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how to use <a href="http://www.r-project.org/"><b>R</b></a> as the main <b>SHELL</b> of <a href="https://www.gnu.org/software/make/manual/html_node/index.html">GNU-Make</a> instead of using a classical linux shell like bash
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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 | |
| > |
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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 | |
| > |
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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 |
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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");) |
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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");) |
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