1-BasicStructures.txt

screen #Get into a screen
ctrl+A D #Detach from the screen
screen -ls #See the ids of the screens you have
screen -r <ID> #reattach to that screen
exit #kill the screen


#ALIASES
alias ll='ls -la'

#LOOPS
while read line
do
cmmnds
cmmnds
cmmnds
done < inputFile.txt > outputFile.txt

#TEXT EDITOR
nano test.sh
for i in `seq ${1} ${2}`
do
cmmnd > tempFile
cmmnd >> tempFile
cmmnd
done > outputFile.txt

#So, if I want to append an empty line at the end of a file called "Lyrics_[1-100].txt", how do I do it?

#Sum a column with awk
cat count.txt | awk '{sum+=$1} END {print sum}'

#Lovely sed
sed 's/,//g'

#To replace all occurrences in all the files with sed in a single line
sed -i 's/old/new/g' *filesufix   #Can you start seeing the beauty of this? there are million ways to do the exact same thing

#Remove the line with a match and the line right after that one with the match
sed '/WorkToSearch/,+1 d' file

#Delete any empty line
sed '/^$/d' file 

#Get the length of a seq in a perl one-liner
pep=`echo $a | perl -nle 'print length' `


#Read from 2 files! or more!!
while read -r a && read -r b <&3 
do
echo -e "$a\n$b";
done < file1 3<file2

while read -r a && read -r b <&3 && read -r c <&4 && read -r d <&5
do
echo -e "$a\n$b\n$c\n$d";
done < PS1.txt 3<PS2.txt 4<PS3.txt 5<PS4.txt


#Have more than one field separator
awk -F"[,=]" '{print $6}' file

#Print the last field with separator ";"
awk -F";" '{print $NF}' 16S.txt 

# And for seqs of letters
for i in $(echo {a..z});do echo $i; done

## Truncating names and more  #<<<<---- VERY useful
${#file} => length of the path/number of letters (with dots and any symbol)
${file%.*} => truncate right of the last dot
${file%%.*} => truncate right of the first dot
${file#*.} => truncate left of the first dot
${file##*.} => truncate left of the last dot 


# Pass a shell variable to awk
awk --assign=var=${line} '{sum+=$1} END {print var"\n"sum}'


##########Exercise:  

#I have a sequence file that looks like this in the header
>cc786992bf3d628b862dfc7e18f86b531c4ef6bf;barcodelabel=Bl1ITS
AACGCACATTGCGCCCCTTGGTATTCCATGGGGCATGCCTGTTCGAGCGTCATTTGTACCTTCAAGCTCTGCTTGGTGTT
GGGTGTTTGTCTCGCCTCTGCGTGTAGACTCGCCTTAAAACAATTGGCAGCCGGCGTATTGATTTCGGAGCGCAGTACAT
CTCGCGCTTTGCACTCACAACGACGACGTCCAAAAGTACATTTTTACACTCTTGACCTCGGATCAGGTAGGGATACCCGC
TGAACTTAA
>cc786992bf3d628b862dfc7e18f86b531c4ef6bf;barcodelabel=Bl1ITS
AACGCACATTGCGCCCCTTGGTATTCCATGGGGCATGCCTGTTCGAGCGTCATTTGTACCTTCAAGCTCTGCTTGGTGTT
GGGTGTTTGTCTCGCCTCTGCGTGTAGACTCGCCTTAAAACAATTGGCAGCCGGCGTATTGATTTCGGAGCGCAGTACAT
CTCGCGCTTTGCACTCACAACGACGACGTCCAAAAGTACATTTTTACACTCTTGACCTCGGATCAGGTAGGGATACCCGC
TGAACTTAA

But I need the header to read so that it only includes the information after the = sign
>Bl1ITS
sequencehere
>Bl1ITS
sequencehere

Is there a sed command to get rid of all of the junk that comes before the = sign above? 





####### If you want to get fancy
# functions in shell
Map(){
local refGenome=$1
local file=$2
cmmnd Using $refGenome ran with $file
}



########################## R

#Use R in a one liner
cut -f 3 all.blast | Rscript -e 'data=scan(file="stdin"); pdf("hist.pdf"); hist(data)' 

##R oneliner
cat datafile | Rscript -e 'print(summary(scan("stdin")))'

#To pass arguments to R
args<- commandArgs(trailingOnly = TRUE)

#With R write/append to an existing file
write(line, file="myfile", append=TRUE)

#Cat with R
cat("line to add", file=FileName, append=TRUE, sep = "\n")


#Input from pipe to Rscript
nano index.R  
#! /usr/bin/env Rscript
d<-scan("stdin", quiet=TRUE)
cat(max(d)/sum(d))

#nano getIndex.sh
for file in `ls *genesHits_L5.txt`
do
awk '{print $1}' $file | ./index.R
echo 
done > ConsistencyIndexes.txt

# PDFs in R
pdf("FileName.pdf")
plot(density(log(as.numeric(RATIOS_nuc[,3]))))
dev.off()

#Loops in R
for(i in 1:14){
cmmnds
}