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$ cat < nums.tab
11.284424023341844 13.29881132278286
15.210930332045214 7.093399689668905
11.997572060631573 7.779530907059893
9.452057374370979 10.911760763046015
8.88551276533381 9.155650726802886

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$ sort -n nums.tab
8.88551276533381 9.155650726802886
9.452057374370979 10.911760763046015
11.284424023341844 13.29881132278286
11.997572060631573 7.779530907059893
15.210930332045214 7.093399689668905
$ sort -n nums.tab | cat -n
1 8.88551276533381 9.155650726802886
2 9.452057374370979 10.911760763046015
3 11.284424023341844 13.29881132278286
4 11.997572060631573 7.779530907059893
5 15.210930332045214 7.093399689668905
$ sort -n nums.tab | cat -n | head -n2
1 8.88551276533381 9.155650726802886
2 9.452057374370979 10.911760763046015

8. • sort
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• cut
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• less file
$ sort nums.tab | less
$ cut -f2 nums.tab

9. wc [options] file ...
• tr
grep
$ sort nums.tab | less
$ wc nums.tab
5 10 183 nums.tab
$ wc -l nums.tab
5 nums.tab

10. re
grep [options] regular_expression file ...
regular_expression
$ cat nums.tab
11.284424023341844 13.29881132278286
15.210930332045214 7.093399689668905
11.997572060631573 7.779530907059893
9.452057374370979 10.911760763046015
8.88551276533381 9.155650726802886
$ grep “12” nums.tab
8.88551276533381 9.155650726802886
$ grep -v “12” nums.tab
11.284424023341844 13.29881132278286
15.210930332045214 7.093399689668905
11.997572060631573 7.779530907059893
9.452057374370979 10.911760763046015

11. $ cat nums.tab
11.284424023341844 13.29881132278286
15.210930332045214 7.093399689668905
11.997572060631573 7.779530907059893
9.452057374370979 10.911760763046015
8.88551276533381 9.155650726802886
$ grep “^8” nums.tab
8.88551276533381 9.155650726802886
$ grep “86$” nums.tab
11.284424023341844 13.29881132278286
8.88551276533381 9.155650726802886
$ grep “5$” nums.tab | wc -l
2
$ cut -f2 nums.tab | grep “^7”
7.093399689668905
7.779530907059893

12. tr [options] string1 string2
sed
$ cat nums.tab
11.284424023341844 13.29881132278286
15.210930332045214 7.093399689668905
11.997572060631573 7.779530907059893
9.452057374370979 10.911760763046015
8.88551276533381 9.155650726802886
$ tr . - < nums.tab
11-284424023341844 13-29881132278286
15-210930332045214 7-093399689668905
11-997572060631573 7-779530907059893
9-452057374370979 10-911760763046015
8-88551276533381 9-155650726802886
$ tr . - < nums.tab $ cat nums.tab | tr . -

13. $ tr 123 abc < nums.tab
aa.b844b40bcc4a844 ac.b988aacbb78b86
a5.ba09c0ccb045ba4 7.09cc99689668905
aa.99757b0606ca57c 7.7795c090705989c
9.45b057c74c70979 a0.9aa76076c0460a5
8.8855ab765ccc8a 9.a556507b680b886
$ tr ‘t’ , < nums.tab
11.284424023341844,13.29881132278286
15.210930332045214,7.093399689668905
11.997572060631573,7.779530907059893
9.452057374370979,10.911760763046015
8.88551276533381,9.155650726802886
$ tr -d . < nums.tab
11284424023341844 1329881132278286
15210930332045214 7093399689668905
11997572060631573 7779530907059893
9452057374370979 10911760763046015
888551276533381 9155650726802886
$ tr 123 abc < nums.tab | tr “[:lower:]” “[:upper:]”
AA.B844B40BCC4A844 AC.B988AACBB78B86
A5.BA09C0CCB045BA4 7.09CC99689668905
AA.99757B0606CA57C 7.7795C090705989C
9.45B057C74C70979 A0.9AA76076C0460A5
8.8855AB765CCC8A 9.A556507B680B886

14. •
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$ sort noexist.txt > stdout.txt
sort: noexist.txt: No such file or directory

15. $ sort noexist.txt > stdout.txt 2> error.log
$ sort noexist.txt > all.txt 2>&1
$ sort noexist.txt 2>&1 | less
$ sort noexist.txt 2>&1 > stdout.txt | cat -n

16. •
jsmbp:~/work/blast sesejun$ ./blast-2.2.16/bin/blastall -p blastn -d
yeast.nt -i myseq.fasta -o myseq.out
jsmbp:~/work/blast sesejun$ ./blast-2.2.16/bin/blastall -p blastn -d
yeast.nt -i myseq.fasta > myseq.out

18. •
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19. cp *.txt dir/
cp a.txt b.txt c.txt dir/
$ cp a* dir/
$ mv b*.txt dir/

20. $ cp {a,b,c}.txt dir/

21. •
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#!/bin/bash
~/work/blast/blast-2.2.16/bin/blastall -p blastn -d yeast.nt -i
myseq.fasta
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22. #!/bin/bash
~/work/blast/blast-2.2.16/bin/blastall -p blastn -d yeast.nt -i
myseq1.fasta
~/work/blast/blast-2.2.16/bin/blastall -p blastn -d yeast.nt -i
myseq2.fasta
~/work/blast/blast-2.2.16/bin/blastall -p blastn -d yeast.nt -i
myseq3.fasta
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23. #!/bin/bash
for i in {1,2,3}.fasta;do
echo $i
~/work/blast/blast-2.2.16/bin/blastall -p blastn -d ../yeast.nt
-i ”$i” > ”$i”.result
done

24. #!/bin/bash
for i in *.fasta;do
echo $i
~/work/blast/blast-2.2.16/bin/blastall -p blastn -d ../yeast.nt
-i ”$i” > ”$i”.result
done

25. a.
b.
c.
d.
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jsmbp:~ sesejun$ cd work/blast
jsmbp:~/work/blast sesejun$ ./blast-2.2.16/bin/blastall -p blastn -d
yeast.nt -i myseq.fasta -o myseq1.out
jsmbp:~/work/blast sesejun$ ./blast-2.2.16/bin/blastall -p blastn -d
yeast.nt -i myseq.fasta > myseq2.out

26. •
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• mv ~/Desktop/bayanus.tar .
• mv ~/Desktop/bayanus.tar ~/work/blast
• tar xvf bayanus.tar
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• mv ~/Desktop/bayanum.tar .; tar zxvf
bayanus.tar.gz
•

27. $ mkdir tmp
$ cp bayanus/{1,3,7,9}.fasta tmp/ <-
$ ls tmp/ <- 1.fasta, 3.fasta,...
$ ls yeast*
$ ls <- 2 ls
$ cd bayanus

28. •$ bash blast.sh
#!/bin/bash
~/work/blast/blast-2.2.16/bin/blastall -p blastn -d yeast.nt -i
myseq.fasta

29. •
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#!/bin/bash
for i in *.fasta;do
echo $i
~/work/blast/blast-2.2.16/bin/blastall -p blastn -d ../yeast.nt
-i ”$i” > ”$i”.result
done
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