Basic bash commands.
Use them to practice with the example file. Even when the example file seems to contain useless information, the commands will help you during the course to extract and format information from sequence files, even if they contain millions of lines.

XXXXXXXXXXXXX
aaaaa	xxxxx
xxxxx	bbbbb
ccccc	xxxxx
xxxxx	ddddd
eeeee	xxxxx
aaaaa	bbbbb
ddddd	fffff
axaxa	bxbxb
XXXXXXXXXXXXX


Play with the following commands. If necessary, make changes to find out what they are doing.
Remember to call the file only in the first command given:
cat ejemplo.txt | grep "xxxxx"

0) Reading files + counting lines
	cat ejemplo.txt
	less ejemplo.txt (press q to exit)
	head -n3 ejemplo.txt
	tail -n2 ejemplo.txt
	
	cat ejemplo.txt | wc -l
	cat ejemplo.txt | uniq
	cat ejemplo.txt | sort | uniq
	cat ejemplo.txt | sort | uniq -c

1) grep
	grep "xxxxx"
	grep "xxxxx" | wc -l
	grep -v "x"
	grep -i "x"
	grep -o "aaaaa"
	grep -a2 "c"
	grep -A2 "c"
	grep -B2 "c"
	grep -E "aaaaa|ccccc"
	
	-> What would you write to find lines that contain both "a" and "b"?

2) Understanding regular expressions.
	grep "^x"
	grep "x$"
	grep "aaaaa..." #How many characters are highlighted?#
	grep "a*"
	grep "a.*"
	grep "a[^a]"
	grep "a[ax]"

	Regular expressions can be combined with the previous options, particularly with -o to extract characters after a pattern.
	-> Try extracting only the first 3 characters of lines that start with "a"

3) sed
	sed s/x/i/
	sed s/x/i/g
	sed s/axaxa/kkkkk/

	Combine with regular expressions.
	-> Try converting the first 3 characters into "iii"
	
	sed + special characters (An special character might be )
	sed s/\t//
	sed -e 's/\t//'

4) cut
	cut -f2
	-> Extract the first column of lines that contain "d"

5) Save/overwrite output (ACHTUNG: do not give same name as input file)
	cut -f2 ejemplo.txt > copy_ejemplo.txt

	To save without overwriting (lines get added to file):
	grep "X" ejemplo.txt >> copy_ejemplo.txt

6) both files vs for-loop
	grep "xxxxx" ejemplo.txt | wc -l
	grep "xxxxx" copy_ejemplo.txt | wc -l
	cat *plo.txt | wc -l

	for i in *plo.txt; do echo $i; done
	for i in *plo.txt; do cat $i | wc -l; done

7) translate
	cat ejemplo.txt | tr -d '\n'