# HG changeset patch
# User petr-novak
# Date 1656494754 0
# Node ID 1aa578e6c8b3c469d034e90d160d86910f8ce232
# Parent  9de392f2fc022d969299cdd248f9bc9a24c12bbd
"planemo upload commit 9488b982bae902f1868785ec4ad47134dac50ff3"

diff -r 9de392f2fc02 -r 1aa578e6c8b3 R/ltr_utils.R
--- a/R/ltr_utils.R	Tue Jun 28 12:33:22 2022 +0000
+++ b/R/ltr_utils.R	Wed Jun 29 09:25:54 2022 +0000
@@ -138,20 +138,20 @@
   gr <- GRanges(seqnames = sapply(gx, function(x)x$seqnames[1]), IRanges(start = S - offset, end = E + offset))
 }
 
-get_ranges_left <- function(gx, offset = OFFSET, offset2 = 10) {
+get_ranges_left <- function(gx, offset = OFFSET, offset2 = 300) {
   ## offset2 - how many nt cen LTR extend to closes protein domain
   ## this is necassary as some detected proteins domains does not have correct bopundaries
   ## if LTR retrotransposons insters to other protein domain.
   S <- sapply(gx, function(x)min(x$start))
-  max_offset <- S - sapply(gx, function(x)min(x$upstream_domain)) + offset2
+  max_offset <- S - sapply(gx, function(x)min(x$upstream_domain)) + 10
   offset_adjusted <- ifelse(max_offset < offset, max_offset, offset)
   gr <- GRanges(seqnames = sapply(gx, function(x)x$seqnames[1]), IRanges(start = S - offset_adjusted, end = S + offset2))
   return(gr)
 }
 
-get_ranges_right <- function(gx, offset = OFFSET, offset2 = 10) {
+get_ranges_right <- function(gx, offset = OFFSET, offset2 = 300) {
   E <- sapply(gx, function(x)max(x$end))
-  max_offset <- sapply(gx, function(x)max(x$downstream_domain)) - E + offset2
+  max_offset <- sapply(gx, function(x)max(x$downstream_domain)) - E + 10
   offset_adjusted <- ifelse(max_offset < offset, max_offset, offset)
   gr <- GRanges(seqnames = sapply(gx, function(x)x$seqnames[1]), IRanges(start = E - offset2, end = E + offset_adjusted))
   return(gr)
diff -r 9de392f2fc02 -r 1aa578e6c8b3 extract_putative_ltr.R
--- a/extract_putative_ltr.R	Tue Jun 28 12:33:22 2022 +0000
+++ b/extract_putative_ltr.R	Wed Jun 29 09:25:54 2022 +0000
@@ -77,6 +77,10 @@
   g <- rtracklayer::import("/mnt/raid/users/petr/workspace/ltr_finder_test/test_data/DANTE_filtered_part.gff3")
   s <- readDNAStringSet("/mnt/raid/users/petr/workspace/ltr_finder_test/test_data/Rbp_part.fa")
 
+  # oriza
+  g <- rtracklayer::import("/mnt/raid/users/petr/workspace/dante_ltr/test_data/big_test_data/DANTE_full_oryza.gff3")
+  s <- readDNAStringSet("/mnt/raid/users/petr/workspace/dante_ltr/test_data/big_test_data/o_sativa_msu7.0.fasta")
+
   g <- rtracklayer::import("/mnt/raid/users/petr/workspace/dante_ltr/test_data
   /DANTE_Vfaba_chr5.gff3")
   s <- readDNAStringSet("/mnt/ceph/454_data/Vicia_faba_assembly/assembly/ver_210910