Mercurial > repos > mingchen0919 > aurora_fastqc_report
changeset 5:b949d2d19a65 draft default tip
get rid of argument replacement procedure
| author | mingchen0919 |
|---|---|
| date | Mon, 26 Feb 2018 23:46:11 -0500 |
| parents | 7918bf4a7bad |
| children | |
| files | fastqc_report.Rmd temp.txt |
| diffstat | 2 files changed, 2 insertions(+), 23 deletions(-) [+] |
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--- a/fastqc_report.Rmd Mon Feb 26 23:34:08 2018 -0500 +++ b/fastqc_report.Rmd Mon Feb 26 23:46:11 2018 -0500 @@ -112,8 +112,8 @@ end_module_lines = grep('END_MODULE', f) end_line = end_module_lines[which(end_module_lines > start_line)[1]] module_data = f[(start_line+1):(end_line-1)] - writeLines(module_data, 'temp.txt') - read.csv('temp.txt', sep = '\t', header = header, comment.char = comment.char) + writeLines(module_data, '/tmp/temp.txt') + read.csv('/tmp/temp.txt', sep = '\t', header = header, comment.char = comment.char) } ```
--- a/temp.txt Mon Feb 26 23:34:08 2018 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,21 +0,0 @@ -#Sequence Count PValue Obs/Exp Max Max Obs/Exp Position -CCGGTAT 20 7.394916E-4 44.530624 1 -TGGGGGG 360 0.0 42.675182 1 -CTCGAGT 40 1.6714475E-5 33.39797 1 -AGGGGGG 45 0.0013009962 24.739237 1 -ATTTCGG 50 0.0024044104 22.260859 10 -CCCCCCC 2485 0.0 21.414124 1 -ATCTACA 55 0.0041787773 20.237143 18 -AGGCAGC 55 0.0041787773 20.237143 10 -TCCAGGA 80 0.0018321791 16.695642 7 -CCCCCCT 1340 0.0 15.117447 3 -CTCCTTT 175 9.111627E-7 13.995339 1 -CCCCCTT 1530 0.0 13.385613 4 -TCAAGTT 135 2.8886713E-4 13.191619 8 -CCCCTTT 1685 0.0 12.154296 5 -GGGGAAA 270 7.1193426E-8 11.547288 29 -CTCCATT 135 0.0043172785 11.544976 1 -CCCTTTT 1795 0.0 11.409464 6 -CCTTTTT 1890 0.0 10.835973 7 -GGGGGAA 275 1.1271768E-6 10.52542 28 -GGGGGGA 300 3.05894E-7 10.390478 27