@jbrowse/plugin-gtf 2.5.0 → 2.6.2
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/dist/GtfAdapter/GtfAdapter.js +0 -1
- package/dist/GtfAdapter/configSchema.js +1 -1
- package/dist/GtfAdapter/index.js +0 -1
- package/dist/index.js +0 -1
- package/dist/util.js +1 -2
- package/esm/GtfAdapter/GtfAdapter.js +0 -1
- package/esm/GtfAdapter/configSchema.js +1 -1
- package/esm/GtfAdapter/index.js +0 -1
- package/esm/index.js +0 -1
- package/esm/util.js +1 -2
- package/package.json +4 -5
- package/dist/GtfAdapter/GtfAdapter.js.map +0 -1
- package/dist/GtfAdapter/configSchema.js.map +0 -1
- package/dist/GtfAdapter/index.js.map +0 -1
- package/dist/index.js.map +0 -1
- package/dist/util.js.map +0 -1
- package/esm/GtfAdapter/GtfAdapter.js.map +0 -1
- package/esm/GtfAdapter/configSchema.js.map +0 -1
- package/esm/GtfAdapter/index.js.map +0 -1
- package/esm/index.js.map +0 -1
- package/esm/util.js.map +0 -1
- package/src/GtfAdapter/GtfAdapter.test.ts +0 -55
- package/src/GtfAdapter/GtfAdapter.ts +0 -130
- package/src/GtfAdapter/__snapshots__/GtfAdapter.test.ts.snap +0 -836
- package/src/GtfAdapter/configSchema.ts +0 -22
- package/src/GtfAdapter/index.ts +0 -1
- package/src/declare.d.ts +0 -1
- package/src/index.ts +0 -48
- package/src/test_data/demo.gtf +0 -26
- package/src/test_data/volvox.sorted.gtf +0 -40
- package/src/util.ts +0 -77
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// Jest Snapshot v1, https://goo.gl/fbAQLP
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exports[`adapter can fetch features from volvox.sorted.gtf test getfeatures on gtf plain text adapter 1`] = `
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[
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{
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"end": 9000,
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"gene_id": "EDEN",
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"gene_name": "EDEN",
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"name": "EDEN.1",
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"phase": 0,
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"refName": "ctgA",
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"source": "example",
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"start": 1049,
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"strand": 1,
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"subfeatures": [
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{
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"end": 1500,
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"gene_id": "EDEN",
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"gene_name": "EDEN",
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"name": "EDEN.1",
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"parentId": "test-ctgA-0",
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"phase": 0,
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"refName": "ctgA",
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"source": "example",
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"start": 1049,
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"strand": 1,
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"transcript_id": "EDEN.1",
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"type": "exon",
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"uniqueId": "test-ctgA-0-0",
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},
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{
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"end": 1200,
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"gene_id": "EDEN",
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"gene_name": "EDEN",
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"name": "EDEN.1",
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"parentId": "test-ctgA-0",
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"refName": "ctgA",
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"source": "example",
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"start": 1049,
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"strand": 1,
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"transcript_id": "EDEN.1",
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"type": "five_prime_UTR",
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"uniqueId": "test-ctgA-0-1",
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},
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{
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"end": 1500,
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"gene_id": "EDEN",
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"gene_name": "EDEN",
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"name": "EDEN.1",
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"parentId": "test-ctgA-0",
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"refName": "ctgA",
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"transcript_id": "EDEN.1",
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"type": "CDS",
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"uniqueId": "test-ctgA-0-2",
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{
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"end": 3902,
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"gene_id": "EDEN",
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"gene_name": "EDEN",
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"name": "EDEN.1",
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"parentId": "test-ctgA-0",
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"refName": "ctgA",
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"source": "example",
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"transcript_id": "EDEN.1",
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"uniqueId": "test-ctgA-0-3",
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{
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"end": 3902,
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"transcript_id": "EDEN.1",
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"uniqueId": "test-ctgA-0-4",
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"uniqueId": "test-ctgA-0-9",
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],
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"subfeatures": [
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"uniqueId": "test-ctgA-1-0",
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"uniqueId": "test-ctgA-1-3",
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"transcript_id": "EDEN.2",
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"uniqueId": "test-ctgA-1-4",
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"type": "CDS",
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"uniqueId": "test-ctgA-1-5",
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"uniqueId": "test-ctgA-1-6",
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|
645
|
-
"refName": "ctgA",
|
|
646
|
-
"source": "exonerate",
|
|
647
|
-
"start": 20999,
|
|
648
|
-
"strand": 1,
|
|
649
|
-
"transcript_id": "rna-Apple3",
|
|
650
|
-
"type": "exon",
|
|
651
|
-
"uniqueId": "test-ctgA-5-6",
|
|
652
|
-
},
|
|
653
|
-
{
|
|
654
|
-
"end": 23000,
|
|
655
|
-
"name": "rna-Apple3",
|
|
656
|
-
"parentId": "test-ctgA-5",
|
|
657
|
-
"phase": 0,
|
|
658
|
-
"refName": "ctgA",
|
|
659
|
-
"source": "exonerate",
|
|
660
|
-
"start": 21200,
|
|
661
|
-
"strand": 1,
|
|
662
|
-
"transcript_id": "rna-Apple3",
|
|
663
|
-
"type": "UTR",
|
|
664
|
-
"uniqueId": "test-ctgA-5-7",
|
|
665
|
-
},
|
|
666
|
-
],
|
|
667
|
-
"transcript_id": "rna-Apple3",
|
|
668
|
-
"type": "transcript",
|
|
669
|
-
"uniqueId": "test-ctgA-5",
|
|
670
|
-
},
|
|
671
|
-
]
|
|
672
|
-
`;
|
|
673
|
-
|
|
674
|
-
exports[`can instantiate new GtfAdapter and check for demo data 1`] = `
|
|
675
|
-
[
|
|
676
|
-
{
|
|
677
|
-
"end": 107987,
|
|
678
|
-
"gene_biotype": "pseudogene",
|
|
679
|
-
"gene_id": "ENSVPAG00000000407",
|
|
680
|
-
"gene_source": "ensembl",
|
|
681
|
-
"gene_version": "1",
|
|
682
|
-
"name": "ENSVPAT00000000407",
|
|
683
|
-
"phase": 0,
|
|
684
|
-
"refName": "GeneScaffold_1",
|
|
685
|
-
"source": "ensembl",
|
|
686
|
-
"start": 107688,
|
|
687
|
-
"strand": 1,
|
|
688
|
-
"subfeatures": [
|
|
689
|
-
{
|
|
690
|
-
"end": 107715,
|
|
691
|
-
"exon_id": "ENSVPAE00000004844",
|
|
692
|
-
"exon_number": "1",
|
|
693
|
-
"exon_version": "1",
|
|
694
|
-
"gene_biotype": "pseudogene",
|
|
695
|
-
"gene_id": "ENSVPAG00000000407",
|
|
696
|
-
"gene_source": "ensembl",
|
|
697
|
-
"gene_version": "1",
|
|
698
|
-
"name": "ENSVPAT00000000407",
|
|
699
|
-
"parentId": "test-GeneScaffold_1-0",
|
|
700
|
-
"phase": 0,
|
|
701
|
-
"refName": "GeneScaffold_1",
|
|
702
|
-
"source": "ensembl",
|
|
703
|
-
"start": 107688,
|
|
704
|
-
"strand": 1,
|
|
705
|
-
"transcript_biotype": "pseudogene",
|
|
706
|
-
"transcript_id": "ENSVPAT00000000407",
|
|
707
|
-
"transcript_source": "ensembl",
|
|
708
|
-
"transcript_version": "1",
|
|
709
|
-
"type": "exon",
|
|
710
|
-
"uniqueId": "test-GeneScaffold_1-0-0",
|
|
711
|
-
},
|
|
712
|
-
{
|
|
713
|
-
"end": 107812,
|
|
714
|
-
"exon_id": "ENSVPAE00000004847",
|
|
715
|
-
"exon_number": "2",
|
|
716
|
-
"exon_version": "1",
|
|
717
|
-
"gene_biotype": "pseudogene",
|
|
718
|
-
"gene_id": "ENSVPAG00000000407",
|
|
719
|
-
"gene_source": "ensembl",
|
|
720
|
-
"gene_version": "1",
|
|
721
|
-
"name": "ENSVPAT00000000407",
|
|
722
|
-
"parentId": "test-GeneScaffold_1-0",
|
|
723
|
-
"phase": 0,
|
|
724
|
-
"refName": "GeneScaffold_1",
|
|
725
|
-
"source": "ensembl",
|
|
726
|
-
"start": 107716,
|
|
727
|
-
"strand": 1,
|
|
728
|
-
"transcript_biotype": "pseudogene",
|
|
729
|
-
"transcript_id": "ENSVPAT00000000407",
|
|
730
|
-
"transcript_source": "ensembl",
|
|
731
|
-
"transcript_version": "1",
|
|
732
|
-
"type": "exon",
|
|
733
|
-
"uniqueId": "test-GeneScaffold_1-0-1",
|
|
734
|
-
},
|
|
735
|
-
{
|
|
736
|
-
"end": 107877,
|
|
737
|
-
"exon_id": "ENSVPAE00000004849",
|
|
738
|
-
"exon_number": "3",
|
|
739
|
-
"exon_version": "1",
|
|
740
|
-
"gene_biotype": "pseudogene",
|
|
741
|
-
"gene_id": "ENSVPAG00000000407",
|
|
742
|
-
"gene_source": "ensembl",
|
|
743
|
-
"gene_version": "1",
|
|
744
|
-
"name": "ENSVPAT00000000407",
|
|
745
|
-
"parentId": "test-GeneScaffold_1-0",
|
|
746
|
-
"phase": 0,
|
|
747
|
-
"refName": "GeneScaffold_1",
|
|
748
|
-
"source": "ensembl",
|
|
749
|
-
"start": 107823,
|
|
750
|
-
"strand": 1,
|
|
751
|
-
"transcript_biotype": "pseudogene",
|
|
752
|
-
"transcript_id": "ENSVPAT00000000407",
|
|
753
|
-
"transcript_source": "ensembl",
|
|
754
|
-
"transcript_version": "1",
|
|
755
|
-
"type": "exon",
|
|
756
|
-
"uniqueId": "test-GeneScaffold_1-0-2",
|
|
757
|
-
},
|
|
758
|
-
{
|
|
759
|
-
"end": 107895,
|
|
760
|
-
"exon_id": "ENSVPAE00000156282",
|
|
761
|
-
"exon_number": "4",
|
|
762
|
-
"exon_version": "1",
|
|
763
|
-
"gene_biotype": "pseudogene",
|
|
764
|
-
"gene_id": "ENSVPAG00000000407",
|
|
765
|
-
"gene_source": "ensembl",
|
|
766
|
-
"gene_version": "1",
|
|
767
|
-
"name": "ENSVPAT00000000407",
|
|
768
|
-
"parentId": "test-GeneScaffold_1-0",
|
|
769
|
-
"phase": 0,
|
|
770
|
-
"refName": "GeneScaffold_1",
|
|
771
|
-
"source": "ensembl",
|
|
772
|
-
"start": 107880,
|
|
773
|
-
"strand": 1,
|
|
774
|
-
"transcript_biotype": "pseudogene",
|
|
775
|
-
"transcript_id": "ENSVPAT00000000407",
|
|
776
|
-
"transcript_source": "ensembl",
|
|
777
|
-
"transcript_version": "1",
|
|
778
|
-
"type": "exon",
|
|
779
|
-
"uniqueId": "test-GeneScaffold_1-0-3",
|
|
780
|
-
},
|
|
781
|
-
{
|
|
782
|
-
"end": 107917,
|
|
783
|
-
"exon_id": "ENSVPAE00000188321",
|
|
784
|
-
"exon_number": "5",
|
|
785
|
-
"exon_version": "1",
|
|
786
|
-
"gene_biotype": "pseudogene",
|
|
787
|
-
"gene_id": "ENSVPAG00000000407",
|
|
788
|
-
"gene_source": "ensembl",
|
|
789
|
-
"gene_version": "1",
|
|
790
|
-
"name": "ENSVPAT00000000407",
|
|
791
|
-
"parentId": "test-GeneScaffold_1-0",
|
|
792
|
-
"phase": 0,
|
|
793
|
-
"refName": "GeneScaffold_1",
|
|
794
|
-
"source": "ensembl",
|
|
795
|
-
"start": 107899,
|
|
796
|
-
"strand": 1,
|
|
797
|
-
"transcript_biotype": "pseudogene",
|
|
798
|
-
"transcript_id": "ENSVPAT00000000407",
|
|
799
|
-
"transcript_source": "ensembl",
|
|
800
|
-
"transcript_version": "1",
|
|
801
|
-
"type": "exon",
|
|
802
|
-
"uniqueId": "test-GeneScaffold_1-0-4",
|
|
803
|
-
},
|
|
804
|
-
{
|
|
805
|
-
"end": 107987,
|
|
806
|
-
"exon_id": "ENSVPAE00000004854",
|
|
807
|
-
"exon_number": "6",
|
|
808
|
-
"exon_version": "1",
|
|
809
|
-
"gene_biotype": "pseudogene",
|
|
810
|
-
"gene_id": "ENSVPAG00000000407",
|
|
811
|
-
"gene_source": "ensembl",
|
|
812
|
-
"gene_version": "1",
|
|
813
|
-
"name": "ENSVPAT00000000407",
|
|
814
|
-
"parentId": "test-GeneScaffold_1-0",
|
|
815
|
-
"phase": 0,
|
|
816
|
-
"refName": "GeneScaffold_1",
|
|
817
|
-
"source": "ensembl",
|
|
818
|
-
"start": 107918,
|
|
819
|
-
"strand": 1,
|
|
820
|
-
"transcript_biotype": "pseudogene",
|
|
821
|
-
"transcript_id": "ENSVPAT00000000407",
|
|
822
|
-
"transcript_source": "ensembl",
|
|
823
|
-
"transcript_version": "1",
|
|
824
|
-
"type": "exon",
|
|
825
|
-
"uniqueId": "test-GeneScaffold_1-0-5",
|
|
826
|
-
},
|
|
827
|
-
],
|
|
828
|
-
"transcript_biotype": "pseudogene",
|
|
829
|
-
"transcript_id": "ENSVPAT00000000407",
|
|
830
|
-
"transcript_source": "ensembl",
|
|
831
|
-
"transcript_version": "1",
|
|
832
|
-
"type": "transcript",
|
|
833
|
-
"uniqueId": "test-GeneScaffold_1-0",
|
|
834
|
-
},
|
|
835
|
-
]
|
|
836
|
-
`;
|