Mercurial > repos > artbio > ngsplot
annotate lib/genedb.r @ 4:9652d08d8441 draft default tip
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit 73a8ef46dddb0a1b224720bcdfe46050ee9a1b8b
author | artbio |
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date | Tue, 26 Dec 2017 08:07:56 -0500 |
parents | 3ca58369469c |
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rev | line source |
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3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
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1 chromFormat <- function(crn, ...){ |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
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2 # Format chromosome names to our standard. |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
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3 # Args: |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
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4 # crn: character vector of chromosome names. |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
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5 # Returns: character vector of formatted chromosome names. |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
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6 |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
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7 crn <- sub('.fa$', '', crn) |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
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8 nochr.i <- grep('^chr', crn, invert=T) |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
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9 crn[nochr.i] <- paste('chr', crn[nochr.i], sep='') |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
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10 crn |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
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11 } |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
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12 |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
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13 FIScoreIntersect <- function(db.info, v.finfo){ |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
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14 # Further info score based on intersection with database FI columns. |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
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15 # Used to select database files. |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
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16 # Args: |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
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17 # db.info: one record of annotation database table. |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
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18 # v.finfo: further info that is split into vector. |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
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19 # Returns: a score for the intersection between database and further info. |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
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20 |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
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21 length(intersect(as.vector(db.info[c("FI.1", "FI.2", "FI.3")]), v.finfo)) |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
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22 } |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
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23 |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
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24 SetupPlotCoord <- function(args.tbl, ctg.tbl, default.tbl, dbfile.tbl, |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
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25 progpath, genome, reg2plot, lgint, flanksize, |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
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26 samprate, galaxy) { |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
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27 # Load genomic coordinates for plot based on the input arguments. |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
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28 # Args: |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
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29 # args.tbl: input argument table |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
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30 # ctg.tbl: coverage-genelist-title table |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
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31 # default.tbl: default settings of databases and plot setting |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
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32 # dbfile.tbl: details of database files(.RData). |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
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33 # progpath: program path derived from NGSPLOT |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
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34 # genome: genome name, such as mm9, hg19. |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
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35 # reg2plot: tss, tes, genebody, etc. |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
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36 # lgint: boolean tag for large interval. |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
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37 # flanksize: flanking region size. |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
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38 # samprate: sampling rate |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
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39 # galaxy: boolean tag for galaxy installation. |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
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40 |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
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41 if(reg2plot!='bed'){ |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
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42 # Subset using genome-region combination. |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
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43 key <- default.tbl$Genome == genome & default.tbl$Region == reg2plot |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
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44 if(sum(key) == 0) { |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
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45 stop("The combination of genome and region does not exist. You |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
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46 may need to install the genome or the region does not exist yet.\n") |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
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47 } |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
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48 anno.parameters <- default.tbl[key, ] |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
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49 db.match.mask <- dbfile.tbl$Genome == genome & |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
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50 dbfile.tbl$Region == reg2plot |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
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51 anno.db.candidates <- dbfile.tbl[db.match.mask, ] |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
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52 |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
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53 # Database flavor. |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
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54 if('-D' %in% names(args.tbl)){ |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
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55 database <- as.character(args.tbl['-D']) |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
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56 database.allowed <- unique(anno.db.candidates$DB) |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
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57 stopifnot(database %in% database.allowed) |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
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58 }else{ |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
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59 database <- as.character(anno.parameters$DefaultDB) |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
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60 } |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
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61 |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
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62 anno.db.candidates <- anno.db.candidates[anno.db.candidates$DB == database, ] |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
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63 |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
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64 if (file.exists(file.path(progpath, 'database', genome, reg2plot))){ |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
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65 prefix <- file.path(progpath, 'database', genome, reg2plot) |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
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66 }else{ |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
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67 prefix <- file.path(progpath, 'database', genome) |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
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68 } |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
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69 |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
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70 # Further info to subset genomic regions. |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
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71 if('-F' %in% names(args.tbl)){ |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
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72 finfo <- as.character(args.tbl['-F']) |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
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73 } else { |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
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74 finfo <- NULL |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
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75 } |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
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diff
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|
76 |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff
changeset
|
77 Labs <- unlist(strsplit(as.character(anno.parameters$PointLab[1]), ",")) |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff
changeset
|
78 if(length(Labs)==1){ |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff
changeset
|
79 pint <- TRUE |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff
changeset
|
80 }else{ |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff
changeset
|
81 pint <- FALSE |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff
changeset
|
82 } |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff
changeset
|
83 |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff
changeset
|
84 if(!is.null(finfo)){ # use finfo to subset DB tables. |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff
changeset
|
85 v.finfo <- unlist(strsplit(finfo, ',')) |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff
changeset
|
86 # Get the intersect of the v.finfo and FI columns of databases, |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff
changeset
|
87 # and choose the best fit. |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff
changeset
|
88 fi.score <- apply(anno.db.candidates, 1, FIScoreIntersect, |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff
changeset
|
89 v.finfo=v.finfo) |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff
changeset
|
90 anno.db.candidates <- anno.db.candidates[fi.score == max(fi.score), ] |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff
changeset
|
91 # RNA-seq tag. |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff
changeset
|
92 if(reg2plot == 'genebody' && 'rnaseq' %in% v.finfo) { |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff
changeset
|
93 rnaseq.gb <- TRUE |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff
changeset
|
94 }else{ |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff
changeset
|
95 rnaseq.gb <- FALSE |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff
changeset
|
96 } |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff
changeset
|
97 } else { |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff
changeset
|
98 rnaseq.gb <- FALSE |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff
changeset
|
99 } |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff
changeset
|
100 anno.db.candidates <- anno.db.candidates[order(anno.db.candidates$dbScore), ] |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff
changeset
|
101 f.load <- file.path(prefix, anno.db.candidates$"db.file"[1]) |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff
changeset
|
102 |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff
changeset
|
103 if (!file.exists(f.load)){ |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff
changeset
|
104 stop("The requested database file does not exist. You may have a |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff
changeset
|
105 corrupted database. Consider reinstalling the genome.\n") |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff
changeset
|
106 # cat("\nDownloading database:\n") |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff
changeset
|
107 # download.file(anno.db.candidates$"URL"[1], destfile=f.load, |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff
changeset
|
108 # method="curl") |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff
changeset
|
109 # stopifnot(file.exists(f.load)) |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff
changeset
|
110 } |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff
changeset
|
111 # Load genomic coordinates. |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff
changeset
|
112 cat("\nUsing database:\n") |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff
changeset
|
113 cat(paste(f.load, "\n", sep="")) |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff
changeset
|
114 load(f.load) # load coordinates into variable: genome.coord |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff
changeset
|
115 |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff
changeset
|
116 } else if(reg2plot == 'bed') { |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff
changeset
|
117 rnaseq.gb <- FALSE |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff
changeset
|
118 } |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff
changeset
|
119 |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff
changeset
|
120 # Identify unique regions. |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff
changeset
|
121 reg.list <- as.factor(ctg.tbl$glist) |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff
changeset
|
122 uniq.reg <- levels(reg.list) |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff
changeset
|
123 |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff
changeset
|
124 # Determine plot coordinates for each unique region. |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff
changeset
|
125 coord.list <- vector('list', length(uniq.reg)) |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff
changeset
|
126 names(coord.list) <- uniq.reg |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff
changeset
|
127 |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff
changeset
|
128 ReadBedCoord <- function(bed.file) { |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff
changeset
|
129 # Read a bed into memory as a dataframe. |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff
changeset
|
130 # Args: |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff
changeset
|
131 # bed.file: path of the bed file to be read. |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff
changeset
|
132 # Returns: genome coordinates as a dataframe. |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff
changeset
|
133 |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff
changeset
|
134 if(!galaxy && |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff
changeset
|
135 length(grep("\\.bed([0-9]+)?$", bed.file, ignore.case=T)) == 0) { |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff
changeset
|
136 warning(sprintf("File name: '%s' does not seem to a correct name |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff
changeset
|
137 for bed file.\n", bed.file)) |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff
changeset
|
138 } |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff
changeset
|
139 bed.coord <- read.table(bed.file, sep="\t", quote="\"") |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff
changeset
|
140 if(ncol(bed.coord) <3){ |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff
changeset
|
141 stop("A bed file must contain at least 3 columns! The format is: |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff
changeset
|
142 chrom, start, end, gname, tid, strand. Columns 4-6 are optional\n") |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff
changeset
|
143 } |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff
changeset
|
144 genome.coord <- data.frame(chrom=chromFormat(bed.coord[, 1]), |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff
changeset
|
145 start=bed.coord[, 2] + 1, |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff
changeset
|
146 end=bed.coord[, 3], |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff
changeset
|
147 gid=NA, gname='N', tid='N', strand='+', |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff
changeset
|
148 byname.uniq=T, bygid.uniq=NA) |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff
changeset
|
149 # Perform sanity check for bed file. |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff
changeset
|
150 if(!all(genome.coord$start <= genome.coord$end)) { |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff
changeset
|
151 stop(sprintf("Sanity check for bed file: %s failed. Bed files are |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff
changeset
|
152 0-based and right-side open.\n", bed.file)) |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff
changeset
|
153 } |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff
changeset
|
154 |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff
changeset
|
155 # Deal with columns 4-6 (Optional). |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff
changeset
|
156 if(ncol(bed.coord) >=4){ |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff
changeset
|
157 genome.coord$gname <- bed.coord[, 4] |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff
changeset
|
158 } |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff
changeset
|
159 if(ncol(bed.coord) >=5){ |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff
changeset
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160 genome.coord$tid <- bed.coord[, 5] |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff
changeset
|
161 } |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff
changeset
|
162 if(ncol(bed.coord) >=6){ |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff
changeset
|
163 genome.coord$strand <- bed.coord[, 6] |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff
changeset
|
164 } |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff
changeset
|
165 |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff
changeset
|
166 genome.coord |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff
changeset
|
167 } |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff
changeset
|
168 |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff
changeset
|
169 # Sample a vector but preserve its original sequential order. |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff
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170 sampleInSequence <- function(x, samprate) { |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff
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171 x[ifelse(runif(length(x)) <= samprate, T, F)] |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff
changeset
|
172 } |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff
changeset
|
173 |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff
changeset
|
174 ValidateGeneSubset <- function(gid.match, tid.match, gname.match) { |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff
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175 # To validate that there is no ambiguous hits in gene match. |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff
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|
176 # Args: |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff
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177 # XXX.match: positional hits with respect to the gene database. 0 means |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
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178 # no hit. |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
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179 |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff
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|
180 subset.matrix <- rbind(gid.match, tid.match, gname.match) |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff
changeset
|
181 g.valid <- sapply(subset.matrix, function(col.hits) { |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff
changeset
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182 length(unique(col.hits[col.hits > 0])) <= 1 |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff
changeset
|
183 }) |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff
changeset
|
184 |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff
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|
185 all(g.valid) |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff
changeset
|
186 } |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff
changeset
|
187 |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff
changeset
|
188 for(i in 1:length(uniq.reg)) { |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff
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|
189 ur <- uniq.reg[i] |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff
changeset
|
190 |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff
changeset
|
191 if(reg2plot == "bed") { |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff
changeset
|
192 coord.list[[i]] <- ReadBedCoord(ur) |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff
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193 } else if(ur == '-1') { # use whole genome. |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff
changeset
|
194 coord.list[[i]] <- genome.coord[genome.coord$byname.uniq, ] |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff
changeset
|
195 } else { # read gene list from text file. |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff
changeset
|
196 gene.list <- read.table(ur, as.is=T, comment.char='#')$V1 |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff
changeset
|
197 gid.match <- match(gene.list, genome.coord$gid, nomatch=0) |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff
changeset
|
198 gname.match <- match(gene.list, genome.coord$gname, nomatch=0) |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff
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|
199 tid.match <- match(gene.list, genome.coord$tid, nomatch=0) |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff
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|
200 if(!ValidateGeneSubset(gid.match, tid.match, gname.match)) { |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff
changeset
|
201 stop("\nAmbiguous hits in gene database. This shall never |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff
changeset
|
202 happen! Contact ngs.plot maintainers.\n") |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff
changeset
|
203 } |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff
changeset
|
204 subset.idx <- pmax(gid.match, tid.match, gname.match) |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff
changeset
|
205 # subset.idx <- gid.match + tid.match + gname.match |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff
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|
206 subset.idx <- subset.idx[subset.idx != 0] |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff
changeset
|
207 if(length(subset.idx) == 0) { |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff
changeset
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208 stop("\nGene subset size becomes zero. Are you using the |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff
changeset
|
209 correct database?\n") |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff
changeset
|
210 } |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff
changeset
|
211 coord.list[[i]] <- genome.coord[subset.idx, ] |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff
changeset
|
212 } |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff
changeset
|
213 |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff
changeset
|
214 # Do sampling. |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff
changeset
|
215 if(samprate < 1) { |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff
changeset
|
216 samp.idx <- sampleInSequence(1:nrow(coord.list[[i]]), samprate) |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff
changeset
|
217 coord.list[[i]] <- coord.list[[i]][samp.idx, ] |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff
changeset
|
218 } |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff
changeset
|
219 } |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff
changeset
|
220 |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff
changeset
|
221 # If bed file, set boolean tag for point interval, i.e. interval=1bp. |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff
changeset
|
222 if(reg2plot == "bed") { |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff
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|
223 pint <- all(sapply(coord.list, function(cd) all(cd$start == cd$end))) |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff
changeset
|
224 if(pint) { |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
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|
225 Labs <- c("Center") |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff
changeset
|
226 } else { |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
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|
227 Labs <- c("5'End", "3'End") |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff
changeset
|
228 } |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff
changeset
|
229 } |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
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230 |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
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231 # Set boolean tag for large interval display. |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
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232 if(!pint && is.na(lgint)) { |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
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233 if(median(sapply(coord.list, function(cd) { |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
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234 median(cd$end - cd$start + 1) |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
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235 })) > flanksize) { |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
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236 lgint <- 1 |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
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237 } else { |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
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238 lgint <- 0 |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
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239 } |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
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240 } |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
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241 |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
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242 res <- list(coord.list=coord.list, rnaseq.gb=rnaseq.gb, lgint=lgint, |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
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243 reg.list=reg.list, uniq.reg=uniq.reg, pint=pint, Labs=Labs) |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
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244 |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
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245 # Add exon models to the result if RNA-seq. |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
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246 if(rnaseq.gb) { |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
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247 em.load <- file.path(prefix, paste(genome, database, 'exonmodel.RData', |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
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248 sep='.')) |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
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249 load(em.load) # load exon models into variable: exonmodel |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
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250 res$exonmodel <- exonmodel |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
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251 } |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
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252 |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
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253 res |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
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254 } |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
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255 |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
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256 |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
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257 |
3ca58369469c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
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258 |