Mercurial > repos > kmace > mtls_analysis
comparison mtls_analyze/gtfToMapFriendlyAnnotation.R @ 4:b465306d00ba draft default tip
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author | kmace |
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date | Mon, 23 Jul 2012 13:00:15 -0400 |
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3:a0306edbf2f8 | 4:b465306d00ba |
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1 rm (list = ls()) | |
2 args <- commandArgs() | |
3 print(args) | |
4 gtf <- read.table(args[6],as.is=T) | |
5 colnames(gtf) <- c("chrom", | |
6 "source", | |
7 "type", | |
8 "five_prime", | |
9 "three_prime", | |
10 "score", | |
11 "strand", | |
12 "frame", | |
13 "nothinggene", | |
14 "gene", | |
15 "nothingSemi1", | |
16 "nothingtranscript", | |
17 "transcript", | |
18 "nothingSemi2") | |
19 gtf.exon <- gtf[which(gtf[,"type"]=="exon"),] | |
20 gtf.exon.slim <-gtf.exon[,c("chrom", "five_prime", "three_prime", "strand", "transcript")] | |
21 gtf.exon.slim.sort <- gtf.exon.slim[sort.list(gtf.exon.slim[,"transcript"]),] | |
22 | |
23 | |
24 | |
25 transcripts <- as.vector(unique(gtf.exon.slim[,"transcript"])) | |
26 #transcripts <- as.vector(unique(gtf.exon.slim[,"transcript"])) | |
27 | |
28 | |
29 | |
30 output <- matrix(0,nr=length(transcripts),nc=ncol(gtf.exon.slim.sort)) | |
31 | |
32 all.chrom <- gtf.exon.slim.sort[,"chrom"] | |
33 all.five_prime <- gtf.exon.slim.sort[,"five_prime"] | |
34 all.three_prime <- gtf.exon.slim.sort[,"three_prime"] | |
35 all.strand <- gtf.exon.slim.sort[,"strand"] | |
36 all.transcript <- gtf.exon.slim.sort[,"transcript"] | |
37 | |
38 colnames(output) <- colnames(gtf.exon.slim.sort) | |
39 | |
40 j <- 0 | |
41 i <- 1 | |
42 | |
43 previous.strand <- gtf.exon.slim.sort[i,"strand"] | |
44 previous.chrom <- gtf.exon.slim.sort[i,"chrom"] | |
45 previous.transcript <- gtf.exon.slim.sort[i,"transcript"] | |
46 previous.five_prime.min <- gtf.exon.slim.sort[i,"five_prime"] | |
47 previous.three_prime.max <- gtf.exon.slim.sort[i,"three_prime"] | |
48 | |
49 # Progress bar: | |
50 total <- dim(gtf.exon.slim.sort)[1] | |
51 # create progress bar | |
52 pb <- txtProgressBar(min = 0, max = total, style = 3) | |
53 | |
54 | |
55 | |
56 | |
57 for ( i in 1:length(all.transcript)) { | |
58 current.transcript <- all.transcript[i] | |
59 setTxtProgressBar(pb, i) | |
60 if (previous.transcript != current.transcript) { | |
61 j <- j + 1 | |
62 # Write out the current transcript info | |
63 output[j,"chrom"] <- previous.chrom | |
64 output[j,"five_prime"] <- previous.five_prime.min | |
65 output[j,"three_prime"] <- previous.three_prime.max | |
66 output[j,"strand"] <- previous.strand | |
67 output[j,"transcript"] <- previous.transcript | |
68 | |
69 # Save the new transcript info (convert the current to previous) | |
70 | |
71 previous.strand <- all.strand[i] | |
72 previous.chrom <- all.chrom[i] | |
73 previous.transcript <- all.transcript[i] # current.transcript | |
74 previous.five_prime.min <- all.five_prime[i] | |
75 previous.three_prime.max <- all.three_prime[i] | |
76 } | |
77 else { | |
78 previous.five_prime.min <- min(previous.five_prime.min, all.five_prime[i]) | |
79 previous.three_prime.max <- max(previous.three_prime.max, all.three_prime[i]) | |
80 previous.transcript <- all.transcript[i] # current.transcript | |
81 } | |
82 } | |
83 # Write the last item | |
84 j <- j + 1 | |
85 # Write out the current transcript info | |
86 output[j,"chrom"] <- previous.chrom | |
87 output[j,"five_prime"] <- previous.five_prime.min | |
88 output[j,"three_prime"] <- previous.three_prime.max | |
89 output[j,"strand"] <- previous.strand | |
90 output[j,"transcript"] <- previous.transcript | |
91 | |
92 close(pb) | |
93 | |
94 colnames(output) <- c("chrom", "txStart", "txEnd", "strand", "name2") | |
95 write.table(output, file="gene_annotation.txt", sep="\t", row.names=F) | |
96 | |
97 #ix <- which(gtf.exon.slim[,"transcript"] == transcripts[i]) | |
98 #output[i,"transcript"] <- transcripts[i] | |
99 #output[i,"five_prime"] <- min(gtf.exon.slim[ix,"five_prime"]) | |
100 #output[i,"three_prime"] <- max(gtf.exon.slim[ix,"three_prime"]) | |
101 #output[i,"strand"] <- gtf.exon.slim[ix,"strand"][1] | |
102 #output[i,"chrom"] <- gtf.exon.slim[ix,"chrom"][1] |