Mercurial > repos > davidvanzessen > mutation_analysis
changeset 109:0096cd454380 draft
Uploaded
| author | davidvanzessen |
|---|---|
| date | Thu, 14 Jul 2016 07:29:56 -0400 |
| parents | 6add3e66f4fa |
| children | ade5cf6fd2dc |
| files | aa_histogram.r tmp/baseline/wrapper.sh |
| diffstat | 2 files changed, 10 insertions(+), 3 deletions(-) [+] |
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--- a/aa_histogram.r Wed Jul 13 09:04:15 2016 -0400 +++ b/aa_histogram.r Thu Jul 14 07:29:56 2016 -0400 @@ -48,13 +48,14 @@ print("---------------- write/print ----------------") + png(filename=paste(outdir, "/aa_histogram_", gene, ".png", sep=""), width=1280, height=720) + print(m) + dev.off() + dat.sums = data.frame(index=1:length(mutations.at.position), mutations.at.position=mutations.at.position, aa.at.position=aa.at.position) write.table(dat.sums, paste(outdir, "/aa_histogram_sum_", gene, ".txt", sep=""), sep="\t",quote=F,row.names=F,col.names=T) write.table(mutations.by.id.gene, paste(outdir, "/aa_histogram_count_", gene, ".txt", sep=""), sep="\t",quote=F,row.names=F,col.names=T) write.table(absent.aa.by.id.gene, paste(outdir, "/aa_histogram_absent_", gene, ".txt", sep=""), sep="\t",quote=F,row.names=F,col.names=T) write.table(dat_dt, paste(outdir, "/aa_histogram_", gene, ".txt", sep=""), sep="\t",quote=F,row.names=F,col.names=T) - png(filename=paste(outdir, "/aa_histogram_", gene, ".png", sep=""), width=1280, height=720) - print(m) - dev.off() }
--- a/tmp/baseline/wrapper.sh Wed Jul 13 09:04:15 2016 -0400 +++ b/tmp/baseline/wrapper.sh Thu Jul 14 07:29:56 2016 -0400 @@ -77,6 +77,12 @@ fi count=$((count+1)) done + +if [[ $(wc -l < $fasta) -eq "1" ]]; then + echo "No sequences in the fasta file, exiting" + exit 0 +fi + workdir="$PWD" cd $dir echo "file: ${inputs[0]}"