Mercurial > repos > petr-novak > dante_ltr

diff extract_putative_ltr.R @ 9:1aa578e6c8b3 draft

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"planemo upload commit 9488b982bae902f1868785ec4ad47134dac50ff3"
author petr-novak
date Wed, 29 Jun 2022 09:25:54 +0000
parents 9de392f2fc02
children
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--- 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