Mercurial > repos > iuc > brew3r_r

comparison brew3r.r_script.R @ 1:3198f52bffaa draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit fa525468780f3dea175da15852b1b8c17e1a80d3
author iuc
date Tue, 18 Jun 2024 05:36:32 +0000
parents 928a52b5c938
children d3b0390f325f
comparison
equal deleted inserted replaced
0:928a52b5c938 1:3198f52bffaa
89 ov.simple <- unique(ov[, c("queryHits", "strand")]) 89 ov.simple <- unique(ov[, c("queryHits", "strand")])
90 # If the queryHits is duplicated it means there are different strands 90 # If the queryHits is duplicated it means there are different strands
91 multi.strand.query <- ov.simple$queryHits[duplicated(ov.simple$queryHits)] 91 multi.strand.query <- ov.simple$queryHits[duplicated(ov.simple$queryHits)]
92 to.remove <- unstranded.intervals[multi.strand.query] 92 to.remove <- unstranded.intervals[multi.strand.query]
93 # Remove these potentially error-prone intervals from the template 93 # Remove these potentially error-prone intervals from the template
94 input_gr_template <- input_gr_template[-to.remove] 94 if (length(to.remove) > 0) {
95 input_gr_template <- input_gr_template[-to.remove]
96 }
95 } 97 }
96 } 98 }
97 99
98 # Run BREW3R.r main function 100 # Run BREW3R.r main function
99 new_gr_exons <- extend_granges( 101 if (length(input_gr_template) > 0) {
100 input_gr_to_extend = input_gr_to_extend, 102 new_gr_exons <- extend_granges(
101 input_gr_to_overlap = input_gr_template, 103 input_gr_to_extend = input_gr_to_extend,
102 add_new_exons = is.null(opt$no_add), 104 input_gr_to_overlap = input_gr_template,
103 overlap_resolution_fn = opt$sup_output 105 add_new_exons = is.null(opt$no_add),
104 ) 106 overlap_resolution_fn = opt$sup_output
107 )
108 } else {
109 new_gr_exons <- subset(input_gr_to_extend, type == "exon")
110 }
105 # Prevent extension using pattern 111 # Prevent extension using pattern
106 if (!is.null(opt$exclude_pattern)) { 112 if (!is.null(opt$exclude_pattern)) {
107 input_gr_pattern <- subset( 113 input_gr_pattern <- subset(
108 input_gr_to_extend, 114 input_gr_to_extend,
109 type == "exon" & grepl(opt$exclude_pattern, gene_name) 115 type == "exon" & grepl(opt$exclude_pattern, gene_name)