| function check_bam { | |
| samtools quickcheck ${1} | |
| if [ $? -ne "0" ]; then | |
| echo ${1} | |
| fi | |
| } | |
| export -f check_bam | |
| parallel check_bam ::: *.bam |
| import | |
| zlib, streams | |
| type | |
| GZipStream* = object of StreamObj | |
| f: GzFile | |
| GzipStreamRef* = ref GZipStream | |
| proc fsClose(s: Stream) = |
| ag -w -o '[A-Za-z0-9\-\_\.]+\/[0-9]+[A-Za-z0-9\-\_\.]+' *.R | sort | uniq | tr ':' '\t' > software.txt | |
| cat software.txt | cut -f 3 | sort | uniq > software.uniq.txt |
| while read f; do | |
| if [[ ! -f "${f}" && ! -d "${f}" ]]; then | |
| echo "$f not found" | |
| fi | |
| done <file_paths.txt |
| # Replace /camp or /lab with volume names | |
| ag -o -w "(/camp)[^\"\t '()$]+" | |
| # Also works with rip grep | |
| rg -w "(/camp)[^\"\t '()$]+" |
| import sugar | |
| import argparse | |
| import colorize | |
| import strformat | |
| import strutils | |
| import tables | |
| proc print_error*(msg: string) = | |
| stderr.write_line "Error".bgWhite.fgRed & fmt": {msg}".fgRed | |
| export PS1='\[\e[0;35m\][\t] 🍔 \[\e[m\] ' |
A super short introduction how to call Nim code from R using the .C
interface.
I’m not an R user normally, so I googled and used this post as a
reference:
https://www.r-bloggers.com/three-ways-to-call-cc-from-r/
Let’s define a simple procedure, which we want Nim to do:
| align = design.combine([8,12,16]) // Cores | |
| .combine([12,32,64]) // Memory (GB) | |
| .combine([1,2,3,7,8,9]) // Method | |
| process alignment { | |
| /* | |
| Alignment as performed identically to the old method | |
| */ |
| function samtools_md5() { | |
| md5=`samtools view ${1} | tr '\t' '\n' | sort | md5sum` | |
| echo -e "${md5}\t${1}" | |
| } | |
| export -f samtools_md5 | |
| parallel --verbose -j 10 samtools_md5 {} ::: `ls *.bam` > hashes.txt | |
