linux101
#01 Rename
cat ala.cds.fasta | awk '{ gsub(/alaSesamum_al;/, "ala_"); print }' > ala.cds.formatted.fasta
#02 split a multifasta file in each set with their corresponding header
cat yourfile.fasta | awk '{
if (substr($0, 1, 1)==">") {filename=(substr($0,2) ".fasta")}
print $0 > filename }'
#03 make a tab separated file as in put for PREP suite online tool
cat ind_accD.fasta | awk 'NR==2{print "indicum"}2' | awk 'NR==3{print "accD"}3' | awk 'NR==4{print "1"}4' | awk 'NR==5{print "0.8"}5'| awk '{if (NR!=1) {print}}' | awk -F'\n' '{$1=$1} 1' RS='\n\n' OFS='\t' > accD.rna.ready
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How To Count Files in Directory on Linux | answer |
*ls | wc -l* -
How to gzip a folder? | answewr is here |
tar -zcvf foldername.tar.gz foldername/| | explanation here | You can confirm its contents:tar ztvf foldername.tar.gz -
want to extract a specifc file in a compressed file in linux? do like this for tar and like this for gz file |
unzip -l unzipfilethenunzip unzipfile fullpathtothefile > yourfile -
want to check parent ID and PID for cleaning zombies do
ps -f -u usernamethenkill yourPIDofinterest -
ps usage 1 | 2 | 3 | 4 | 5
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oneliners | The reads that passed the base caller quality filter were then filtered with seqtk v1.3 (seqtk, RRID:SCR_018927) [19] to remove reads <10 kb (seq -A -L 10 000), yielding a final set of 1,050,302 reads with a total size of 38.2 Gb and ∼45× coverage (Supplementary Table S2). | blog point 9
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Linux Command Line Full course: Beginners to Advance. Bash Command Line Tutorials
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7 System Monitoring Tools for Linux to Keep an Eye on Vital System Stats
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CPU and Memory usage record for a multiple algorithm process
Hello everyone.
Here is a bash script for long-reads assembly using CANU.
#!/bin/bash
set -e export
PATH='/home/raymond/devel/canu/canu/Linux-amd64/bin/':$PATH
inputFile=$1
outputDir=$2
name='Epau'
genomeSize=160kb
threads=40
gnuplotPath=/home/raymond/devel/gnuplot/install/bin/gnuplot
echo $inputFile
echo $outputDir
canu \ -p $name \
-d $outputDir \
correctedErrorRate=$correctedErrorRate \ genomesize=$genomeSize \
-nanopore-raw $inputFile\
gnuplot=$gnuplotPath \
useGrid=false \ maxThreads=$threads
I would like to incorporate a command line in order to get CPU and memort usage every 5 mn from the begining to the end of the CANU assembly.
How could I get this info in a specific file as an output since CANU running deals with a bunch of multiple processes?
Thanks.
There are lots of different ways to attack this problem.
System stats are all in files in /proc, so to get memory usage you might parse /proc/meminfo. For CPU utilization /proc/loadavg might be what you want. Here is a link to some documentation. You could write a bash script to get these values and write to a file.
You could also add in a middle man and use the psutil package for Python and just use that
There are probably lots of other ways to do this as well
f its running as a systems process, firefox for example, use
top| grep firefox --line-buffered > outfile.txt I couldn't figure out how to get my cut to work in-line though, it seems the delimiters are scrambled after field 2.
answer depends on OS and environment to some extent-- is this a machine with few other users or a dedicated VM, or a shared host, and what's the OS/distribution you're running?
quick and dirty would be to run top in batch mode if that's available. Reports of the host's memory usage are available via free and vmstat -- those are useful to see if your process is eating all available memory and then failing. Unlikely with such a small genome.
Thank you for your reply. I am working on Centos 7 OS.
Probably easiest is calling top -b -n 99 -s 13 or something similar with parameters appropriate to your work.
If you are hoping for a machine-readable log and a way to summariza a proces tree by a piece of code, then more work will be necessary, but this will give you output good for human eyes to understand what's happening.
A4