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Support *.gff3.gz files as Genes annotations source #151

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iromeo opened this issue Jul 8, 2021 · 3 comments
Open

Support *.gff3.gz files as Genes annotations source #151

iromeo opened this issue Jul 8, 2021 · 3 comments

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@iromeo
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iromeo commented Jul 8, 2021

New CHM13 genome provides only *.gff3.gz files for genes annotations, see https://github.com/marbl/CHM13#v11. So we cannot configure genes markup for new genome in JBR
@iromeo
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iromeo commented Jul 8, 2021

image

Is result of opening new chm13t2t-v1.1 session after #150 workaround

@iromeo
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iromeo commented Jul 8, 2021

https://learn.gencore.bio.nyu.edu/ngs-file-formats/gff3-format/

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iromeo commented Jul 8, 2021 •
edited
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NB:

GFF3 file format is weird, e.g. here we have several transcripts with same ID ENST00000457736.1. Our GTF parser doesn't expect such usecase. We assume encode transcript is unique:

chr4	Liftoff	transcript	9127305	9128897	.	+	.	gene_name=USP17L11;source_gene=ENSG00000233136.2;gene_biotype=protein_coding;transcript_biotype=protein_coding;source_transcript=ENST00000457736.1;Name=USP17L11;source_gene_common_name=USP17L11;extra_paralog=True;gene_id=LOFF_G0002011;Parent=LOFF_G0002011;transcript_id=LOFF_T0002506;transcript_name=USP17L11-1;ID=LOFF_T0002506;alignment_id=N/A;alternative_source_transcripts=N/A;paralogy=N/A;unfiltered_paralogy=N/A;collapsed_gene_ids=N/A;collapsed_gene_names=N/A;frameshift=N/A;exon_annotation_support=N/A;intron_annotation_support=N/A;transcript_class=paralog;transcript_modes=Liftoff;valid_start=N/A;valid_stop=N/A;proper_orf=N/A
chr4	Liftoff	exon	9127305	9128897	.	+	.	gene_name=USP17L11;source_gene=ENSG00000233136.2;gene_biotype=protein_coding;transcript_biotype=protein_coding;source_transcript=ENST00000457736.1;Name=USP17L11;source_gene_common_name=USP17L11;extra_paralog=True;gene_id=LOFF_G0002011;transcript_id=LOFF_T0002506;transcript_name=USP17L11-0;Parent=LOFF_T0002506;ID=exon:LOFF_T0002506:0;alignment_id=N/A;alternative_source_transcripts=N/A;paralogy=N/A;unfiltered_paralogy=N/A;collapsed_gene_ids=N/A;collapsed_gene_names=N/A;frameshift=N/A;exon_annotation_support=N/A;intron_annotation_support=N/A;transcript_class=paralog;transcript_modes=Liftoff;valid_start=N/A;valid_stop=N/A;proper_orf=N/A
chr4	Liftoff	CDS	9127305	9128897	.	+	0	gene_name=USP17L11;source_gene=ENSG00000233136.2;gene_biotype=protein_coding;transcript_biotype=protein_coding;source_transcript=ENST00000457736.1;Name=USP17L11;source_gene_common_name=USP17L11;extra_paralog=True;gene_id=LOFF_G0002011;transcript_id=LOFF_T0002506;transcript_name=USP17L11-0;Parent=LOFF_T0002506;ID=CDS:LOFF_T0002506:0;alignment_id=N/A;alternative_source_transcripts=N/A;paralogy=N/A;unfiltered_paralogy=N/A;collapsed_gene_ids=N/A;collapsed_gene_names=N/A;frameshift=N/A;exon_annotation_support=N/A;intron_annotation_support=N/A;transcript_class=paralog;transcript_modes=Liftoff;valid_start=N/A;valid_stop=N/A;proper_orf=N/A
chr4	Liftoff	transcript	9132054	9133646	.	+	.	gene_name=USP17L11;source_gene=ENSG00000233136.2;gene_biotype=protein_coding;transcript_biotype=protein_coding;source_transcript=ENST00000457736.1;Name=USP17L11;source_gene_common_name=USP17L11;extra_paralog=True;gene_id=LOFF_G0002012;Parent=LOFF_G0002012;transcript_id=LOFF_T0002508;transcript_name=USP17L11-1;ID=LOFF_T0002508;alignment_id=N/A;alternative_source_transcripts=N/A;paralogy=N/A;unfiltered_paralogy=N/A;collapsed_gene_ids=N/A;collapsed_gene_names=N/A;frameshift=N/A;exon_annotation_support=N/A;intron_annotation_support=N/A;transcript_class=paralog;transcript_modes=Liftoff;valid_start=N/A;valid_stop=N/A;proper_orf=N/A
chr4	Liftoff	exon	9132054	9133646	.	+	.	gene_name=USP17L11;source_gene=ENSG00000233136.2;gene_biotype=protein_coding;transcript_biotype=protein_coding;source_transcript=ENST00000457736.1;Name=USP17L11;source_gene_common_name=USP17L11;extra_paralog=True;gene_id=LOFF_G0002012;transcript_id=LOFF_T0002508;transcript_name=USP17L11-0;Parent=LOFF_T0002508;ID=exon:LOFF_T0002508:0;alignment_id=N/A;alternative_source_transcripts=N/A;paralogy=N/A;unfiltered_paralogy=N/A;collapsed_gene_ids=N/A;collapsed_gene_names=N/A;frameshift=N/A;exon_annotation_support=N/A;intron_annotation_support=N/A;transcript_class=paralog;transcript_modes=Liftoff;valid_start=N/A;valid_stop=N/A;proper_orf=N/A
chr4	Liftoff	CDS	9132054	9133646	.	+	0	gene_name=USP17L11;source_gene=ENSG00000233136.2;gene_biotype=protein_coding;transcript_biotype=protein_coding;source_transcript=ENST00000457736.1;Name=USP17L11;source_gene_common_name=USP17L11;extra_paralog=True;gene_id=LOFF_G0002012;transcript_id=LOFF_T0002508;transcript_name=USP17L11-0;Parent=LOFF_T0002508;ID=CDS:LOFF_T0002508:0;alignment_id=N/A;alternative_source_transcripts=N/A;paralogy=N/A;unfiltered_paralogy=N/A;collapsed_gene_ids=N/A;collapsed_gene_names=N/A;frameshift=N/A;exon_annotation_support=N/A;intron_annotation_support=N/A;transcript_class=paralog;transcript_modes=Liftoff;valid_start=N/A;valid_stop=N/A;proper_orf=N/A
chr4	Liftoff	transcript	9136804	9138396	.	+	.	gene_name=USP17L11;source_gene=ENSG00000233136.2;gene_biotype=protein_coding;transcript_biotype=protein_coding;source_transcript=ENST00000457736.1;Name=USP17L11;source_gene_common_name=USP17L11;extra_paralog=True;gene_id=LOFF_G0002013;Parent=LOFF_G0002013;transcript_id=LOFF_T0002510;transcript_name=USP17L11-1;ID=LOFF_T0002510;alignment_id=N/A;alternative_source_transcripts=N/A;paralogy=N/A;unfiltered_paralogy=N/A;collapsed_gene_ids=N/A;collapsed_gene_names=N/A;frameshift=N/A;exon_annotation_support=N/A;intron_annotation_support=N/A;transcript_class=paralog;transcript_modes=Liftoff;valid_start=N/A;valid_stop=N/A;proper_orf=N/A
chr4	Liftoff	exon	9136804	9138396	.	+	.	gene_name=USP17L11;source_gene=ENSG00000233136.2;gene_biotype=protein_coding;transcript_biotype=protein_coding;source_transcript=ENST00000457736.1;Name=USP17L11;source_gene_common_name=USP17L11;extra_paralog=True;gene_id=LOFF_G0002013;transcript_id=LOFF_T0002510;transcript_name=USP17L11-0;Parent=LOFF_T0002510;ID=exon:LOFF_T0002510:0;alignment_id=N/A;alternative_source_transcripts=N/A;paralogy=N/A;unfiltered_paralogy=N/A;collapsed_gene_ids=N/A;collapsed_gene_names=N/A;frameshift=N/A;exon_annotation_support=N/A;intron_annotation_support=N/A;transcript_class=paralog;transcript_modes=Liftoff;valid_start=N/A;valid_stop=N/A;proper_orf=N/A
chr4	Liftoff	CDS	9136804	9138396	.	+	0	gene_name=USP17L11;source_gene=ENSG00000233136.2;gene_biotype=protein_coding;transcript_biotype=protein_coding;source_transcript=ENST00000457736.1;Name=USP17L11;source_gene_common_name=USP17L11;extra_paralog=True;gene_id=LOFF_G0002013;transcript_id=LOFF_T0002510;transcript_name=USP17L11-0;Parent=LOFF_T0002510;ID=CDS:LOFF_T0002510:0;alignment_id=N/A;alternative_source_transcripts=N/A;paralogy=N/A;unfiltered_paralogy=N/A;collapsed_gene_ids=N/A;collapsed_gene_names=N/A;frameshift=N/A;exon_annotation_support=N/A;intron_annotation_support=N/A;transcript_class=paralog;transcript_modes=Liftoff;valid_start=N/A;valid_stop=N/A;proper_orf=N/A
chr4	Liftoff	transcript	9141553	9143145	.	+	.	gene_name=USP17L11;source_gene=ENSG00000233136.2;gene_biotype=protein_coding;transcript_biotype=protein_coding;source_transcript=ENST00000457736.1;Name=USP17L11;source_gene_common_name=USP17L11;extra_paralog=True;gene_id=LOFF_G0002014;Parent=LOFF_G0002014;transcript_id=LOFF_T0002512;transcript_name=USP17L11-1;ID=LOFF_T0002512;alignment_id=N/A;alternative_source_transcripts=N/A;paralogy=N/A;unfiltered_paralogy=N/A;collapsed_gene_ids=N/A;collapsed_gene_names=N/A;frameshift=N/A;exon_annotation_support=N/A;intron_annotation_support=N/A;transcript_class=paralog;transcript_modes=Liftoff;valid_start=N/A;valid_stop=N/A;proper_orf=N/A
chr4	Liftoff	exon	9141553	9143145	.	+	.	gene_name=USP17L11;source_gene=ENSG00000233136.2;gene_biotype=protein_coding;transcript_biotype=protein_coding;source_transcript=ENST00000457736.1;Name=USP17L11;source_gene_common_name=USP17L11;extra_paralog=True;gene_id=LOFF_G0002014;transcript_id=LOFF_T0002512;transcript_name=USP17L11-0;Parent=LOFF_T0002512;ID=exon:LOFF_T0002512:0;alignment_id=N/A;alternative_source_transcripts=N/A;paralogy=N/A;unfiltered_paralogy=N/A;collapsed_gene_ids=N/A;collapsed_gene_names=N/A;frameshift=N/A;exon_annotation_support=N/A;intron_annotation_support=N/A;transcript_class=paralog;transcript_modes=Liftoff;valid_start=N/A;valid_stop=N/A;proper_orf=N/A
chr4	Liftoff	CDS	9141553	9143145	.	+	0	gene_name=USP17L11;source_gene=ENSG00000233136.2;gene_biotype=protein_coding;transcript_biotype=protein_coding;source_transcript=ENST00000457736.1;Name=USP17L11;source_gene_common_name=USP17L11;extra_paralog=True;gene_id=LOFF_G0002014;transcript_id=LOFF_T0002512;transcript_name=USP17L11-0;Parent=LOFF_T0002512;ID=CDS:LOFF_T0002512:0;alignment_id=N/A;alternative_source_transcripts=N/A;paralogy=N/A;unfiltered_paralogy=N/A;collapsed_gene_ids=N/A;collapsed_gene_names=N/A;frameshift=N/A;exon_annotation_support=N/A;intron_annotation_support=N/A;transcript_class=paralog;transcript_modes=Liftoff;valid_start=N/A;valid_stop=N/A;proper_orf=N/A
chr4	Liftoff	transcript	9146303	9147895	.	+	.	gene_name=USP17L11;source_gene=ENSG00000233136.2;gene_biotype=protein_coding;transcript_biotype=protein_coding;source_transcript=ENST00000457736.1;Name=USP17L11;source_gene_common_name=USP17L11;extra_paralog=True;gene_id=LOFF_G0002015;Parent=LOFF_G0002015;transcript_id=LOFF_T0002514;transcript_name=USP17L11-1;ID=LOFF_T0002514;alignment_id=N/A;alternative_source_transcripts=N/A;paralogy=N/A;unfiltered_paralogy=N/A;collapsed_gene_ids=N/A;collapsed_gene_names=N/A;frameshift=N/A;exon_annotation_support=N/A;intron_annotation_support=N/A;transcript_class=paralog;transcript_modes=Liftoff;valid_start=N/A;valid_stop=N/A;proper_orf=N/A
chr4	Liftoff	exon	9146303	9147895	.	+	.	gene_name=USP17L11;source_gene=ENSG00000233136.2;gene_biotype=protein_coding;transcript_biotype=protein_coding;source_transcript=ENST00000457736.1;Name=USP17L11;source_gene_common_name=USP17L11;extra_paralog=True;gene_id=LOFF_G0002015;transcript_id=LOFF_T0002514;transcript_name=USP17L11-0;Parent=LOFF_T0002514;ID=exon:LOFF_T0002514:0;alignment_id=N/A;alternative_source_transcripts=N/A;paralogy=N/A;unfiltered_paralogy=N/A;collapsed_gene_ids=N/A;collapsed_gene_names=N/A;frameshift=N/A;exon_annotation_support=N/A;intron_annotation_support=N/A;transcript_class=paralog;transcript_modes=Liftoff;valid_start=N/A;valid_stop=N/A;proper_orf=N/A
chr4	Liftoff	CDS	9146303	9147895	.	+	0	gene_name=USP17L11;source_gene=ENSG00000233136.2;gene_biotype=protein_coding;transcript_biotype=protein_coding;source_transcript=ENST00000457736.1;Name=USP17L11;source_gene_common_name=USP17L11;extra_paralog=True;gene_id=LOFF_G0002015;transcript_id=LOFF_T0002514;transcript_name=USP17L11-0;Parent=LOFF_T0002514;ID=CDS:LOFF_T0002514:0;alignment_id=N/A;alternative_source_transcripts=N/A;paralogy=N/A;unfiltered_paralogy=N/A;collapsed_gene_ids=N/A;collapsed_gene_names=N/A;frameshift=N/A;exon_annotation_support=N/A;intron_annotation_support=N/A;transcript_class=paralog;transcript_modes=Liftoff;valid_start=N/A;valid_stop=N/A;proper_orf=N/A
chr4	Liftoff	transcript	9151054	9152646	.	+	.	gene_name=USP17L11;source_gene=ENSG00000233136.2;gene_biotype=protein_coding;transcript_biotype=protein_coding;source_transcript=ENST00000457736.1;Name=USP17L11;source_gene_common_name=USP17L11;extra_paralog=True;gene_id=LOFF_G0002016;Parent=LOFF_G0002016;transcript_id=LOFF_T0002516;transcript_name=USP17L11-1;ID=LOFF_T0002516;alignment_id=N/A;alternative_source_transcripts=N/A;paralogy=N/A;unfiltered_paralogy=N/A;collapsed_gene_ids=N/A;collapsed_gene_names=N/A;frameshift=N/A;exon_annotation_support=N/A;intron_annotation_support=N/A;transcript_class=paralog;transcript_modes=Liftoff;valid_start=N/A;valid_stop=N/A;proper_orf=N/A
chr4	Liftoff	exon	9151054	9152646	.	+	.	gene_name=USP17L11;source_gene=ENSG00000233136.2;gene_biotype=protein_coding;transcript_biotype=protein_coding;source_transcript=ENST00000457736.1;Name=USP17L11;source_gene_common_name=USP17L11;extra_paralog=True;gene_id=LOFF_G0002016;transcript_id=LOFF_T0002516;transcript_name=USP17L11-0;Parent=LOFF_T0002516;ID=exon:LOFF_T0002516:0;alignment_id=N/A;alternative_source_transcripts=N/A;paralogy=N/A;unfiltered_paralogy=N/A;collapsed_gene_ids=N/A;collapsed_gene_names=N/A;frameshift=N/A;exon_annotation_support=N/A;intron_annotation_support=N/A;transcript_class=paralog;transcript_modes=Liftoff;valid_start=N/A;valid_stop=N/A;proper_orf=N/A
chr4	Liftoff	CDS	9151054	9152646	.	+	0	gene_name=USP17L11;source_gene=ENSG00000233136.2;gene_biotype=protein_coding;transcript_biotype=protein_coding;source_transcript=ENST00000457736.1;Name=USP17L11;source_gene_common_name=USP17L11;extra_paralog=True;gene_id=LOFF_G0002016;transcript_id=LOFF_T0002516;transcript_name=USP17L11-0;Parent=LOFF_T0002516;ID=CDS:LOFF_T0002516:0;alignment_id=N/A;alternative_source_transcripts=N/A;paralogy=N/A;unfiltered_paralogy=N/A;collapsed_gene_ids=N/A;collapsed_gene_names=N/A;frameshift=N/A;exon_annotation_support=N/A;intron_annotation_support=N/A;transcript_class=paralog;transcript_modes=Liftoff;valid_start=N/A;valid_stop=N/A;proper_orf=N/A
chr4	Liftoff	transcript	9165302	9166894	.	+	.	gene_name=USP17L11;source_gene=ENSG00000233136.2;gene_biotype=protein_coding;transcript_biotype=protein_coding;source_transcript=ENST00000457736.1;Name=USP17L11;source_gene_common_name=USP17L11;extra_paralog=True;gene_id=LOFF_G0002019;Parent=LOFF_G0002019;transcript_id=LOFF_T0002521;transcript_name=USP17L11-1;ID=LOFF_T0002521;alignment_id=N/A;alternative_source_transcripts=N/A;paralogy=N/A;unfiltered_paralogy=N/A;collapsed_gene_ids=N/A;collapsed_gene_names=N/A;frameshift=N/A;exon_annotation_support=N/A;intron_annotation_support=N/A;transcript_class=paralog;transcript_modes=Liftoff;valid_start=N/A;valid_stop=N/A;proper_orf=N/A
chr4	Liftoff	exon	9165302	9166894	.	+	.	gene_name=USP17L11;source_gene=ENSG00000233136.2;gene_biotype=protein_coding;transcript_biotype=protein_coding;source_transcript=ENST00000457736.1;Name=USP17L11;source_gene_common_name=USP17L11;extra_paralog=True;gene_id=LOFF_G0002019;transcript_id=LOFF_T0002521;transcript_name=USP17L11-0;Parent=LOFF_T0002521;ID=exon:LOFF_T0002521:0;alignment_id=N/A;alternative_source_transcripts=N/A;paralogy=N/A;unfiltered_paralogy=N/A;collapsed_gene_ids=N/A;collapsed_gene_names=N/A;frameshift=N/A;exon_annotation_support=N/A;intron_annotation_support=N/A;transcript_class=paralog;transcript_modes=Liftoff;valid_start=N/A;valid_stop=N/A;proper_orf=N/A
chr4	Liftoff	CDS	9165302	9166894	.	+	0	gene_name=USP17L11;source_gene=ENSG00000233136.2;gene_biotype=protein_coding;transcript_biotype=protein_coding;source_transcript=ENST00000457736.1;Name=USP17L11;source_gene_common_name=USP17L11;extra_paralog=True;gene_id=LOFF_G0002019;transcript_id=LOFF_T0002521;transcript_name=USP17L11-0;Parent=LOFF_T0002521;ID=CDS:LOFF_T0002521:0;alignment_id=N/A;alternative_source_transcripts=N/A;paralogy=N/A;unfiltered_paralogy=N/A;collapsed_gene_ids=N/A;collapsed_gene_names=N/A;frameshift=N/A;exon_annotation_support=N/A;intron_annotation_support=N/A;transcript_class=paralog;transcript_modes=Liftoff;valid_start=N/A;valid_stop=N/A;proper_orf=N/A
chr4	Liftoff	transcript	9170051	9171643	.	+	.	gene_name=USP17L11;source_gene=ENSG00000233136.2;gene_biotype=protein_coding;transcript_biotype=protein_coding;source_transcript=ENST00000457736.1;Name=USP17L11;source_gene_common_name=USP17L11;extra_paralog=True;gene_id=LOFF_G0002020;Parent=LOFF_G0002020;transcript_id=LOFF_T0002523;transcript_name=USP17L11-1;ID=LOFF_T0002523;alignment_id=N/A;alternative_source_transcripts=N/A;paralogy=N/A;unfiltered_paralogy=N/A;collapsed_gene_ids=N/A;collapsed_gene_names=N/A;frameshift=N/A;exon_annotation_support=N/A;intron_annotation_support=N/A;transcript_class=paralog;transcript_modes=Liftoff;valid_start=N/A;valid_stop=N/A;proper_orf=N/A
chr4	Liftoff	exon	9170051	9171643	.	+	.	gene_name=USP17L11;source_gene=ENSG00000233136.2;gene_biotype=protein_coding;transcript_biotype=protein_coding;source_transcript=ENST00000457736.1;Name=USP17L11;source_gene_common_name=USP17L11;extra_paralog=True;gene_id=LOFF_G0002020;transcript_id=LOFF_T0002523;transcript_name=USP17L11-0;Parent=LOFF_T0002523;ID=exon:LOFF_T0002523:0;alignment_id=N/A;alternative_source_transcripts=N/A;paralogy=N/A;unfiltered_paralogy=N/A;collapsed_gene_ids=N/A;collapsed_gene_names=N/A;frameshift=N/A;exon_annotation_support=N/A;intron_annotation_support=N/A;transcript_class=paralog;transcript_modes=Liftoff;valid_start=N/A;valid_stop=N/A;proper_orf=N/A
chr4	Liftoff	CDS	9170051	9171643	.	+	0	gene_name=USP17L11;source_gene=ENSG00000233136.2;gene_biotype=protein_coding;transcript_biotype=protein_coding;source_transcript=ENST00000457736.1;Name=USP17L11;source_gene_common_name=USP17L11;extra_paralog=True;gene_id=LOFF_G0002020;transcript_id=LOFF_T0002523;transcript_name=USP17L11-0;Parent=LOFF_T0002523;ID=CDS:LOFF_T0002523:0;alignment_id=N/A;alternative_source_transcripts=N/A;paralogy=N/A;unfiltered_paralogy=N/A;collapsed_gene_ids=N/A;collapsed_gene_names=N/A;frameshift=N/A;exon_annotation_support=N/A;intron_annotation_support=N/A;transcript_class=paralog;transcript_modes=Liftoff;valid_start=N/A;valid_stop=N/A;proper_orf=N/A
chr4	Liftoff	transcript	9174798	9176390	.	+	.	gene_name=USP17L11;source_gene=ENSG00000233136.2;gene_biotype=protein_coding;transcript_biotype=protein_coding;source_transcript=ENST00000457736.1;Name=USP17L11;source_gene_common_name=USP17L11;extra_paralog=True;gene_id=LOFF_G0002021;Parent=LOFF_G0002021;transcript_id=LOFF_T0002525;transcript_name=USP17L11-1;ID=LOFF_T0002525;alignment_id=N/A;alternative_source_transcripts=N/A;paralogy=N/A;unfiltered_paralogy=N/A;collapsed_gene_ids=N/A;collapsed_gene_names=N/A;frameshift=N/A;exon_annotation_support=N/A;intron_annotation_support=N/A;transcript_class=paralog;transcript_modes=Liftoff;valid_start=N/A;valid_stop=N/A;proper_orf=N/A
chr4	Liftoff	exon	9174798	9176390	.	+	.	gene_name=USP17L11;source_gene=ENSG00000233136.2;gene_biotype=protein_coding;transcript_biotype=protein_coding;source_transcript=ENST00000457736.1;Name=USP17L11;source_gene_common_name=USP17L11;extra_paralog=True;gene_id=LOFF_G0002021;transcript_id=LOFF_T0002525;transcript_name=USP17L11-0;Parent=LOFF_T0002525;ID=exon:LOFF_T0002525:0;alignment_id=N/A;alternative_source_transcripts=N/A;paralogy=N/A;unfiltered_paralogy=N/A;collapsed_gene_ids=N/A;collapsed_gene_names=N/A;frameshift=N/A;exon_annotation_support=N/A;intron_annotation_support=N/A;transcript_class=paralog;transcript_modes=Liftoff;valid_start=N/A;valid_stop=N/A;proper_orf=N/A
chr4	Liftoff	CDS	9174798	9176390	.	+	0	gene_name=USP17L11;source_gene=ENSG00000233136.2;gene_biotype=protein_coding;transcript_biotype=protein_coding;source_transcript=ENST00000457736.1;Name=USP17L11;source_gene_common_name=USP17L11;extra_paralog=True;gene_id=LOFF_G0002021;transcript_id=LOFF_T0002525;transcript_name=USP17L11-0;Parent=LOFF_T0002525;ID=CDS:LOFF_T0002525:0;alignment_id=N/A;alternative_source_transcripts=N/A;paralogy=N/A;unfiltered_paralogy=N/A;collapsed_gene_ids=N/A;collapsed_gene_names=N/A;frameshift=N/A;exon_annotation_support=N/A;intron_annotation_support=N/A;transcript_class=paralog;transcript_modes=Liftoff;valid_start=N/A;valid_stop=N/A;proper_orf=N/A
chr4	Liftoff	transcript	9184299	9185891	.	+	.	gene_name=USP17L11;source_gene=ENSG00000233136.2;gene_biotype=protein_coding;transcript_biotype=protein_coding;source_transcript=ENST00000457736.1;Name=USP17L11;source_gene_common_name=USP17L11;extra_paralog=True;gene_id=LOFF_G0002023;Parent=LOFF_G0002023;transcript_id=LOFF_T0002528;transcript_name=USP17L11-1;ID=LOFF_T0002528;alignment_id=N/A;alternative_source_transcripts=N/A;paralogy=N/A;unfiltered_paralogy=N/A;collapsed_gene_ids=N/A;collapsed_gene_names=N/A;frameshift=N/A;exon_annotation_support=N/A;intron_annotation_support=N/A;transcript_class=paralog;transcript_modes=Liftoff;valid_start=N/A;valid_stop=N/A;proper_orf=N/A
chr4	Liftoff	exon	9184299	9185891	.	+	.	gene_name=USP17L11;source_gene=ENSG00000233136.2;gene_biotype=protein_coding;transcript_biotype=protein_coding;source_transcript=ENST00000457736.1;Name=USP17L11;source_gene_common_name=USP17L11;extra_paralog=True;gene_id=LOFF_G0002023;transcript_id=LOFF_T0002528;transcript_name=USP17L11-0;Parent=LOFF_T0002528;ID=exon:LOFF_T0002528:0;alignment_id=N/A;alternative_source_transcripts=N/A;paralogy=N/A;unfiltered_paralogy=N/A;collapsed_gene_ids=N/A;collapsed_gene_names=N/A;frameshift=N/A;exon_annotation_support=N/A;intron_annotation_support=N/A;transcript_class=paralog;transcript_modes=Liftoff;valid_start=N/A;valid_stop=N/A;proper_orf=N/A
chr4	Liftoff	CDS	9184299	9185891	.	+	0	gene_name=USP17L11;source_gene=ENSG00000233136.2;gene_biotype=protein_coding;transcript_biotype=protein_coding;source_transcript=ENST00000457736.1;Name=USP17L11;source_gene_common_name=USP17L11;extra_paralog=True;gene_id=LOFF_G0002023;transcript_id=LOFF_T0002528;transcript_name=USP17L11-0;Parent=LOFF_T0002528;ID=CDS:LOFF_T0002528:0;alignment_id=N/A;alternative_source_transcripts=N/A;paralogy=N/A;unfiltered_paralogy=N/A;collapsed_gene_ids=N/A;collapsed_gene_names=N/A;frameshift=N/A;exon_annotation_support=N/A;intron_annotation_support=N/A;transcript_class=paralog;transcript_modes=Liftoff;valid_start=N/A;valid_stop=N/A;proper_orf=N/A
chr4	Liftoff	transcript	9189049	9190641	.	+	.	gene_name=USP17L11;source_gene=ENSG00000233136.2;gene_biotype=protein_coding;transcript_biotype=protein_coding;source_transcript=ENST00000457736.1;Name=USP17L11;source_gene_common_name=USP17L11;extra_paralog=True;gene_id=LOFF_G0002024;Parent=LOFF_G0002024;transcript_id=LOFF_T0002530;transcript_name=USP17L11-1;ID=LOFF_T0002530;alignment_id=N/A;alternative_source_transcripts=N/A;paralogy=N/A;unfiltered_paralogy=N/A;collapsed_gene_ids=N/A;collapsed_gene_names=N/A;frameshift=N/A;exon_annotation_support=N/A;intron_annotation_support=N/A;transcript_class=paralog;transcript_modes=Liftoff;valid_start=N/A;valid_stop=N/A;proper_orf=N/A
chr4	Liftoff	exon	9189049	9190641	.	+	.	gene_name=USP17L11;source_gene=ENSG00000233136.2;gene_biotype=protein_coding;transcript_biotype=protein_coding;source_transcript=ENST00000457736.1;Name=USP17L11;source_gene_common_name=USP17L11;extra_paralog=True;gene_id=LOFF_G0002024;transcript_id=LOFF_T0002530;transcript_name=USP17L11-0;Parent=LOFF_T0002530;ID=exon:LOFF_T0002530:0;alignment_id=N/A;alternative_source_transcripts=N/A;paralogy=N/A;unfiltered_paralogy=N/A;collapsed_gene_ids=N/A;collapsed_gene_names=N/A;frameshift=N/A;exon_annotation_support=N/A;intron_annotation_support=N/A;transcript_class=paralog;transcript_modes=Liftoff;valid_start=N/A;valid_stop=N/A;proper_orf=N/A
chr4	Liftoff	CDS	9189049	9190641	.	+	0	gene_name=USP17L11;source_gene=ENSG00000233136.2;gene_biotype=protein_coding;transcript_biotype=protein_coding;source_transcript=ENST00000457736.1;Name=USP17L11;source_gene_common_name=USP17L11;extra_paralog=True;gene_id=LOFF_G0002024;transcript_id=LOFF_T0002530;transcript_name=USP17L11-0;Parent=LOFF_T0002530;ID=CDS:LOFF_T0002530:0;alignment_id=N/A;alternative_source_transcripts=N/A;paralogy=N/A;unfiltered_paralogy=N/A;collapsed_gene_ids=N/A;collapsed_gene_names=N/A;frameshift=N/A;exon_annotation_support=N/A;intron_annotation_support=N/A;transcript_class=paralog;transcript_modes=Liftoff;valid_start=N/A;valid_stop=N/A;proper_orf=N/A
chr4	Liftoff	transcript	9193800	9195392	.	+	.	gene_name=USP17L11;source_gene=ENSG00000233136.2;gene_biotype=protein_coding;transcript_biotype=protein_coding;source_transcript=ENST00000457736.1;Name=USP17L11;source_gene_common_name=USP17L11;extra_paralog=True;gene_id=LOFF_G0002025;Parent=LOFF_G0002025;transcript_id=LOFF_T0002532;transcript_name=USP17L11-1;ID=LOFF_T0002532;alignment_id=N/A;alternative_source_transcripts=N/A;paralogy=N/A;unfiltered_paralogy=N/A;collapsed_gene_ids=N/A;collapsed_gene_names=N/A;frameshift=N/A;exon_annotation_support=N/A;intron_annotation_support=N/A;transcript_class=paralog;transcript_modes=Liftoff;valid_start=N/A;valid_stop=N/A;proper_orf=N/A
chr4	Liftoff	exon	9193800	9195392	.	+	.	gene_name=USP17L11;source_gene=ENSG00000233136.2;gene_biotype=protein_coding;transcript_biotype=protein_coding;source_transcript=ENST00000457736.1;Name=USP17L11;source_gene_common_name=USP17L11;extra_paralog=True;gene_id=LOFF_G0002025;transcript_id=LOFF_T0002532;transcript_name=USP17L11-0;Parent=LOFF_T0002532;ID=exon:LOFF_T0002532:0;alignment_id=N/A;alternative_source_transcripts=N/A;paralogy=N/A;unfiltered_paralogy=N/A;collapsed_gene_ids=N/A;collapsed_gene_names=N/A;frameshift=N/A;exon_annotation_support=N/A;intron_annotation_support=N/A;transcript_class=paralog;transcript_modes=Liftoff;valid_start=N/A;valid_stop=N/A;proper_orf=N/A
chr4	Liftoff	CDS	9193800	9195392	.	+	0	gene_name=USP17L11;source_gene=ENSG00000233136.2;gene_biotype=protein_coding;transcript_biotype=protein_coding;source_transcript=ENST00000457736.1;Name=USP17L11;source_gene_common_name=USP17L11;extra_paralog=True;gene_id=LOFF_G0002025;transcript_id=LOFF_T0002532;transcript_name=USP17L11-0;Parent=LOFF_T0002532;ID=CDS:LOFF_T0002532:0;alignment_id=N/A;alternative_source_transcripts=N/A;paralogy=N/A;unfiltered_paralogy=N/A;collapsed_gene_ids=N/A;collapsed_gene_names=N/A;frameshift=N/A;exon_annotation_support=N/A;intron_annotation_support=N/A;transcript_class=paralog;transcript_modes=Liftoff;valid_start=N/A;valid_stop=N/A;proper_orf=N/A
chr4	Liftoff	transcript	9198551	9200143	.	+	.	gene_name=USP17L11;source_gene=ENSG00000233136.2;gene_biotype=protein_coding;transcript_biotype=protein_coding;source_transcript=ENST00000457736.1;Name=USP17L11;source_gene_common_name=USP17L11;extra_paralog=True;gene_id=LOFF_G0002026;Parent=LOFF_G0002026;transcript_id=LOFF_T0002534;transcript_name=USP17L11-1;ID=LOFF_T0002534;alignment_id=N/A;alternative_source_transcripts=N/A;paralogy=N/A;unfiltered_paralogy=N/A;collapsed_gene_ids=N/A;collapsed_gene_names=N/A;frameshift=N/A;exon_annotation_support=N/A;intron_annotation_support=N/A;transcript_class=paralog;transcript_modes=Liftoff;valid_start=N/A;valid_stop=N/A;proper_orf=N/A
chr4	Liftoff	exon	9198551	9200143	.	+	.	gene_name=USP17L11;source_gene=ENSG00000233136.2;gene_biotype=protein_coding;transcript_biotype=protein_coding;source_transcript=ENST00000457736.1;Name=USP17L11;source_gene_common_name=USP17L11;extra_paralog=True;gene_id=LOFF_G0002026;transcript_id=LOFF_T0002534;transcript_name=USP17L11-0;Parent=LOFF_T0002534;ID=exon:LOFF_T0002534:0;alignment_id=N/A;alternative_source_transcripts=N/A;paralogy=N/A;unfiltered_paralogy=N/A;collapsed_gene_ids=N/A;collapsed_gene_names=N/A;frameshift=N/A;exon_annotation_support=N/A;intron_annotation_support=N/A;transcript_class=paralog;transcript_modes=Liftoff;valid_start=N/A;valid_stop=N/A;proper_orf=N/A
chr4	Liftoff	CDS	9198551	9200143	.	+	0	gene_name=USP17L11;source_gene=ENSG00000233136.2;gene_biotype=protein_coding;transcript_biotype=protein_coding;source_transcript=ENST00000457736.1;Name=USP17L11;source_gene_common_name=USP17L11;extra_paralog=True;gene_id=LOFF_G0002026;transcript_id=LOFF_T0002534;transcript_name=USP17L11-0;Parent=LOFF_T0002534;ID=CDS:LOFF_T0002534:0;alignment_id=N/A;alternative_source_transcripts=N/A;paralogy=N/A;unfiltered_paralogy=N/A;collapsed_gene_ids=N/A;collapsed_gene_names=N/A;frameshift=N/A;exon_annotation_support=N/A;intron_annotation_support=N/A;transcript_class=paralog;transcript_modes=Liftoff;valid_start=N/A;valid_stop=N/A;proper_orf=N/A
chr4	Liftoff	transcript	9227046	9228638	.	+	.	gene_name=USP17L11;source_gene=ENSG00000233136.3;gene_biotype=protein_coding;transcript_biotype=protein_coding;source_transcript=ENST00000457736.1;Name=USP17L11;source_gene_common_name=USP17L11;extra_paralog=False;gene_id=LOFF_G0002032;Parent=LOFF_G0002032;transcript_id=LOFF_T0002541;transcript_name=USP17L11-1;ID=LOFF_T0002541;alignment_id=N/A;alternative_source_transcripts=N/A;paralogy=N/A;unfiltered_paralogy=N/A;collapsed_gene_ids=N/A;collapsed_gene_names=N/A;frameshift=N/A;exon_annotation_support=N/A;intron_annotation_support=N/A;transcript_class=ortholog;transcript_modes=Liftoff;valid_start=N/A;valid_stop=N/A;proper_orf=N/A
chr4	Liftoff	start_codon	9227046	9227048	.	+	.	gene_name=USP17L11;source_gene=ENSG00000233136.3;gene_biotype=protein_coding;transcript_biotype=protein_coding;source_transcript=ENST00000457736.1;Name=USP17L11;source_gene_common_name=USP17L11;extra_paralog=False;gene_id=LOFF_G0002032;transcript_id=LOFF_T0002541;transcript_name=USP17L11-0;Parent=LOFF_T0002541;ID=start_codon:LOFF_T0002541;alignment_id=N/A;alternative_source_transcripts=N/A;paralogy=N/A;unfiltered_paralogy=N/A;collapsed_gene_ids=N/A;collapsed_gene_names=N/A;frameshift=N/A;exon_annotation_support=N/A;intron_annotation_support=N/A;transcript_class=ortholog;transcript_modes=Liftoff;valid_start=N/A;valid_stop=N/A;proper_orf=N/A
chr4	Liftoff	exon	9227046	9228638	.	+	.	gene_name=USP17L11;source_gene=ENSG00000233136.3;gene_biotype=protein_coding;transcript_biotype=protein_coding;source_transcript=ENST00000457736.1;Name=USP17L11;source_gene_common_name=USP17L11;extra_paralog=False;gene_id=LOFF_G0002032;transcript_id=LOFF_T0002541;transcript_name=USP17L11-0;Parent=LOFF_T0002541;ID=exon:LOFF_T0002541:0;alignment_id=N/A;alternative_source_transcripts=N/A;paralogy=N/A;unfiltered_paralogy=N/A;collapsed_gene_ids=N/A;collapsed_gene_names=N/A;frameshift=N/A;exon_annotation_support=N/A;intron_annotation_support=N/A;transcript_class=ortholog;transcript_modes=Liftoff;valid_start=N/A;valid_stop=N/A;proper_orf=N/A
chr4	Liftoff	CDS	9227046	9228638	.	+	0	gene_name=USP17L11;source_gene=ENSG00000233136.3;gene_biotype=protein_coding;transcript_biotype=protein_coding;source_transcript=ENST00000457736.1;Name=USP17L11;source_gene_common_name=USP17L11;extra_paralog=False;gene_id=LOFF_G0002032;transcript_id=LOFF_T0002541;transcript_name=USP17L11-0;Parent=LOFF_T0002541;ID=CDS:LOFF_T0002541:0;alignment_id=N/A;alternative_source_transcripts=N/A;paralogy=N/A;unfiltered_paralogy=N/A;collapsed_gene_ids=N/A;collapsed_gene_names=N/A;frameshift=N/A;exon_annotation_support=N/A;intron_annotation_support=N/A;transcript_class=ortholog;transcript_modes=Liftoff;valid_start=N/A;valid_stop=N/A;proper_orf=N/A
chr4	Liftoff	stop_codon	9228636	9228638	.	+	.	gene_name=USP17L11;source_gene=ENSG00000233136.3;gene_biotype=protein_coding;transcript_biotype=protein_coding;source_transcript=ENST00000457736.1;Name=USP17L11;source_gene_common_name=USP17L11;extra_paralog=False;gene_id=LOFF_G0002032;transcript_id=LOFF_T0002541;transcript_name=USP17L11-0;Parent=LOFF_T0002541;ID=stop_codon:LOFF_T0002541;alignment_id=N/A;alternative_source_transcripts=N/A;paralogy=N/A;unfiltered_paralogy=N/A;collapsed_gene_ids=N/A;collapsed_gene_names=N/A;frameshift=N/A;exon_annotation_support=N/A;intron_annotation_support=N/A;transcript_class=ortholog;transcript_modes=Liftoff;valid_start=N/A;valid_stop=N/A;proper_orf=N/A

Leads to error like:

[9 Jul 2021 01:37:37] ERROR PathExtensions Processing genes: recalculating /Users/romeo/.jbr_browser/genomes/chm13t2t-v1.1/chm13t2t-v1.1.gene_annotation.v4.gff3.json.gz: [FAILED] after 17.61 s
Caused by: ERROR IllegalStateException [START_CODON] We assume 'start_codon' (9227045) starts in CDS 5'end (9127304) but is false here. Gene: ENST00000457736.1
org.jetbrains.bio.genome.GtfReader.readTranscripts(Ensembl.kt:92)
org.jetbrains.bio.genome.Transcripts$loadTranscripts$1$transcripts$1.invoke(Transcripts.kt:287)
org.jetbrains.bio.genome.Transcripts$loadTranscripts$1$transcripts$1.invoke(Transcripts.kt:219)
org.jetbrains.bio.util.LoggerExtensionsKt.time(LoggerExtensions.kt:18)
...

iromeo added a commit to JetBrains-Research/bioinf-commons that referenced this issue Jul 8, 2021
@iromeo
fix: Initial impl (proof of concept) for GFF3 annotations support, Je…
2e411c0 
…tBrains-Research/jbr#151
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