Mercurial > repos > davidvanzessen > mutation_analysis
changeset 80:a4c2ddeadec0 draft
Uploaded
| author | davidvanzessen |
|---|---|
| date | Thu, 12 May 2016 10:51:55 -0400 |
| parents | 0513b46178c4 |
| children | a778156dad3d |
| files | naive_output.r wrapper.sh |
| diffstat | 2 files changed, 5 insertions(+), 5 deletions(-) [+] |
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--- a/naive_output.r Thu May 12 07:35:07 2016 -0400 +++ b/naive_output.r Thu May 12 10:51:55 2016 -0400 @@ -17,9 +17,9 @@ final.numeric[is.na(final.numeric)] = 0 final[,sapply(final, is.numeric)] = final.numeric -final.ca = final[grepl("ca", final$Sample),] -final.cg = final[grepl("cg", final$Sample),] -final.cm = final[grepl("cm", final$Sample),] +final.ca = final[grepl("^ca", final$Sample),] +final.cg = final[grepl("^cg", final$Sample),] +final.cm = final[grepl("^cm", final$Sample),] if(nrow(final.ca) > 0){ final.ca$Replicate = 1
--- a/wrapper.sh Thu May 12 07:35:07 2016 -0400 +++ b/wrapper.sh Thu May 12 10:51:55 2016 -0400 @@ -227,9 +227,9 @@ then echo "---------------- imgt_loader.r ----------------" #python $dir/imgt_loader.py --summ $PWD/summary.txt --aa $PWD/aa.txt --junction $PWD/junction.txt --output $naive_output - Rscript --verbose $dir/imgt_loader.r $PWD/summary.txt $PWD/aa.txt $PWD/junction.txt ${naive_output_ca} 2>&1 + Rscript --verbose $dir/imgt_loader.r $PWD/summary.txt $PWD/aa.txt $PWD/junction.txt $outdir/loader_output.txt 2>&1 echo "---------------- naive_output.r ----------------" - Rscript $dir/naive_output.r $naive_output_ca $outdir/merged.txt $naive_output_ca $naive_output_cg $naive_output_cm 2>&1 + Rscript $dir/naive_output.r $outdir/loader_output.txt $outdir/merged.txt ${naive_output_ca} ${naive_output_cg} ${naive_output_cm} 2>&1 fi echo "---------------- sequence_overview.r ----------------"