Discover and read the best of Twitter Threads about #unix
Most recents (14)
' With the help of the Python #glob #module, we can search for all the path names which are looking for files matching a specific pattern (which is defined by us). The specified pattern for file matching is defined according to the rules dictated by the #Unix shell.
#SQL
#SQL
The result obtained by following these rules for specific pattern file matching is returned in arbitrary order in output of program While using file matching pattern we have to fulfil some requirements of the glob #module because the module can travel through the list of the file
1/ If someone tells you that you can learn computation overnight, it is a lie. What I wish I had known 10 years ago with resource links👇🧵 #rstats #computationalbiology
2/ Spend time learning Linux commands. Fancy tools can become obsolete tomorrow, and Linux skills persist.
I started with this book linuxcommand.org/tlcl.php #unix
I started with this book linuxcommand.org/tlcl.php #unix
3/ Learn a language and learn it well. It does not matter if you pick R or python. If you can use it to solve your practical problems in the lab, that will be good. There is so much data wrangling to do, start with r4ds.had.co.nz #rstats
Καλή χρονιά με υγεία!
Happy new year ppl!
#σημερα εκτός από Πρωτοχρονιά στα κράτη που ακολουθούν το #gregoriancalendar και την #japan είναι η δεύτερη μέρα του #hogmanay στη #scotland, τελευταία μέρα του #kwanzaa για τους Αφροαμερικανούς, ημέρα Σύνταγματος στην #italy,
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Happy new year ppl!
#σημερα εκτός από Πρωτοχρονιά στα κράτη που ακολουθούν το #gregoriancalendar και την #japan είναι η δεύτερη μέρα του #hogmanay στη #scotland, τελευταία μέρα του #kwanzaa για τους Αφροαμερικανούς, ημέρα Σύνταγματος στην #italy,
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ημέρα ίδρυσης της Σλοβακικής Δημοκρατίας στη #slovakia, ημέρα αποκατάστασης της ανεξαρτησίας στην #CzechRepublic, ημέρα απελευθέρωσης των σκλάβων στις #usa και μερικά κράτη της #carribean, ημέρα της σημαίας στη #lithuania, ημέρα ίδρυσης στην #taiwan,
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#παγκοσμιαΗμεραΟικογενοιας, ημέρα ανεξαρτησίας σε #brunei, #cameroon, #Haiti και #sudan, #kamakuraEbisu στην Ιαπωνία και ημέρα θριάμβου της επανάστασης στην #cuba.
#σανσημερα το 45 BCE η υιοθέτηση του Ιουλιανού ημερολογίου στη #rome, προκαλεί την πρώτη Πρωτοχρονιά.
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#σανσημερα το 45 BCE η υιοθέτηση του Ιουλιανού ημερολογίου στη #rome, προκαλεί την πρώτη Πρωτοχρονιά.
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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
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
3/
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
awk -F "\t" '$3 == "transcript" { print $9 }' myensembl.gtf| tr -s ";" " " | cut -d " " -f6,8| sed 's/\"//g' | awk '{print $1"."$2}' > transcripts.txt
paste transcripts.txt genes.txt > tx2genes.txt
1/ Do not give me excel files (which is impossible :)).
8 tools to deal with tsv/csv files on the command line:
visidata.org Data exploration at your fingertips
#unix #data #commandline
8 tools to deal with tsv/csv files on the command line:
visidata.org Data exploration at your fingertips
#unix #data #commandline
2/ csvkit csvkit.readthedocs.io/en/latest/inde…
3/ csvtk bioinf.shenwei.me/csvtk/usage/
Bioinformatics one-line Day 18
1/
delete the blank lines
```
sed /^$/d'
```
delete the last line
```
sed $d
```
sed '1d' to remove the header for all csv files
```
ls *csv | parallel 'cut -f, -d 2 | sed '1d' > {/.}.list'
```
1/
delete the blank lines
```
sed /^$/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
sed -n '2{p;q}'
#unix #oneliner #bioinformatics #sed
That's a wrap!
If you enjoyed this thread:
1. Follow me @tangming2005 for more of these
2. RT the tweet below to share this thread with your audience
If you enjoyed this thread:
1. Follow me @tangming2005 for more of these
2. RT the tweet below to share this thread with your audience
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
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
2/
memory usage: free -mg
open `top -M` with human readable size in Mb, Gb.
install htop htop.dev for better visualization.
#unix #onliner
memory usage: free -mg
open `top -M` with human readable size in Mb, Gb.
install htop htop.dev for better visualization.
#unix #onliner
That's a wrap!
If you enjoyed this thread:
1. Follow me @tangming2005 for more of these
2. RT the tweet below to share this thread with your audience
If you enjoyed this thread:
1. Follow me @tangming2005 for more of these
2. RT the tweet below to share this thread with your audience
#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
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*
*always look at your trash reads to understand why they're trashed*
Open Source Software Favorites:
System Monitoring and Telemetry:
github.com/aksakalli/gtop
gtop is a straightforward and easy to use Visual System monitoring dashboard. #gtop #unix
gtop is a straightforward and easy to use Visual System monitoring dashboard. #gtop #unix
[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. 
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 vim.fandom.com/wiki/Su-write?… back in 2005.
#vim
:w !sudo tee "%"
Learnt it from vim.fandom.com/wiki/Su-write?… back in 2005.
#vim
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}.
#vim
: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}.
#vim
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
: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
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:
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]
royalsocietypublishing.org/doi/10.1098/rs…
[@PLOSBiology]
doi.org/10.1371/journa…
...and this interview she did for @QuantaMagazine:
quantamagazine.org/with-food-webs…
#Ecology #Ecologist
[@royalsociety Proceedings B]
royalsocietypublishing.org/doi/10.1098/rs…
[@PLOSBiology]
doi.org/10.1371/journa…
...and this interview she did for @QuantaMagazine:
quantamagazine.org/with-food-webs…
#Ecology #Ecologist
Next, two papers on how humans navigate and process #information co-authored by SFI External Prof @DaniSBassett (@Penn):
[@NatureHumBehav]
nature.com/articles/s4156…
+ summary:
blog.seas.upenn.edu/studying-hunte…
[@nature]
nature.com/articles/s4156…
+ summary:
penntoday.upenn.edu/news/what-do-b…
[@NatureHumBehav]
nature.com/articles/s4156…
+ summary:
blog.seas.upenn.edu/studying-hunte…
[@nature]
nature.com/articles/s4156…
+ summary:
penntoday.upenn.edu/news/what-do-b…
Few Computer Science Legends you should know about
🧵👇
(They are really inspiring developers)
🧵👇
(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: en.wikipedia.org/wiki/Dennis_Ri…
#UNIX
"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: en.wikipedia.org/wiki/Dennis_Ri…
#UNIX
* 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: en.wikipedia.org/wiki/Linus_Tor…
#Linux #git #android
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: en.wikipedia.org/wiki/Linus_Tor…
#Linux #git #android
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
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
Sıfırdan kodlama ihtiyacınız büyük ihtimalle hiç olmayacak. Ancak ihtiyaç anında doğru yerde doğrusunu seçebilmek için o veri yapısının veya algoritmanın nasıl çalıştığını bilmeniz şart
