536159	139372255	139374362	NM_001168388

scout/demo/resources/hgnc_reduced_set.txt

@@ -263,3 +263,5 @@ HGNC:12791	WRN	Werner syndrome RecQ like helicase	protein-coding gene	gene with
 HGNC:32550	ZBTB42	zinc finger and BTB domain containing 42	protein-coding gene	gene with protein product	Approved	14q32.33	14q32.33	ZNF925				"Zinc fingers C2H2-type|BTB domain containing"	"28|861"	2006-03-15			2015-08-26	100128927	ENSG00000179627	OTTHUMG00000170790	uc021sem.3	AX721091	NM_001137601	CCDS45174	B2RXF5		MGI:3644133	RGD:1582758		ZBTB42	613915					471346						591
 HGNC:12873	ZIC2	Zic family member 2	protein-coding gene	gene with protein product	Approved	13q32.3	13q32.3	HPE5	Zinc finger protein of the cerebellum 2		"Zic family member 2 (odd-paired Drosophila homolog)|Zic family member 2 (odd-paired homolog, Drosophila)"	Zinc fingers C2H2-type	28	1998-04-27		2011-05-19	2018-04-21	7546	ENSG00000043355	OTTHUMG00000017279	uc001von.4	AF104902	NM_007129	CCDS9495	O95409	9771712	MGI:106679	RGD:1311174	LRG_1157|http://www.lrg-sequence.org/LRG/LRG_1157	ZIC2	603073					120610
 HGNC:29277	ZNF687	zinc finger protein 687	protein-coding gene	gene with protein product	Approved	1q21.3	01q21.3	KIAA1441						2005-05-06			2016-10-05	57592	ENSG00000143373	OTTHUMG00000012347	uc001exq.4		NM_020832	CCDS992	Q8N1G0	10718198	MGI:1925516	RGD:2323182		ZNF687	610568					451453
+HGNC:11117	SMN1	survival of motor neuron 1, telomeric	protein-coding gene	gene with protein product	Approved	5q13.2	05q13.2	"BCD541|SMNT|SMA1|SMA2|SMA3|GEMIN1|TDRD16A"	"gemin-1|tudor domain containing 16A"	"SMA@|SMA"	spinal muscular atrophy (Werdnig-Hoffmann disease, Kugelberg-Welander disease)	"Tudor domain containing|SMN complex|Proteins encoded by multiple genes"	"780|1500|2293"	1996-12-12			2023-01-20	6606	ENSG00000172062	OTTHUMG00000099361	uc003kak.4	U18423	NM_000344		Q16637	7813012	MGI:109257	RGD:620755	"SMN1 - Spinal Muscular Atrophy (SMA)|http://www.LOVD.nl/SMN1|Leiden Muscular Dystrophy pages|http://www.dmd.nl/nmdb2/home.php?select_db=SMN1|ALSOD, the Amyotrophic Lateral Sclerosis Online Genetic Database|http://alsod.iop.kcl.ac.uk/|LRG_676|http://ftp.ebi.ac.uk/pub/databases/lrgex/LRG_676.xml"		600354					133452															HGNC:11117	"ENST00000380707.9|NM_000344.4"	HGNC:11117
+HGNC:11118	SMN2	survival of motor neuron 2, centromeric	protein-coding gene	gene with protein product	Approved	5q13.2	05q13.2	"BCD541|SMNC|GEMIN1|TDRD16B"	tudor domain containing 16B			"Tudor domain containing|SMN complex|Proteins encoded by multiple genes"	"780|1500|2293"	1996-12-12			2023-01-20	6607	ENSG00000205571	OTTHUMG00000099389	uc003jyd.4		NM_017411		Q16637	7813012	MGI:109257		"ALSOD, the Amyotrophic Lateral Sclerosis Online Genetic Database|http://alsod.iop.kcl.ac.uk/|LRG_677|http://ftp.ebi.ac.uk/pub/databases/lrgex/LRG_677.xml"		601627					119750															HGNC:11118	"ENST00000380743.9|NM_017411.4"	

scout/log/handlers.py

@@ -1,9 +1,10 @@
 # -*- coding: utf-8 -*-
-import logging
 import logging.handlers
 
 
 class TlsSMTPHandler(logging.handlers.SMTPHandler):
+    """Used by the app to send emails."""
+
     def emit(self, record):
         """Emit a record.
         Format the record and send it to the specified addressees.

scout/log/log.py

@@ -1,62 +1,49 @@
 import logging
-import os
-import sys
-
-
-def init_log(logger, filename=None, loglevel=None):
-    """
-    Initializes the log file in the proper format.
-
-    Arguments:
-
-        filename (str): Path to a file. Or None if logging is to
-                         be disabled.
-        loglevel (str): Determines the level of the log output.
-    """
-    template = "[%(asctime)s] %(levelname)-8s: %(name)-25s: %(message)s"
-    formatter = logging.Formatter(template)
-
-    if loglevel:
-        logger.setLevel(getattr(logging, loglevel))
-
-    # We will always print warnings and higher to stderr
-    console = logging.StreamHandler()
-    console.setLevel("WARNING")
-    console.setFormatter(formatter)
-
-    if filename:
-        file_handler = logging.FileHandler(filename, encoding="utf-8")
-        if loglevel:
-            file_handler.setLevel(getattr(logging, loglevel))
-        file_handler.setFormatter(formatter)
-        logger.addHandler(file_handler)
-    # If no logfile is provided we print all log messages that the user has
-    # defined to stderr
-    else:
-        if loglevel:
-            console.setLevel(getattr(logging, loglevel))
-
-    logger.addHandler(console)
-
-
-def get_log_stream(logger):
-    """
-    Returns a stream to the root log file.
-    If there is no logfile return the stderr log stream
-
-    Returns:
-        A stream to the root log file or stderr stream.
-    """
-
-    file_stream = None
-    log_stream = None
-    for handler in logger.handlers:
-        if isinstance(handler, logging.FileHandler):
-            file_stream = handler.stream
-        else:
-            log_stream = handler.stream
-
-    if file_stream:
-        return file_stream
-
-    return log_stream
+
+import coloredlogs
+from flask.app import Flask
+
+USERS_LOGGER_PATH_PARAM = "USERS_ACTIVITY_LOG_PATH"
+ACTIVITY_LOG_IGNORE_TRIGGERS = [
+    "static",
+    "ideograms",
+    "custom_images",
+    "autozygous_images",
+    "coverage_images",
+    "upd_regions_images",
+    "favicon",
+    "GET /",
+    "Closing",
+    "Enable",
+    "enabled",
+    "Collecting IGV tracks",
+]  # Substrings used when filtering messages to show if users activity log is on
+
+
+class ActivityLogFilter(logging.Filter):
+    """When monitoring users activity, log only navigation on main pages.
+    - Do not log messages that contain the substrings specified in ACTIVITY_LOG_IGNORE_TRIGGERS"""
+
+    def filter(self, record):
+        return (
+            any(sub_url in record.getMessage() for sub_url in ACTIVITY_LOG_IGNORE_TRIGGERS) is False
+        )
+
+
+def set_activity_log(log: logging.Logger, app: Flask):
+    """Log users' activity to a file, if specified in the scout config."""
+    app.logger.setLevel("INFO")
+    app.logger.addFilter(ActivityLogFilter())
+    file_handler = logging.FileHandler(app.config[USERS_LOGGER_PATH_PARAM])
+    file_handler.setFormatter(logging.Formatter("%(asctime)s - %(message)s"))
+    log.addHandler(file_handler)
+
+
+def init_log(log: logging.Logger, app: Flask):
+    """Initializes the log file in the proper format."""
+
+    current_log_level = log.getEffectiveLevel()
+    coloredlogs.install(level="DEBUG" if app.debug else current_log_level)
+
+    if USERS_LOGGER_PATH_PARAM in app.config:
+        set_activity_log(log=log, app=app)

scout/models/case/case_loading_models.py

@@ -58,6 +58,7 @@ CASE_FILE_PATH_CHECKS = [
     "RNAfusion_inspector_research",
     "RNAfusion_report",
     "RNAfusion_report_research",
+    "rna_delivery_report",
 ]
 
 VCF_FILE_PATH_CHECKS = FILE_TYPE_MAP.keys()
@@ -431,6 +432,7 @@ class CaseLoader(BaseModel):
     RNAfusion_inspector_research: Optional[str] = None
     RNAfusion_report: Optional[str] = None
     RNAfusion_report_research: Optional[str] = None
+    rna_delivery_report: Optional[str] = None
     smn_tsv: Optional[str] = None
     sv_rank_model_version: Optional[str] = None
     synopsis: Optional[Union[List[str], str]] = None

scout/parse/omim.py

@@ -49,7 +49,7 @@ def parse_genemap2_diseases(phenotype_entry, mim_number=None):
         i = 0
         splitted_info = phenotype_info.split(",")
         for i, text in enumerate(splitted_info):
-            # Everything before ([1,2,3])
+            # Everything before ([1,2,3,4])
             # We check if we are in the part where the mim number exists
             match = ENTRY_PATTERN.search(text)
             if not match:
@@ -75,7 +75,7 @@ def parse_genemap2_diseases(phenotype_entry, mim_number=None):
             {
                 "mim_number": disease_mim,
                 "inheritance": inheritance,
-                "description": disease_description.strip("?\{\}"),
+                "description": disease_description.strip(r"?{}"),
                 "status": disease_status,
             }
         )

scout/server/app.py

@@ -2,17 +2,19 @@
 
 import logging
 import os
+import re
 from datetime import timedelta
 from typing import Dict, Union
 from urllib.parse import parse_qsl, unquote, urlsplit
 
-import coloredlogs
 from flask import Flask, redirect, request, url_for
 from flask_cors import CORS
 from flask_login import current_user
 from markdown import markdown as python_markdown
 from markupsafe import Markup
 
+from scout.log import init_log
+
 from . import extensions
 from .blueprints import (
     alignviewers,
@@ -36,6 +38,8 @@ from .blueprints import (
 
 LOG = logging.getLogger(__name__)
 
+USERS_LOGGER_PATH_PARAM = "USERS_ACTIVITY_LOG_PATH"
+
 
 def create_app(config_file=None, config=None):
     """Flask app factory function."""
@@ -60,8 +64,7 @@ def create_app(config_file=None, config=None):
 
     app.json.sort_keys = False
 
-    current_log_level = LOG.getEffectiveLevel()
-    coloredlogs.install(level="DEBUG" if app.debug else current_log_level)
+    init_log(log=LOG, app=app)
     configure_extensions(app)
     register_blueprints(app)
     register_filters(app)
@@ -83,10 +86,15 @@ def create_app(config_file=None, config=None):
             relevant_endpoint = not (static_endpoint or public_endpoint)
             # if endpoint requires auth, check if user is authenticated
             if relevant_endpoint and not current_user.is_authenticated:
-                # combine visited URL (convert byte string query string to unicode!)
-                next_url = "{}?{}".format(request.path, request.query_string.decode())
-                login_url = url_for("public.index", next=next_url)
-                return redirect(login_url)
+                return redirect(url_for("public.index"))
+
+    @app.before_request
+    def log_users_activity():
+        """Log users' navigation to file, if specified in the app setting.s"""
+        if USERS_LOGGER_PATH_PARAM not in app.config:
+            return
+        user = current_user.email if current_user.is_authenticated else "anonymous"
+        LOG.info(" - ".join([user, request.path]))
 
     return app
 
@@ -246,6 +254,14 @@ def register_filters(app):
             return "COSM" + str(cosmicId)
         return cosmicId
 
+    @app.template_filter()
+    def upper_na(string):
+        """
+        Uppercase ocurences of "dna" and "rna" for nice display.
+        """
+
+        return re.sub(r"[Dd][Nn][Aa]", r"DNA", re.sub(r"[Rr][Nn][Aa]", r"RNA", string))
+
     @app.template_filter()
     def count_cursor(pymongo_cursor):
         """Count number of returned documents (deprecated pymongo.cursor.count())"""

scout/server/blueprints/alignviewers/controllers.py

@@ -125,7 +125,9 @@ def make_sashimi_tracks(
     case_obj: dict, variant_id: Optional[str] = None, omics_variant_id: Optional[str] = None
 ):
     """Create a dictionary containing the required tracks for a splice junction plot
-    If either a regular variant_id or an omics variant id is passed, set display to a particular locus.
+    If a regular variant_id is passed, set display to a particular gene locus.
+    If an omics_variant_id is passed, set display to a window surrounding the variant, which can be a
+    gene or an affected region.
     Otherwise defaults to whole genome "All" view.
 
     Returns:
@@ -133,18 +135,16 @@ def make_sashimi_tracks(
     """
 
     locus = "All"
-    variant_obj = None
-
-    if variant_id:
-        variant_obj = store.variant(document_id=variant_id)
-    if omics_variant_id:
-        variant_obj = store.omics_variant(variant_id=omics_variant_id)
 
     build = "38"
     if "37" in str(case_obj.get("rna_genome_build", "38")):
         build = "37"
 
-    if variant_obj:
+    if variant_id:
+        variant_obj = store.variant(document_id=variant_id)
+        locus = make_locus_from_gene(variant_obj, case_obj, build)
+    if omics_variant_id:
+        variant_obj = store.omics_variant(variant_id=omics_variant_id)
         locus = make_locus_from_variant(variant_obj, case_obj, build)
 
     display_obj = {"locus": locus, "tracks": []}
@@ -195,17 +195,16 @@ def make_merged_splice_track(ind: dict) -> dict:
     return track
 
 
-def make_locus_from_variant(variant_obj: Dict, case_obj: Dict, build: str) -> str:
-    """Given a variant obj, construct a locus string across any gene touched for IGV to display.
-
-    Initialize locus coordinates with variant coordinates so it won't crash if variant gene(s) no longer exist in database.
+def get_locus_from_variant(variant_obj: Dict, case_obj: Dict, build: str) -> tuple:
+    """
     Check if variant coordinates are in genome build 38, otherwise do variant coords liftover.
     Use original coordinates only if genome build was already 38 or liftover didn't work.
-    Collect locus coordinates. Take into account that variant can hit multiple genes.
-    The returned locus will so span all genes the variant falls into.
+    Collect locus coordinates.
     """
-    locus_start_coords = []
-    locus_end_coords = []
+    MIN_LOCUS_SIZE_OFFSET = 100
+
+    locus_start_coord = variant_obj.get("position")
+    locus_end_coord = variant_obj.get("end")
 
     if build not in str(case_obj.get("genome_build")):
         client = EnsemblRestApiClient()
@@ -218,13 +217,37 @@ def make_locus_from_variant(variant_obj: Dict, case_obj: Dict, build: str) -> st
         if mapped_coords:
             mapped_start = mapped_coords[0]["mapped"].get("start")
             mapped_end = mapped_coords[0]["mapped"].get("end") or mapped_start
-            locus_start_coords.append(mapped_start)
-            locus_end_coords.append(mapped_end)
+            locus_start_coord = mapped_start
+            locus_end_coord = mapped_end
+
+    variant_size_offset = (variant_obj.get("end") - variant_obj.get("position")) / 10
+    if variant_size_offset < (MIN_LOCUS_SIZE_OFFSET * 2):
+        variant_size_offset = MIN_LOCUS_SIZE_OFFSET
+    locus_start_coord -= variant_size_offset
+    locus_end_coord += variant_size_offset
+
+    return (variant_obj["chromosome"], locus_start_coord, locus_end_coord)
+
+
+def make_locus_from_variant(variant_obj: Dict, case_obj: Dict, build: str) -> str:
+    """Given a variant obj, construct a locus string across variant plus a percent size offset around the variant."""
+
+    (chrom, locus_start, locus_end) = get_locus_from_variant(variant_obj, case_obj, build)
+    return f"{chrom}:{locus_start}-{locus_end}"
+
+
+def make_locus_from_gene(variant_obj: Dict, case_obj: Dict, build: str) -> str:
+    """Given a variant obj, construct a locus string across any gene touched for IGV to display.
+    Initialize locus coordinates with variant coordinates so it won't crash if variant gene(s) no longer exist in database.
+    Check if variant coordinates are in genome build 38, otherwise do variant coords liftover.
+    Use original coordinates only if genome build was already 38 or liftover didn't work.
+    Collect locus coordinates. Take into account that variant can hit multiple genes.
+    The returned locus will so span all genes the variant falls into.
+    """
 
-    if not locus_start_coords:
-        locus_start_coords.append(variant_obj.get("position"))
-    if not locus_end_coords:
-        locus_end_coords.append(variant_obj.get("end"))
+    (chrom, locus_start, locus_end) = get_locus_from_variant(variant_obj, case_obj, build)
+    locus_start_coords = [locus_start]
+    locus_end_coords = [locus_end]
 
     variant_genes_ids = [gene["hgnc_id"] for gene in variant_obj.get("genes", [])]
     for gene_id in variant_genes_ids:
@@ -237,7 +260,7 @@ def make_locus_from_variant(variant_obj: Dict, case_obj: Dict, build: str) -> st
     locus_start = min(locus_start_coords)
     locus_end = max(locus_end_coords)
 
-    return f"{variant_obj['chromosome']}:{locus_start}-{locus_end}"
+    return f"{chrom}:{locus_start}-{locus_end}"
 
 
 def set_tracks(name, file_list):