Mercurial > repos > petr-novak > dante_ltr
comparison extract_putative_ltr.R @ 9:1aa578e6c8b3 draft
"planemo upload commit 9488b982bae902f1868785ec4ad47134dac50ff3"
| author | petr-novak |
|---|---|
| date | Wed, 29 Jun 2022 09:25:54 +0000 |
| parents | 9de392f2fc02 |
| children |
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| 8:9de392f2fc02 | 9:1aa578e6c8b3 |
|---|---|
| 75 | 75 |
| 76 g <- rtracklayer::import("/mnt/raid/users/petr/workspace/dante_ltr/test_data/sample_DANTE_unfiltered.gff3") | 76 g <- rtracklayer::import("/mnt/raid/users/petr/workspace/dante_ltr/test_data/sample_DANTE_unfiltered.gff3") |
| 77 g <- rtracklayer::import("/mnt/raid/users/petr/workspace/ltr_finder_test/test_data/DANTE_filtered_part.gff3") | 77 g <- rtracklayer::import("/mnt/raid/users/petr/workspace/ltr_finder_test/test_data/DANTE_filtered_part.gff3") |
| 78 s <- readDNAStringSet("/mnt/raid/users/petr/workspace/ltr_finder_test/test_data/Rbp_part.fa") | 78 s <- readDNAStringSet("/mnt/raid/users/petr/workspace/ltr_finder_test/test_data/Rbp_part.fa") |
| 79 | 79 |
| 80 # oriza | |
| 81 g <- rtracklayer::import("/mnt/raid/users/petr/workspace/dante_ltr/test_data/big_test_data/DANTE_full_oryza.gff3") | |
| 82 s <- readDNAStringSet("/mnt/raid/users/petr/workspace/dante_ltr/test_data/big_test_data/o_sativa_msu7.0.fasta") | |
| 83 | |
| 80 g <- rtracklayer::import("/mnt/raid/users/petr/workspace/dante_ltr/test_data | 84 g <- rtracklayer::import("/mnt/raid/users/petr/workspace/dante_ltr/test_data |
| 81 /DANTE_Vfaba_chr5.gff3") | 85 /DANTE_Vfaba_chr5.gff3") |
| 82 s <- readDNAStringSet("/mnt/ceph/454_data/Vicia_faba_assembly/assembly/ver_210910 | 86 s <- readDNAStringSet("/mnt/ceph/454_data/Vicia_faba_assembly/assembly/ver_210910 |
| 83 /fasta_parts/211010_Vfaba_chr5.fasta") | 87 /fasta_parts/211010_Vfaba_chr5.fasta") |
| 84 | 88 |