Discover and read the best of Twitter Threads about #unix

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Bioinformatics one-liner * Day 19
1/ create a tx2gene mapping file from ensemble gtf retaining the version number of genes and transcripts. A thread. #bioinformatics #oneliner #unix
2/ awk -F "\t" '$3 == "transcript" { print $9 }' myensembl.gtf| tr -s ";" " " | cut -d " " -f2,4| sed 's/\"//g' | awk '{print $1"."$2}' > genes.txt
awk -F "\t" '$3 == "transcript" { print $9 }' myensembl.gtf| tr -s ";" " " | cut -d " " -f6,8| sed 's/\"//g' | awk '{print $1"."$2}' > transcripts.txt
paste transcripts.txt genes.txt > tx2genes.txt
Read 4 tweets
1/ Do not give me excel files (which is impossible :)).
8 tools to deal with tsv/csv files on the command line: Data exploration at your fingertips

#unix #data #commandline
Read 9 tweets
Bioinformatics one-line Day 18

delete the blank lines
sed /^$/d'
delete the last line
sed $d
sed '1d' to remove the header for all csv files

ls *csv | parallel 'cut -f, -d 2 | sed '1d' > {/.}.list'
2/ print the second line of a LARGE file and quit:

sed -n '2{p;q}'

#unix #oneliner #bioinformatics #sed
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Read 4 tweets
1/ Bioinformatics one-liner day Day 15
get all the folders' sizes in the current folder: du -h --max-depth=1
the total size of the current directory: du -sh .
display disk space: df -h
memory usage: free -mg
open `top -M` with human readable size in Mb, Gb.
install htop for better visualization.
#unix #onliner
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Read 4 tweets
#bioinformatics tip of the day: FOLLOW THE DATA. Trace a read through its journey. Example is when I look at a fresh @PacBio Iso-Seq run (but really for any sequencing data for any application).

I start w CCS reads, scroll through them to viz the primers and polyA tail. /1
@PacBio 2/ I run lima to strip the cDNA primers, check the summary file to see a good percentage actually has the expected 5'/3' cDNA primers. if a high % failed, look for reasons why - is it user error (wrong primers?), prep error, or biological?
3/ then run `isoseq3 refine` to identify (unintended) concatemers and missing polyA tails. if reads are lost here, it usually indicates serious library prep issues, less about bioinfx.

*always look at your trash reads to understand why they're trashed*
Read 11 tweets
Open Source Software Favorites:
System Monitoring and Telemetry:
gtop is a straightforward and easy to use Visual System monitoring dashboard. #gtop #unix
Read 7 tweets
[THREAD] #Linux a 30 ans aujourd'hui 🥳🐧
Il y a 30 ans, un fringuant jeune homme, Linus Torvalds, ingénieur de son état, envoyait un mail sur un newsgroup qui allait secouer durablement Internet.
L'objet du délit s'appelle #Minix, un proof of concept assez avancé d'un début de système d'exploitation, et surtout, un noyau logiciel pour lequel il explique alors avoir déjà porté l'interpréteur de commandes #Bash et le compilateur #GCC que nous utilisons encore, 30 ans après.
Read 13 tweets
The famous Vim sudo-write trick: You open a file, edit it, and save it only to get the E45 error message. You now realize that only root can edit the file. What do you? Start over? No, instead try this:

:w !sudo tee "%"

Learnt it from… back in 2005.

How does :w !sudo tee "%" work?

:w !{cmd} - Executes {cmd} with all lines in buffer as standard input.

% - Expands to current filename. Quotes around it keep it as a single argument even if the filename contains whitespace.

tee {file} - Copies stdin to stdout and {file}.

For more information on the command :w !sudo tee "%", enter the following commands in Vim:

:help :w_c
:help current-file
:help :_%

Also, enter the following command in shell:

man tee

I hope this was fun!

#vim #unix #linux #shell #programming
Read 3 tweets
On #InternationalWomensDay we'd like to pause and celebrate just a small slice of the enormous contributions to science women have made here at SFI.

Read the thread below for links to some of their own favorite research papers, and a few nominated by other SFI faculty members:
First off, these papers on #FoodWebs led by our VP for #Science, Jennifer Dunne:

[@royalsociety Proceedings B]…


...and this interview she did for @QuantaMagazine:…

#Ecology #Ecologist
Next, two papers on how humans navigate and process #information co-authored by SFI External Prof @DaniSBassett (@Penn):

+ summary:…

+ summary:…
Read 21 tweets
Few Computer Science Legends you should know about


(They are really inspiring developers)
* Dennis Ritchie *

"Father of the 'C' programming language"
Created UNIX operating system with colleague Ken Thompson .
Received Turing Award in 1983.
Modern computing would not have existed without Dennis Ritchie.

Read More:…
* Linus Torvalds *

Created Linux Kernel and Git.
Linux kernel is the kernel for Linux operating systems (distributions) and other operating systems such as Android and Chrome OS.

Read More:…
#Linux #git #android
Read 15 tweets
Bir yazılım geliştiricinin bilmesi gerekenlerle ilgili 15 maddelik flood geliyor.. Mümkün olduğunca fazla keywordü bir araya toplamaya çalıştım.
Hadi Başlıyoruz!

#Developer #Software #Java #code #kod #yazılım #development #computer #bilgisayar #tool #PC #IT #web #tech #data
1-Temel veri yapıları (linkedList, map, tree vb) ve temel algoritmalar (sıralama, arama vb)

Sıfırdan kodlama ihtiyacınız büyük ihtimalle hiç olmayacak. Ancak ihtiyaç anında doğru yerde doğrusunu seçebilmek için o veri yapısının veya algoritmanın nasıl çalıştığını bilmeniz şart
2- Network Temelleri

OSI Modelini ve 7 katmanı; temel protokolleri(#TCP-IP, TCP-UDP, #HTTP, #FTP), güvenlik protokollerini(#HTTPS, #SFTP, #SSL), monitoring protokolleri(#SNMP, ICMP) bilmekte fayda var. Ayrıca ağ ekipmanlarının görevlerini tanımak ve 7Layer yerlerini bilmek lazım
Read 16 tweets

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