Unix Tips and Tricks - Part 1
January 29, 2008
Exercises

Perform the following tasks and answer the questions.
Everything can be done with a Unix command or commands.

Exercises are at
	http://iona.wi.mit.edu/bio/education/hot_topics/unix1/unix_tips_tricks_1_ex.txt
These solutions are at
	http://iona.wi.mit.edu/bio/education/hot_topics/unix1/solutions_1.txt


0 - Open a Unix terminal on your computer

1 - mkdir unix1
    cd unix1

2 - wget http://iona.wi.mit.edu/bio/education/hot_topics/unix1/refSeq_hg18.zip
	
3 - unzip refSeq_hg18.zip
	
4 - head refSeq_hg18.txt
    How many fields wide is it? 6
    wc -l refSeq_hg18.txt
    How many lines long is it? 25990

5 - 
	
6 - cat -A refSeq_hg18.txt | head
    ^I refers to tabs, so it's a tab-delimited file

7 - cut -f2 refSeq_hg18.txt | sort -u | wc -l
    cut -f2 refSeq_hg18.txt | sort | uniq | wc -l
    25031

8 - cut -f1 refSeq_hg18.txt | sort -u | wc -l
    cut -f1 refSeq_hg18.txt | sort | uniq | wc -l
    18593

9 - cut -f2 refSeq_hg18.txt | sort | uniq -d | wc -l
    579 appear more than once, largely because mRNA sequence maps to multiple places in the genome
    cut -f2 refSeq_hg18.txt | sort | uniq -d > mult_transcripts.txt

10- cut -f3 refSeq_hg18.txt | sort -u | wc -l
    42 (Note that there are some random bits of the genome that can't be placed in context.)
	
11- grep chrY refSeq_hg18.txt | cut -f1 > chrY_genes.txt

12- sort -k3,3 -k4,4 -k 5,5n refSeq_hg18.txt > refSeq_hg18_sorted.txt

13- awk -F"\t" '$4 == "+" {print $0}' refSeq_hg18.txt > refSeq_hg18_plus.txt
	awk -F"\t" '$4 == "-" {print $0}' refSeq_hg18.txt > refSeq_hg18_neg.txt
	
14- wc -l refSeq_hg18.txt
    [25990 lines / 4 ==> ~ 6498]
    split -l 6498 -d refSeq_hg18.txt Part_
    mv Part_00 Part_1.txt
    mv Part_01 Part_2.txt
    mv Part_02 Part_3.txt
    mv Part_03 Part_4.txt

15- grep chr19 refSeq_hg18.txt | sort -k6nr | cut -f1 | head -7
    CHMP2A
    MZF1
    TRIM28
    UBE2M
    ZBTB45
	
16- sort -k6nr  refSeq_hg18.txt | head -1
    chr1 is at least 247179967 nt
	
17- grep BMP refSeq_hg18.txt > BMP_etc.txt

18- cut -f1 BMP_etc.txt | sort | uniq -d

19- awk -F"\t" '{print $0 "\t" $6 - $5}' refSeq_hg18.txt | sort -k7nr | head -1
    CNTNAP2 (NM_014141)
    awk -F"\t" '{print $0 "\t" $6 - $5}' refSeq_hg18.txt | sort -k7n | head -1
    KRTAP22-1 (NM_181620)

20- awk -F"\t" '{ print $2 "\t" $3 ":" $5 "-" $6}' refSeq_hg18.txt> refSeq_hg18_coords.txt

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