Mercurial > repos > iuc > brew3r_r

annotate test-data/generate_test.R @ 1:3198f52bffaa draft

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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
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928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
parents:
diff changeset
1 library(GenomicRanges)
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
parents:
diff changeset
2 input_to_overlap_case1_2_3_4_6_7_8 <- GenomicRanges::GRanges(
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
parents:
diff changeset
3 seqnames = "chr1",
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
parents:
diff changeset
4 ranges = IRanges::IRanges(
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
parents:
diff changeset
5 start = 3,
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
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6 end = 25
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
parents:
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7 ),
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
parents:
diff changeset
8 strand = "+",
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
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9 gene_id = "geneA",
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
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10 transcript_id = "transcriptA",
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
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11 type = "exon",
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
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12 exon_id = "exonA"
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
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13 )
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
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14 big_gr <- NULL
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
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15 for (i in c(1:5, 7:10)) {
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
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16 temp.gr <- input_to_overlap_case1_2_3_4_6_7_8
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
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17 temp.gr <- shift(temp.gr, 100 * (i - 1))
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
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18 temp.gr$gene_id <- paste0("gene", LETTERS[i])
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
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19 temp.gr$transcript_id <- paste0("transcript", LETTERS[i])
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
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diff changeset
20 temp.gr$exon_id <- paste0("exon", LETTERS[i])
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
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21 temp.gr$exon_number <- 1
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
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22 big_gr <- c(big_gr, temp.gr)
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
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23 }
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
parents:
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24 input_to_overlap_case5_9 <- GenomicRanges::GRanges(
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
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25 seqnames = "chr1",
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
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26 ranges = IRanges::IRanges(
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
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27 start = c(1, 33, 45, 72),
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
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28 end = c(25, 40, 60, 75)
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
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29 ),
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
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30 strand = "+",
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
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31 gene_id = "geneA",
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
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32 transcript_id = "transcriptA",
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
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33 type = "exon",
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
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34 exon_id = c("exonA", "exonB", "exonC", "exonD")
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
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35 )
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
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36 for (i in c(6, 11)) {
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
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37 temp.gr <- input_to_overlap_case5_9
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
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38 temp.gr <- shift(temp.gr, 100 * (i - 1))
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
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39 temp.gr$gene_id <- paste0("gene", LETTERS[i])
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
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40 temp.gr$transcript_id <- paste0("transcript", LETTERS[i])
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
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41 temp.gr$exon_id <- paste0("exon", LETTERS[i], letters[1:4])
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
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42 temp.gr$exon_number <- 1:4
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
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43 big_gr <- c(big_gr, temp.gr)
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
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44 }
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
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45 big_gr <- unlist(as(big_gr, "GRangesList"))
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
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46
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
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47
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
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48
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
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49 input_gr <- c(
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
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50 # 1
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
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51 GenomicRanges::GRanges(
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
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52 seqnames = "chr1",
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
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53 ranges = IRanges::IRanges(
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
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54 start = c(5, 20),
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
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55 end = c(10, 30)
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
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56 ),
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
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57 strand = "+",
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
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58 gene_id = c("gene11", "gene12"),
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
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59 transcript_id = c("transcript11", "transcript12"),
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
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60 type = "exon",
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
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61 exon_id = c("exon11", "exon12")
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
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62 ),
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
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63 # 2
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
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64 shift(
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
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65 GenomicRanges::GRanges(
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
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66 seqnames = "chr1",
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
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67 ranges = IRanges::IRanges(
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
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68 start = c(5, 20),
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
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69 end = c(10, 25)
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
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70 ),
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
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71 strand = "+",
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
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72 gene_id = c("gene21", "gene22"),
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
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73 transcript_id = c("transcript21", "transcript22"),
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
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74 type = "exon",
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
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75 exon_id = c("exon21", "exon22")
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76 ),
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
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77 100
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
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78 ),
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
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79 # 3_5
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80 shift(
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
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81 GenomicRanges::GRanges(
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
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82 seqnames = "chr1",
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
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83 ranges = IRanges::IRanges(
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
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84 start = c(5, 20),
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iuc
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85 end = c(10, 22)
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
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diff changeset
86 ),
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
parents:
diff changeset
87 strand = "+",
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
parents:
diff changeset
88 gene_id = c("gene31", "gene32"),
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
parents:
diff changeset
89 transcript_id = c("transcript31", "transcript32"),
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
parents:
diff changeset
90 type = "exon",
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
parents:
diff changeset
91 exon_id = c("exon31", "exon32")
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
parents:
diff changeset
92 ),
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
parents:
diff changeset
93 200
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
parents:
diff changeset
94 ),
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
parents:
diff changeset
95 # 4
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
parents:
diff changeset
96 shift(
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
parents:
diff changeset
97 GenomicRanges::GRanges(
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
parents:
diff changeset
98 seqnames = "chr1",
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
parents:
diff changeset
99 ranges = IRanges::IRanges(
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
parents:
diff changeset
100 start = c(5, 5),
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
parents:
diff changeset
101 end = c(10, 22)
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
parents:
diff changeset
102 ),
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
parents:
diff changeset
103 strand = "+",
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
parents:
diff changeset
104 gene_id = c("gene41", "gene42"),
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
parents:
diff changeset
105 transcript_id = c("transcript41", "transcript42"),
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
parents:
diff changeset
106 type = "exon",
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
parents:
diff changeset
107 exon_id = c("exon41", "exon42")
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
parents:
diff changeset
108 ),
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
parents:
diff changeset
109 300
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
parents:
diff changeset
110 ),
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
parents:
diff changeset
111 # 4bis
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
parents:
diff changeset
112 shift(
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
parents:
diff changeset
113 GenomicRanges::GRanges(
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
parents:
diff changeset
114 seqnames = "chr1",
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
parents:
diff changeset
115 ranges = IRanges::IRanges(
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
parents:
diff changeset
116 start = c(5, 5),
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
parents:
diff changeset
117 end = c(10, 25)
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
parents:
diff changeset
118 ),
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
parents:
diff changeset
119 strand = "+",
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
parents:
diff changeset
120 gene_id = c("gene51", "gene52"),
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
parents:
diff changeset
121 transcript_id = c("transcript51", "transcript52"),
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
parents:
diff changeset
122 type = "exon",
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
parents:
diff changeset
123 exon_id = c("exon51", "exon52")
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
parents:
diff changeset
124 ),
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
parents:
diff changeset
125 400
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
parents:
diff changeset
126 ),
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
parents:
diff changeset
127 # 3_5
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
parents:
diff changeset
128 shift(
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
parents:
diff changeset
129 GenomicRanges::GRanges(
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
parents:
diff changeset
130 seqnames = "chr1",
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
parents:
diff changeset
131 ranges = IRanges::IRanges(
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
parents:
diff changeset
132 start = c(5, 20),
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
parents:
diff changeset
133 end = c(10, 22)
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
parents:
diff changeset
134 ),
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
parents:
diff changeset
135 strand = "+",
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
parents:
diff changeset
136 gene_id = c("gene61", "gene62"),
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
parents:
diff changeset
137 transcript_id = c("transcript61", "transcript62"),
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
parents:
diff changeset
138 type = "exon",
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
parents:
diff changeset
139 exon_id = c("exon61", "exon62")
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
parents:
diff changeset
140 ),
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
parents:
diff changeset
141 500
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
parents:
diff changeset
142 ),
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
parents:
diff changeset
143 # 6
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
parents:
diff changeset
144 shift(
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
parents:
diff changeset
145 GenomicRanges::GRanges(
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
parents:
diff changeset
146 seqnames = "chr1",
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
parents:
diff changeset
147 ranges = IRanges::IRanges(
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
parents:
diff changeset
148 start = c(1, 1, 30),
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
parents:
diff changeset
149 end = c(10, 10, 40)
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
parents:
diff changeset
150 ),
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
parents:
diff changeset
151 strand = "+",
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
parents:
diff changeset
152 gene_id = "gene71",
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
parents:
diff changeset
153 transcript_id = c("transcript71", "transcript72", "transcript72"),
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
parents:
diff changeset
154 type = "exon",
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
parents:
diff changeset
155 exon_id = c("exon71", "exon71", "exon72")
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
parents:
diff changeset
156 ),
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
parents:
diff changeset
157 600
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
parents:
diff changeset
158 ),
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
parents:
diff changeset
159 # 6bis
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
parents:
diff changeset
160 shift(
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
parents:
diff changeset
161 GenomicRanges::GRanges(
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
parents:
diff changeset
162 seqnames = "chr1",
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
parents:
diff changeset
163 ranges = IRanges::IRanges(
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
parents:
diff changeset
164 start = c(1, 1, 30),
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
parents:
diff changeset
165 end = c(10, 10, 40)
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
parents:
diff changeset
166 ),
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
parents:
diff changeset
167 strand = "+",
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
parents:
diff changeset
168 gene_id = c("gene81", "gene82", "gene82"),
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
parents:
diff changeset
169 transcript_id = c("transcript81", "transcript82", "transcript82"),
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
parents:
diff changeset
170 type = "exon",
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
parents:
diff changeset
171 exon_id = c("exon81", "exon82", "exon83")
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
parents:
diff changeset
172 ),
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
parents:
diff changeset
173 700
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
parents:
diff changeset
174 ),
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
parents:
diff changeset
175 # 7
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
parents:
diff changeset
176 shift(
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
parents:
diff changeset
177 GenomicRanges::GRanges(
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
parents:
diff changeset
178 seqnames = "chr1",
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
parents:
diff changeset
179 ranges = IRanges::IRanges(
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
parents:
diff changeset
180 start = c(1, 1, 30),
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
parents:
diff changeset
181 end = c(8, 10, 40)
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
parents:
diff changeset
182 ),
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
parents:
diff changeset
183 strand = "+",
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
parents:
diff changeset
184 gene_id = "gene1",
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
parents:
diff changeset
185 transcript_id = c("transcript91", "transcript92", "transcript92"),
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
parents:
diff changeset
186 type = "exon",
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
parents:
diff changeset
187 exon_id = c("exon91", "exon92", "exon93")
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
parents:
diff changeset
188 ),
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
parents:
diff changeset
189 800
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
parents:
diff changeset
190 ),
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
parents:
diff changeset
191 # 8
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
parents:
diff changeset
192 shift(
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
parents:
diff changeset
193 GenomicRanges::GRanges(
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
parents:
diff changeset
194 seqnames = "chr1",
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
parents:
diff changeset
195 ranges = IRanges::IRanges(
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
parents:
diff changeset
196 start = c(1, 1, 30),
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
parents:
diff changeset
197 end = c(8, 10, 40)
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
parents:
diff changeset
198 ),
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
parents:
diff changeset
199 strand = "+",
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
parents:
diff changeset
200 gene_id = c("gene101", "gene102", "gene102"),
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
parents:
diff changeset
201 transcript_id = c("transcript101", "transcript102", "transcript102"),
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
parents:
diff changeset
202 type = "exon",
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
parents:
diff changeset
203 exon_id = c("exon101", "exon102", "exon103")
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
parents:
diff changeset
204 ),
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
parents:
diff changeset
205 900
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
parents:
diff changeset
206 ),
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
parents:
diff changeset
207 # 9
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
parents:
diff changeset
208 shift(
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
parents:
diff changeset
209 GenomicRanges::GRanges(
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
parents:
diff changeset
210 seqnames = "chr1",
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
parents:
diff changeset
211 ranges = IRanges::IRanges(
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
parents:
diff changeset
212 start = c(5, 55),
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
parents:
diff changeset
213 end = c(10, 70)
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
parents:
diff changeset
214 ),
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
parents:
diff changeset
215 strand = "+",
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
parents:
diff changeset
216 gene_id = c("gene111", "gene112"),
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
parents:
diff changeset
217 transcript_id = c("transcript111", "transcript112"),
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
parents:
diff changeset
218 type = "exon",
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
parents:
diff changeset
219 exon_id = c("exon111", "exon112")
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
parents:
diff changeset
220 ),
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
parents:
diff changeset
221 1000
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
parents:
diff changeset
222 )
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
parents:
diff changeset
223 )
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
parents:
diff changeset
224 ## Add convergent genes overlapping a unstranded
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
parents:
diff changeset
225 input_gr <- c(
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
parents:
diff changeset
226 input_gr,
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
parents:
diff changeset
227 GenomicRanges::GRanges(
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
parents:
diff changeset
228 seqnames = "chr1",
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
parents:
diff changeset
229 ranges = IRanges::IRanges(
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
parents:
diff changeset
230 start = c(1100, 1110),
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
parents:
diff changeset
231 end = c(1105, 1120)
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
parents:
diff changeset
232 ),
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
parents:
diff changeset
233 strand = c("+", "-"),
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
parents:
diff changeset
234 gene_id = c("gene121", "gene122"),
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
parents:
diff changeset
235 transcript_id = c("transcript121", "transcript122"),
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
parents:
diff changeset
236 type = "exon",
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
parents:
diff changeset
237 exon_id = c("exon121", "exon122")
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
parents:
diff changeset
238 )
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
parents:
diff changeset
239 )
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
parents:
diff changeset
240 big_gr <- c(
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
parents:
diff changeset
241 big_gr,
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
parents:
diff changeset
242 GenomicRanges::GRanges(
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
parents:
diff changeset
243 seqnames = "chr1",
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
parents:
diff changeset
244 ranges = IRanges::IRanges(
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
parents:
diff changeset
245 start = 1103,
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
parents:
diff changeset
246 end = 1113
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
parents:
diff changeset
247 ),
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
parents:
diff changeset
248 strand = "*",
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
parents:
diff changeset
249 gene_id = "geneL",
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
parents:
diff changeset
250 transcript_id = "transcriptL",
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
parents:
diff changeset
251 type = "exon",
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
parents:
diff changeset
252 exon_id = "exonL"
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
parents:
diff changeset
253 )
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
parents:
diff changeset
254 )
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
parents:
diff changeset
255 input_gr$gene_name <- input_gr$gene_id
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
parents:
diff changeset
256 input_gr$gene_name[input_gr$gene_id == "gene111"] <- "Gm001"
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
parents:
diff changeset
257 library(BREW3R.r)
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
parents:
diff changeset
258 new.gr <- extend_granges(input_gr, big_gr)
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
parents:
diff changeset
259 library("rtracklayer")
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
parents:
diff changeset
260 export.gff(input_gr, "input.gtf")
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
parents:
diff changeset
261 export.gff(big_gr, "second_input.gtf")
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
parents:
diff changeset
262 export.gff(sort(new.gr, ignore.strand = TRUE), "output.gtf")