Advlinux, cheat sheet

Assignment – Ownership and permissions

Q:
Change permission from

----------

to

-rw-rw—wx

One answer:

chmod ug+rw filename  
chmod o+wx filename  

Assignment - Symbolic links - files

Q Did editing the information in the link change the information in the original?
A: Yes.

Q: what happens to a symbolic link when we move whatever its pointing to?
A: it breaks.

Q: is the link re-activated?
A: yes.

Assignments - Grep

command to grep all lines with chr1 and send to other file.

ex:

grep "chr1" sample_1.sam > chr1.txt

Assignment - WC

grep "chr1" sample_1.sam | wc -l
samtools view outbam.bam | grep "CATCATCAT" | wc -l

Extra material 1.

Task1:

grep "^@" sample_1.sam > at.txt

Task2:

grep "[0-9]\{3\}$" sample_1.sam

Extra material 2.

sed 's/chr1/chr2/' sample_1.sam > sample_2.sam

Extra material 3

for f in *.sam; do mv $f ${f/.sam}.bam; done