This repo contains all random things I'm doing, some are usefull some aren't This README also contain several oneliners used time to time
Python object reminder, long time no object in python Python dict-like class that forgets things. I need to rename this... This script is based on https://github.com/gitpan/Tie-Hash-Cannabinol
Python3; automatic generation for some part of roxygen documentation See inside for more details
Python3; convert robotguide waypoints files to URscript Quickly done
Python3; transform GPS Degrees Minutes Seconds locations into Decimal Degrees
Concat files without their 1st line
find . -name "*.txt" | xargs -n 1 tail -n +2 > outfileExtract all columns but the one matching regex
awk 'NR==1{for(i=1;i<=NF;i++)if(!($i~/REGEX_HERE:_[kv][0-9]+$/)){a[i]=1;m=i}}{for(i=1;i<=NF;i++)if(a[i])printf "%s%s",$i,(i==m?RS:FS)}' FILE.tsv |column -tCreate N files of size S
# Create 20 000 files of size = 1MB; change bs to change size
for i in $(seq 1 20000); do touch $i; dd if=/dev/urandom of=$i bs=1024 count=1024 >/dev/null 2>&1; donePython, create a test email server that prints mail in terminal instead of sending them
# Mail is sent to localhost on port 8025 in this example
python -m smtpd -n -c DebuggingServer localhost:8025Extract only even/odd lines from a file
# even
sed -n '0~2p' file.csv > output.csv
# odd
sed -n '1~2p' file.csv > output.csvCount number of reads in fasta/fastq files
# Fasta
grep '>' file.fasta | wc -l
# Fastq
awk '{lines++}END{print lines/4}' file.fastqExtract sequences from a fasta based on a list of IDs
# Change the value in 'cut' to strip unneccessary characters before your id
cut -c 1- FILE_IDs.TXT | xargs -n 1 samtools faidx FILE.FASTAExtract specific regions from a fasta file (using bedtools)
bedtools getfasta -fi file.fasta -bed file.bed -fo output.fasta -name
# See the bed file format here: https://felixfan.github.io/bedtools/Rename a tilda (or xterm compatible terminal programs) tab
NAME="tab name here"
echo -e "\e]2;$NAME\a tab --> [$NAME]"Create multiple screens to run several commands in it
#!/bin/bash
# Run this script with this command: screen -c "./SCRIPT_NAME" && pkill screen
# && pkill screen will just kill all the existing screens once you detach; on macos use pkill SCREEN instead
# split is going to split your window; the -v option is for vertical splitting and only available for screen > 4.01.0
# focus gonna change the focus to the newly created window
# using ;sh as the final bash command will allow you to keep the screen running. Otherwise it will terminate itself once the command is done running
screen -t "YOUR TITLE 1" bash -c "<your bash command>; sh"
split -v
focus
screen -t "YOUR TITLE 2" bash -c "<your bash command>; sh"
split -v
focus
screen -t "YOUR TITLE 3" bash -c "<your bash command>; sh"
split -v
focus
screen -t "YOUR TITLE 4" bash -c "<your bash command>; sh"
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