#How to write a bash for loop
#Written by E Heppenheimer, Fall 2017 

#For loops are awesome and can save you a lot of time! 
#the basic idea is that you would like to repeat the same set of commands on many files 

#the general syntax is: 
for BLANK in FILES do SOMECOMMAND done 

#walking through the simplest example: 

#first specify the files of interest 

#you can do this by listing all the file names
$ files="sample1
sample2
sample3" 
#but that becomes really inefficient for more than a handful of files 

#it is usually easier to use a wildcard character (*) 
#for example, if all the file names start with "sample": 
$ files=sample*

#or if all the files end with ".txt" 
$ files= *.txt 

#and so on... 

#once you have your files specified, open the loop:

$ for f in $files 
#note the "f" could be any letter, "i" and "j" are also popular choices 
do


#then specify the set of commands. Here is a simple cat command, but it could be anything 

cat $f > outputfile.txt 

#then you close the loop with the word "done" 
done 

#Now some more complicated things: 

#Extracting the file name prefix: 
#this is possibly the hardest part of for loops 
#in short, you want to generate one output file for every input file, and keep the same prefix of the file name 

#This can be done with awk
#assuming everything before the first period is the prefix (e.g. Important_Data_File_1.txt, prefix would be "Important_Data_File_1")
pre=$(echo $f |awk -F'.' '{print $1 }')

#you may also want to specify a suffix for the output file 
#for example, if your output is a sorted text file: 
suf="_sorted.txt" 

#putting this all together 
#this is a for loop to sort a set of files
#maintains the original file prefix 
#suffix indicates the file is sorted

files=*.txt
for f in $files 
do 
pre=$(echo $f |awk -F'.' '{print $1 }')
suf="_sorted.txt" 
sort -n $f > $pre$suf
done