From e5d6389117fddef8086f0dadb81933ac5d32541e Mon Sep 17 00:00:00 2001 From: Helena Rasche Date: Wed, 31 Jan 2024 11:07:40 +0100 Subject: [PATCH] manually add --- arrow/commands/annotations/load_gff3.py | 9 +++++++-- 1 file changed, 7 insertions(+), 2 deletions(-) diff --git a/arrow/commands/annotations/load_gff3.py b/arrow/commands/annotations/load_gff3.py index 0559664c..48f0dcc0 100644 --- a/arrow/commands/annotations/load_gff3.py +++ b/arrow/commands/annotations/load_gff3.py @@ -33,6 +33,11 @@ help="Disable CDS recalculation and instead use the one provided", is_flag=True ) +@click.option( + "--cds_cleaning", + help="This changes the behaviour of creating GFF3 features in apollo to match more closely to what it expects. Generally you'll probably want this on if you have transcripts with multiple exons and CDSs, but we don't want to change existing scripts so we are not defaulting this on." + is_flag=True +) @click.option( "--timing", help="Output loading performance metrics", @@ -41,11 +46,11 @@ @pass_context @custom_exception @str_output -def cli(ctx, organism, gff3, source="", batch_size=1, test=False, use_name=False, disable_cds_recalculation=False, timing=False): +def cli(ctx, organism, gff3, source="", batch_size=1, test=False, use_name=False, disable_cds_recalculation=False, cds_cleaning=False, timing=False): """Load a full GFF3 into annotation track Output: Loading report """ - return ctx.gi.annotations.load_gff3(organism, gff3, source=source, batch_size=batch_size, test=test, use_name=use_name, disable_cds_recalculation=disable_cds_recalculation, timing=timing) + return ctx.gi.annotations.load_gff3(organism, gff3, source=source, batch_size=batch_size, test=test, use_name=use_name, disable_cds_recalculation=disable_cds_recalculation, cds_cleaning=cds_cleaning, timing=timing)