Parallelizing #RStats using #make
In the current post, I'll show how to use R as the main SHELL of GNU-Make instead of using a classical linux shell like 'bash'. Why would you do this ?
- awesomeness
- Make-based workflow management
- Make-based execution with --jobs. GNU make knows how to execute several recipes at once. Normally, make will execute only one recipe at a time, waiting for it to finish before executing the next. However, the '-j' or '--jobs' option tells make to execute many recipes simultaneously.
The only problem is that R doesn't accept a multiline-argument on the command line (see http://stackoverflow.com/questions/21442674) so I created a wrapper 'mockR' that save the argument '-e "code"' into a file and pipe it into R:
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| #!/bin/bash | |
| while getopts "e:" opt; do | |
| case $opt in | |
| e) | |
| R=$OPTARG | |
| ;; | |
| \:) | |
| echo "Argument missing: -$OPTARG" >&2 | |
| exit -1 | |
| ;; | |
| \?) | |
| echo "Invalid option: -$OPTARG" >&2 | |
| exit -1 | |
| ;; | |
| esac | |
| done | |
| if [[ -n "$R" ]] | |
| then | |
| TMP=$(mktemp) | |
| trap "{ rm -f ${TMP}; exit 255; }" SIGINT | |
| echo "${R}" > ${TMP} | |
| R --vanilla --no-readline --quiet < ${TMP} | |
| rm -f ${TMP} | |
| else | |
| echo "Undefined script" >&2 | |
| exit -1 | |
| fi |
(Edit1: A comment from madscientist : Re your script; you can save yourself some wear-and-tear on your disk and avoid the need for temp files and cleanup by just piping the input directly:
echo "$R" | R --vanilla --no-readline --quiet . Just a thought. ")(Edit2: the exit value of 'R' should also be returned by 'mockR'.)
This file is set as executable:
$ chmod u+x ./mockRIn the makefile, we tell 'make' to use 'mockR' instead of '/usr/bin/sh':
SHELL = ./mockRThe R code will be passed to 'mockR' using the argument '-e "code"'
.SHELLFLAGS= -eWe also set 'ONESHELL': "If .ONESHELL is mentioned as a target, then when a target is built all lines of the recipe will be given to a single invocation of the shell rather than each line being invoked separately"
.ONESHELL:
Example 1
We download the table 'knownGene' from the UCSC and we plot a pdf file 'countExons=f(txStart)'. Please, note that the targets are created using some R statements, NOT bash statements:
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| .PHONY: all clean | |
| SHELL = ./mockR | |
| .SHELLFLAGS= -e | |
| .ONESHELL: | |
| CHROM=1 2 | |
| UCSC=http://hgdownload.cse.ucsc.edu/goldenpath/hg19/database/ | |
| all: $(foreach C,${CHROM}, chr${C}.pdf) | |
| chr1.pdf: knownGene.txt.gz | |
| gold <- read.delim(gzfile("$<")) | |
| colnames(gold)= c("name", "chrom", "strand", "txStart", "txEnd", "cdsStart", "cdsEnd", "exonCount", "exonStarts", "exonEnds", "proteinID", "alignID") | |
| gold=subset(gold,chrom=='chr1') | |
| pdf(file="$@") | |
| plot(gold$$txStart,gold$$exonCount) | |
| dev.off() | |
| chr2.pdf: knownGene.txt.gz | |
| gold <- read.delim(gzfile("$<")) | |
| colnames(gold)= c("name", "chrom", "strand", "txStart", "txEnd", "cdsStart", "cdsEnd", "exonCount", "exonStarts", "exonEnds", "proteinID", "alignID") | |
| gold=subset(gold,chrom=='chr2') | |
| pdf(file="$@") | |
| plot(gold$$txStart,gold$$exonCount) | |
| dev.off() | |
| knownGene.txt.gz: | |
| download.file("${UCSC}/$@","$@") | |
| clean: | |
| $(foreach F,knownGene.txt.gz $(foreach C,${CHROM}, chr${C}.pdf) ,file.remove("$F");) |
Now Invoke make
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| $ make-4.0/make -f R01.mk | |
| download.file("http://hgdownload.cse.ucsc.edu/goldenpath/hg19/database//knownGene.txt.gz","knownGene.txt.gz") | |
| > download.file("http://hgdownload.cse.ucsc.edu/goldenpath/hg19/database//knownGene.txt.gz","knownGene.txt.gz") | |
| trying URL 'http://hgdownload.cse.ucsc.edu/goldenpath/hg19/database//knownGene.txt.gz' | |
| Content type 'application/x-gzip' length 4270683 bytes (4.1 Mb) | |
| opened URL | |
| ================================================== | |
| downloaded 4.1 Mb | |
| > | |
| gold <- read.delim(gzfile("knownGene.txt.gz")) | |
| colnames(gold)= c("name", "chrom", "strand", "txStart", "txEnd", "cdsStart", "cdsEnd", "exonCount", "exonStarts", "exonEnds", "proteinID", "alignID") | |
| gold=subset(gold,chrom=='chr1') | |
| pdf(file="chr1.pdf") | |
| plot(gold$txStart,gold$exonCount) | |
| dev.off() | |
| > gold <- read.delim(gzfile("knownGene.txt.gz")) | |
| > colnames(gold)= c("name", "chrom", "strand", "txStart", "txEnd", "cdsStart", "cdsEnd", "exonCount", "exonStarts", "exonEnds", "proteinID", "alignID") | |
| > gold=subset(gold,chrom=='chr1') | |
| > pdf(file="chr1.pdf") | |
| > plot(gold$txStart,gold$exonCount) | |
| > dev.off() | |
| null device | |
| 1 | |
| > | |
| gold <- read.delim(gzfile("knownGene.txt.gz")) | |
| colnames(gold)= c("name", "chrom", "strand", "txStart", "txEnd", "cdsStart", "cdsEnd", "exonCount", "exonStarts", "exonEnds", "proteinID", "alignID") | |
| gold=subset(gold,chrom=='chr2') | |
| pdf(file="chr2.pdf") | |
| plot(gold$txStart,gold$exonCount) | |
| dev.off() | |
| > gold <- read.delim(gzfile("knownGene.txt.gz")) | |
| > colnames(gold)= c("name", "chrom", "strand", "txStart", "txEnd", "cdsStart", "cdsEnd", "exonCount", "exonStarts", "exonEnds", "proteinID", "alignID") | |
| > gold=subset(gold,chrom=='chr2') | |
| > pdf(file="chr2.pdf") | |
| > plot(gold$txStart,gold$exonCount) | |
| > dev.off() | |
| null device | |
| 1 | |
| > |
Example 2
Using a theeval and the call function we can make the previous 'Makefile' applicable for all the chromosomes:
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| .PHONY: all clean | |
| SHELL = ./mockR | |
| .SHELLFLAGS= -e | |
| .ONESHELL: | |
| CHROM=1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X Y | |
| UCSC=http://hgdownload.cse.ucsc.edu/goldenpath/hg19/database/ | |
| define plot_knownGene | |
| chr$(1).pdf: knownGene.txt.gz | |
| gold <- read.delim(gzfile("$$<")) | |
| colnames(gold)= c("name", "chrom", "strand", "txStart", "txEnd", "cdsStart", "cdsEnd", "exonCount", "exonStarts", "exonEnds", "proteinID", "alignID") | |
| gold=subset(gold,chrom=='chr$(1)') | |
| pdf(file="$$@") | |
| plot(gold$$$$txStart,gold$$$$exonCount) | |
| dev.off() | |
| endef | |
| all: $(foreach C,${CHROM}, chr${C}.pdf) | |
| $(foreach C,${CHROM}, $(eval $(call plot_knownGene,$C))) | |
| knownGene.txt.gz: | |
| download.file("${UCSC}/$@","$@") | |
| clean: | |
| $(foreach F,knownGene.txt.gz $(foreach C,${CHROM}, chr${C}.pdf) ,file.remove("$F");) |
Now Invoke make USING TRHEE PARALLEL JOBS
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| $ ./make -j 3 -f R02.mk all | |
| download.file("http://hgdownload.cse.ucsc.edu/goldenpath/hg19/database//knownGene.txt.gz","knownGene.txt.gz") | |
| > download.file("http://hgdownload.cse.ucsc.edu/goldenpath/hg19/database//knownGene.txt.gz","knownGene.txt.gz") | |
| trying URL 'http://hgdownload.cse.ucsc.edu/goldenpath/hg19/database//knownGene.txt.gz' | |
| Content type 'application/x-gzip' length 4270683 bytes (4.1 Mb) | |
| opened URL | |
| ================================================== | |
| downloaded 4.1 Mb | |
| > | |
| gold <- read.delim(gzfile("knownGene.txt.gz")) | |
| colnames(gold)= c("name", "chrom", "strand", "txStart", "txEnd", "cdsStart", "cdsEnd", "exonCount", "exonStarts", "exonEnds", "proteinID", "alignID") | |
| gold=subset(gold,chrom=='chr1') | |
| pdf(file="chr1.pdf") | |
| plot(gold$txStart,gold$exonCount) | |
| dev.off() | |
| gold <- read.delim(gzfile("knownGene.txt.gz")) | |
| colnames(gold)= c("name", "chrom", "strand", "txStart", "txEnd", "cdsStart", "cdsEnd", "exonCount", "exonStarts", "exonEnds", "proteinID", "alignID") | |
| gold=subset(gold,chrom=='chr2') | |
| pdf(file="chr2.pdf") | |
| plot(gold$txStart,gold$exonCount) | |
| dev.off() | |
| gold <- read.delim(gzfile("knownGene.txt.gz")) | |
| colnames(gold)= c("name", "chrom", "strand", "txStart", "txEnd", "cdsStart", "cdsEnd", "exonCount", "exonStarts", "exonEnds", "proteinID", "alignID") | |
| gold=subset(gold,chrom=='chr3') | |
| pdf(file="chr3.pdf") | |
| plot(gold$txStart,gold$exonCount) | |
| dev.off() | |
| > gold <- read.delim(gzfile("knownGene.txt.gz")) | |
| > gold <- read.delim(gzfile("knownGene.txt.gz")) | |
| > gold <- read.delim(gzfile("knownGene.txt.gz")) | |
| > colnames(gold)= c("name", "chrom", "strand", "txStart", "txEnd", "cdsStart", "cdsEnd", "exonCount", "exonStarts", "exonEnds", "proteinID", "alignID") | |
| > colnames(gold)= c("name", "chrom", "strand", "txStart", "txEnd", "cdsStart", "cdsEnd", "exonCount", "exonStarts", "exonEnds", "proteinID", "alignID") | |
| > colnames(gold)= c("name", "chrom", "strand", "txStart", "txEnd", "cdsStart", "cdsEnd", "exonCount", "exonStarts", "exonEnds", "proteinID", "alignID") | |
| > gold=subset(gold,chrom=='chr3') | |
| > gold=subset(gold,chrom=='chr1') | |
| > pdf(file="chr3.pdf") | |
| > gold=subset(gold,chrom=='chr2') | |
| > plot(gold$txStart,gold$exonCount) | |
| > dev.off() | |
| null device | |
| 1 | |
| > | |
| gold <- read.delim(gzfile("knownGene.txt.gz")) | |
| colnames(gold)= c("name", "chrom", "strand", "txStart", "txEnd", "cdsStart", "cdsEnd", "exonCount", "exonStarts", "exonEnds", "proteinID", "alignID") | |
| gold=subset(gold,chrom=='chr4') | |
| pdf(file="chr4.pdf") | |
| plot(gold$txStart,gold$exonCount) | |
| dev.off() | |
| > pdf(file="chr1.pdf") | |
| > pdf(file="chr2.pdf") | |
| > plot(gold$txStart,gold$exonCount) | |
| > plot(gold$txStart,gold$exonCount) | |
| > dev.off() | |
| null device | |
| 1 | |
| > | |
| gold <- read.delim(gzfile("knownGene.txt.gz")) | |
| colnames(gold)= c("name", "chrom", "strand", "txStart", "txEnd", "cdsStart", "cdsEnd", "exonCount", "exonStarts", "exonEnds", "proteinID", "alignID") | |
| gold=subset(gold,chrom=='chr5') | |
| pdf(file="chr5.pdf") | |
| plot(gold$txStart,gold$exonCount) | |
| dev.off() | |
| > dev.off() | |
| null device | |
| 1 | |
| > | |
| gold <- read.delim(gzfile("knownGene.txt.gz")) | |
| colnames(gold)= c("name", "chrom", "strand", "txStart", "txEnd", "cdsStart", "cdsEnd", "exonCount", "exonStarts", "exonEnds", "proteinID", "alignID") | |
| gold=subset(gold,chrom=='chr6') | |
| pdf(file="chr6.pdf") | |
| plot(gold$txStart,gold$exonCount) | |
| dev.off() | |
| > gold <- read.delim(gzfile("knownGene.txt.gz")) | |
| > gold <- read.delim(gzfile("knownGene.txt.gz")) | |
| > gold <- read.delim(gzfile("knownGene.txt.gz")) | |
| > colnames(gold)= c("name", "chrom", "strand", "txStart", "txEnd", "cdsStart", "cdsEnd", "exonCount", "exonStarts", "exonEnds", "proteinID", "alignID") | |
| > colnames(gold)= c("name", "chrom", "strand", "txStart", "txEnd", "cdsStart", "cdsEnd", "exonCount", "exonStarts", "exonEnds", "proteinID", "alignID") | |
| > gold=subset(gold,chrom=='chr5') | |
| > gold=subset(gold,chrom=='chr6') | |
| > pdf(file="chr5.pdf") | |
| > plot(gold$txStart,gold$exonCount) | |
| > dev.off() | |
| null device | |
| 1 | |
| > | |
| gold <- read.delim(gzfile("knownGene.txt.gz")) | |
| colnames(gold)= c("name", "chrom", "strand", "txStart", "txEnd", "cdsStart", "cdsEnd", "exonCount", "exonStarts", "exonEnds", "proteinID", "alignID") | |
| gold=subset(gold,chrom=='chr7') | |
| pdf(file="chr7.pdf") | |
| plot(gold$txStart,gold$exonCount) | |
| dev.off() | |
| > pdf(file="chr6.pdf") | |
| > plot(gold$txStart,gold$exonCount) | |
| > dev.off() | |
| null device | |
| 1 | |
| > | |
| gold <- read.delim(gzfile("knownGene.txt.gz")) | |
| colnames(gold)= c("name", "chrom", "strand", "txStart", "txEnd", "cdsStart", "cdsEnd", "exonCount", "exonStarts", "exonEnds", "proteinID", "alignID") | |
| gold=subset(gold,chrom=='chr8') | |
| pdf(file="chr8.pdf") | |
| plot(gold$txStart,gold$exonCount) | |
| dev.off() | |
| > gold <- read.delim(gzfile("knownGene.txt.gz")) | |
| > gold <- read.delim(gzfile("knownGene.txt.gz")) | |
| > colnames(gold)= c("name", "chrom", "strand", "txStart", "txEnd", "cdsStart", "cdsEnd", "exonCount", "exonStarts", "exonEnds", "proteinID", "alignID") | |
| > gold=subset(gold,chrom=='chr4') | |
| > pdf(file="chr4.pdf") | |
| > plot(gold$txStart,gold$exonCount) | |
| > dev.off() | |
| null device | |
| 1 | |
| > | |
| gold <- read.delim(gzfile("knownGene.txt.gz")) | |
| colnames(gold)= c("name", "chrom", "strand", "txStart", "txEnd", "cdsStart", "cdsEnd", "exonCount", "exonStarts", "exonEnds", "proteinID", "alignID") | |
| gold=subset(gold,chrom=='chr9') | |
| pdf(file="chr9.pdf") | |
| plot(gold$txStart,gold$exonCount) | |
| dev.off() | |
| > gold <- read.delim(gzfile("knownGene.txt.gz")) | |
| > colnames(gold)= c("name", "chrom", "strand", "txStart", "txEnd", "cdsStart", "cdsEnd", "exonCount", "exonStarts", "exonEnds", "proteinID", "alignID") | |
| > gold=subset(gold,chrom=='chr7') | |
| > pdf(file="chr7.pdf") | |
| > plot(gold$txStart,gold$exonCount) | |
| > dev.off() | |
| null device | |
| 1 | |
| > | |
| gold <- read.delim(gzfile("knownGene.txt.gz")) | |
| colnames(gold)= c("name", "chrom", "strand", "txStart", "txEnd", "cdsStart", "cdsEnd", "exonCount", "exonStarts", "exonEnds", "proteinID", "alignID") | |
| gold=subset(gold,chrom=='chr10') | |
| pdf(file="chr10.pdf") | |
| plot(gold$txStart,gold$exonCount) | |
| dev.off() | |
| > gold <- read.delim(gzfile("knownGene.txt.gz")) | |
| > colnames(gold)= c("name", "chrom", "strand", "txStart", "txEnd", "cdsStart", "cdsEnd", "exonCount", "exonStarts", "exonEnds", "proteinID", "alignID") | |
| > gold=subset(gold,chrom=='chr9') | |
| > pdf(file="chr9.pdf") | |
| > plot(gold$txStart,gold$exonCount) | |
| > dev.off() | |
| null device | |
| 1 | |
| > | |
| gold <- read.delim(gzfile("knownGene.txt.gz")) | |
| colnames(gold)= c("name", "chrom", "strand", "txStart", "txEnd", "cdsStart", "cdsEnd", "exonCount", "exonStarts", "exonEnds", "proteinID", "alignID") | |
| gold=subset(gold,chrom=='chr11') | |
| pdf(file="chr11.pdf") | |
| plot(gold$txStart,gold$exonCount) | |
| dev.off() | |
| > colnames(gold)= c("name", "chrom", "strand", "txStart", "txEnd", "cdsStart", "cdsEnd", "exonCount", "exonStarts", "exonEnds", "proteinID", "alignID") | |
| > gold <- read.delim(gzfile("knownGene.txt.gz")) | |
| > gold=subset(gold,chrom=='chr8') | |
| > pdf(file="chr8.pdf") | |
| > plot(gold$txStart,gold$exonCount) | |
| > dev.off() | |
| null device | |
| 1 | |
| > | |
| gold <- read.delim(gzfile("knownGene.txt.gz")) | |
| colnames(gold)= c("name", "chrom", "strand", "txStart", "txEnd", "cdsStart", "cdsEnd", "exonCount", "exonStarts", "exonEnds", "proteinID", "alignID") | |
| gold=subset(gold,chrom=='chr12') | |
| pdf(file="chr12.pdf") | |
| plot(gold$txStart,gold$exonCount) | |
| dev.off() | |
| > gold <- read.delim(gzfile("knownGene.txt.gz")) | |
| > colnames(gold)= c("name", "chrom", "strand", "txStart", "txEnd", "cdsStart", "cdsEnd", "exonCount", "exonStarts", "exonEnds", "proteinID", "alignID") | |
| > gold=subset(gold,chrom=='chr10') | |
| > pdf(file="chr10.pdf") | |
| > plot(gold$txStart,gold$exonCount) | |
| > dev.off() | |
| null device | |
| 1 | |
| > | |
| gold <- read.delim(gzfile("knownGene.txt.gz")) | |
| colnames(gold)= c("name", "chrom", "strand", "txStart", "txEnd", "cdsStart", "cdsEnd", "exonCount", "exonStarts", "exonEnds", "proteinID", "alignID") | |
| gold=subset(gold,chrom=='chr13') | |
| pdf(file="chr13.pdf") | |
| plot(gold$txStart,gold$exonCount) | |
| dev.off() | |
| > gold <- read.delim(gzfile("knownGene.txt.gz")) | |
| > colnames(gold)= c("name", "chrom", "strand", "txStart", "txEnd", "cdsStart", "cdsEnd", "exonCount", "exonStarts", "exonEnds", "proteinID", "alignID") | |
| > gold=subset(gold,chrom=='chr11') | |
| > pdf(file="chr11.pdf") | |
| > plot(gold$txStart,gold$exonCount) | |
| > dev.off() | |
| null device | |
| 1 | |
| > | |
| gold <- read.delim(gzfile("knownGene.txt.gz")) | |
| colnames(gold)= c("name", "chrom", "strand", "txStart", "txEnd", "cdsStart", "cdsEnd", "exonCount", "exonStarts", "exonEnds", "proteinID", "alignID") | |
| gold=subset(gold,chrom=='chr14') | |
| pdf(file="chr14.pdf") | |
| plot(gold$txStart,gold$exonCount) | |
| dev.off() | |
| > gold <- read.delim(gzfile("knownGene.txt.gz")) | |
| > colnames(gold)= c("name", "chrom", "strand", "txStart", "txEnd", "cdsStart", "cdsEnd", "exonCount", "exonStarts", "exonEnds", "proteinID", "alignID") | |
| > gold=subset(gold,chrom=='chr12') | |
| > pdf(file="chr12.pdf") | |
| > plot(gold$txStart,gold$exonCount) | |
| > dev.off() | |
| null device | |
| 1 | |
| > | |
| gold <- read.delim(gzfile("knownGene.txt.gz")) | |
| colnames(gold)= c("name", "chrom", "strand", "txStart", "txEnd", "cdsStart", "cdsEnd", "exonCount", "exonStarts", "exonEnds", "proteinID", "alignID") | |
| gold=subset(gold,chrom=='chr15') | |
| pdf(file="chr15.pdf") | |
| plot(gold$txStart,gold$exonCount) | |
| dev.off() | |
| > gold <- read.delim(gzfile("knownGene.txt.gz")) | |
| > colnames(gold)= c("name", "chrom", "strand", "txStart", "txEnd", "cdsStart", "cdsEnd", "exonCount", "exonStarts", "exonEnds", "proteinID", "alignID") | |
| > gold=subset(gold,chrom=='chr13') | |
| > pdf(file="chr13.pdf") | |
| > plot(gold$txStart,gold$exonCount) | |
| > dev.off() | |
| null device | |
| 1 | |
| > | |
| gold <- read.delim(gzfile("knownGene.txt.gz")) | |
| colnames(gold)= c("name", "chrom", "strand", "txStart", "txEnd", "cdsStart", "cdsEnd", "exonCount", "exonStarts", "exonEnds", "proteinID", "alignID") | |
| gold=subset(gold,chrom=='chr16') | |
| pdf(file="chr16.pdf") | |
| plot(gold$txStart,gold$exonCount) | |
| dev.off() | |
| > gold <- read.delim(gzfile("knownGene.txt.gz")) | |
| > colnames(gold)= c("name", "chrom", "strand", "txStart", "txEnd", "cdsStart", "cdsEnd", "exonCount", "exonStarts", "exonEnds", "proteinID", "alignID") | |
| > gold=subset(gold,chrom=='chr14') | |
| > pdf(file="chr14.pdf") | |
| > plot(gold$txStart,gold$exonCount) | |
| > dev.off() | |
| null device | |
| 1 | |
| > | |
| gold <- read.delim(gzfile("knownGene.txt.gz")) | |
| colnames(gold)= c("name", "chrom", "strand", "txStart", "txEnd", "cdsStart", "cdsEnd", "exonCount", "exonStarts", "exonEnds", "proteinID", "alignID") | |
| gold=subset(gold,chrom=='chr17') | |
| pdf(file="chr17.pdf") | |
| plot(gold$txStart,gold$exonCount) | |
| dev.off() | |
| > gold <- read.delim(gzfile("knownGene.txt.gz")) | |
| > colnames(gold)= c("name", "chrom", "strand", "txStart", "txEnd", "cdsStart", "cdsEnd", "exonCount", "exonStarts", "exonEnds", "proteinID", "alignID") | |
| > gold=subset(gold,chrom=='chr15') | |
| > pdf(file="chr15.pdf") | |
| > plot(gold$txStart,gold$exonCount) | |
| > dev.off() | |
| null device | |
| 1 | |
| > | |
| gold <- read.delim(gzfile("knownGene.txt.gz")) | |
| colnames(gold)= c("name", "chrom", "strand", "txStart", "txEnd", "cdsStart", "cdsEnd", "exonCount", "exonStarts", "exonEnds", "proteinID", "alignID") | |
| gold=subset(gold,chrom=='chr18') | |
| pdf(file="chr18.pdf") | |
| plot(gold$txStart,gold$exonCount) | |
| dev.off() | |
| > gold <- read.delim(gzfile("knownGene.txt.gz")) | |
| > colnames(gold)= c("name", "chrom", "strand", "txStart", "txEnd", "cdsStart", "cdsEnd", "exonCount", "exonStarts", "exonEnds", "proteinID", "alignID") | |
| > gold=subset(gold,chrom=='chr16') | |
| > pdf(file="chr16.pdf") | |
| > plot(gold$txStart,gold$exonCount) | |
| > dev.off() | |
| null device | |
| 1 | |
| > | |
| gold <- read.delim(gzfile("knownGene.txt.gz")) | |
| colnames(gold)= c("name", "chrom", "strand", "txStart", "txEnd", "cdsStart", "cdsEnd", "exonCount", "exonStarts", "exonEnds", "proteinID", "alignID") | |
| gold=subset(gold,chrom=='chr19') | |
| pdf(file="chr19.pdf") | |
| plot(gold$txStart,gold$exonCount) | |
| dev.off() | |
| > gold <- read.delim(gzfile("knownGene.txt.gz")) | |
| > colnames(gold)= c("name", "chrom", "strand", "txStart", "txEnd", "cdsStart", "cdsEnd", "exonCount", "exonStarts", "exonEnds", "proteinID", "alignID") | |
| > gold=subset(gold,chrom=='chr17') | |
| > pdf(file="chr17.pdf") | |
| > plot(gold$txStart,gold$exonCount) | |
| > dev.off() | |
| null device | |
| 1 | |
| > | |
| gold <- read.delim(gzfile("knownGene.txt.gz")) | |
| colnames(gold)= c("name", "chrom", "strand", "txStart", "txEnd", "cdsStart", "cdsEnd", "exonCount", "exonStarts", "exonEnds", "proteinID", "alignID") | |
| gold=subset(gold,chrom=='chr20') | |
| pdf(file="chr20.pdf") | |
| plot(gold$txStart,gold$exonCount) | |
| dev.off() | |
| > gold <- read.delim(gzfile("knownGene.txt.gz")) | |
| > colnames(gold)= c("name", "chrom", "strand", "txStart", "txEnd", "cdsStart", "cdsEnd", "exonCount", "exonStarts", "exonEnds", "proteinID", "alignID") | |
| > gold=subset(gold,chrom=='chr18') | |
| > pdf(file="chr18.pdf") | |
| > plot(gold$txStart,gold$exonCount) | |
| > dev.off() | |
| null device | |
| 1 | |
| > | |
| gold <- read.delim(gzfile("knownGene.txt.gz")) | |
| colnames(gold)= c("name", "chrom", "strand", "txStart", "txEnd", "cdsStart", "cdsEnd", "exonCount", "exonStarts", "exonEnds", "proteinID", "alignID") | |
| gold=subset(gold,chrom=='chr21') | |
| pdf(file="chr21.pdf") | |
| plot(gold$txStart,gold$exonCount) | |
| dev.off() | |
| > gold <- read.delim(gzfile("knownGene.txt.gz")) | |
| > colnames(gold)= c("name", "chrom", "strand", "txStart", "txEnd", "cdsStart", "cdsEnd", "exonCount", "exonStarts", "exonEnds", "proteinID", "alignID") | |
| > gold=subset(gold,chrom=='chr19') | |
| > pdf(file="chr19.pdf") | |
| > plot(gold$txStart,gold$exonCount) | |
| > dev.off() | |
| null device | |
| 1 | |
| > | |
| gold <- read.delim(gzfile("knownGene.txt.gz")) | |
| colnames(gold)= c("name", "chrom", "strand", "txStart", "txEnd", "cdsStart", "cdsEnd", "exonCount", "exonStarts", "exonEnds", "proteinID", "alignID") | |
| gold=subset(gold,chrom=='chr22') | |
| pdf(file="chr22.pdf") | |
| plot(gold$txStart,gold$exonCount) | |
| dev.off() | |
| > gold <- read.delim(gzfile("knownGene.txt.gz")) | |
| > colnames(gold)= c("name", "chrom", "strand", "txStart", "txEnd", "cdsStart", "cdsEnd", "exonCount", "exonStarts", "exonEnds", "proteinID", "alignID") | |
| > gold=subset(gold,chrom=='chr20') | |
| > pdf(file="chr20.pdf") | |
| > plot(gold$txStart,gold$exonCount) | |
| > dev.off() | |
| null device | |
| 1 | |
| > | |
| gold <- read.delim(gzfile("knownGene.txt.gz")) | |
| colnames(gold)= c("name", "chrom", "strand", "txStart", "txEnd", "cdsStart", "cdsEnd", "exonCount", "exonStarts", "exonEnds", "proteinID", "alignID") | |
| gold=subset(gold,chrom=='chrX') | |
| pdf(file="chrX.pdf") | |
| plot(gold$txStart,gold$exonCount) | |
| dev.off() | |
| > colnames(gold)= c("name", "chrom", "strand", "txStart", "txEnd", "cdsStart", "cdsEnd", "exonCount", "exonStarts", "exonEnds", "proteinID", "alignID") | |
| > gold <- read.delim(gzfile("knownGene.txt.gz")) | |
| > gold=subset(gold,chrom=='chr21') | |
| > pdf(file="chr21.pdf") | |
| > plot(gold$txStart,gold$exonCount) | |
| > dev.off() | |
| null device | |
| 1 | |
| > | |
| gold <- read.delim(gzfile("knownGene.txt.gz")) | |
| colnames(gold)= c("name", "chrom", "strand", "txStart", "txEnd", "cdsStart", "cdsEnd", "exonCount", "exonStarts", "exonEnds", "proteinID", "alignID") | |
| gold=subset(gold,chrom=='chrY') | |
| pdf(file="chrY.pdf") | |
| plot(gold$txStart,gold$exonCount) | |
| dev.off() | |
| > gold <- read.delim(gzfile("knownGene.txt.gz")) | |
| > colnames(gold)= c("name", "chrom", "strand", "txStart", "txEnd", "cdsStart", "cdsEnd", "exonCount", "exonStarts", "exonEnds", "proteinID", "alignID") | |
| > gold=subset(gold,chrom=='chr22') | |
| > pdf(file="chr22.pdf") | |
| > plot(gold$txStart,gold$exonCount) | |
| > dev.off() | |
| null device | |
| 1 | |
| > | |
| > colnames(gold)= c("name", "chrom", "strand", "txStart", "txEnd", "cdsStart", "cdsEnd", "exonCount", "exonStarts", "exonEnds", "proteinID", "alignID") | |
| > colnames(gold)= c("name", "chrom", "strand", "txStart", "txEnd", "cdsStart", "cdsEnd", "exonCount", "exonStarts", "exonEnds", "proteinID", "alignID") | |
| > gold=subset(gold,chrom=='chrX') | |
| > gold=subset(gold,chrom=='chrY') | |
| > pdf(file="chrX.pdf") | |
| > pdf(file="chrY.pdf") | |
| > plot(gold$txStart,gold$exonCount) | |
| > dev.off() | |
| null device | |
| 1 | |
| > | |
| > plot(gold$txStart,gold$exonCount) | |
| > dev.off() | |
| null device | |
| 1 | |
| > |
You can now watch the final pdf files:
That's it,
Pierre
1 comment:
Very cool.
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