From 5306339a6b5c57285d65d25432d433215b0982dd Mon Sep 17 00:00:00 2001 From: francois-a Date: Fri, 29 Nov 2024 16:26:38 +0000 Subject: [PATCH] Updated docstring --- qtl/annotation.py | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/qtl/annotation.py b/qtl/annotation.py index 311562e..5552362 100644 --- a/qtl/annotation.py +++ b/qtl/annotation.py @@ -261,8 +261,10 @@ def __init__(self, gene_id, gene_name, gene_type, chrom, strand, start_pos, end_ self.end_pos = end_pos if strand == '+': self.tss = start_pos + self.tes = end_pos else: self.tss = end_pos + self.tes = start_pos self.transcripts = [] self.exclude_biotypes = [] self.mappability = None @@ -1252,8 +1254,10 @@ def write_gtf(self, gtf_path): def write_bed(self, bed_path, overwrite=False): """ - Write to BED format. - Columns: chr, start, end, gff3_attributes (ID, name, biotype), score (1000), strand, thick_start, thick_end, ., #exons, sizes, starts + Write to BED format, with GFF3 attributes for optimal display in IGV (transcript + names are shown on gene model, with remaining attributes shown on overlay/hover). + Columns: chr, start, end, gff3_attributes (ID, name, biotype), score (1000), + strand, thick_start, thick_end, ., num_exons, sizes, starts """ if not os.path.exists(bed_path) or overwrite: with open(bed_path, 'w') as bed: