Workshop in Computational Bioskills - Spring 2008
Lesson 1 - Unix Shell Programming
Part I - The basics of text manipulation in
UNIX
Part II - Primitive motif search - E.Coli
sigma70 sites
Part III - Visualization of E.Coli genes'
length
<201|0>bioskill:~> cal
February 2005
Su Mo Tu We Th Fr Sa
1 2 3 4 5
6 7 8 9 10 11 12
13 14 15 16 17 18 19
20 21 22 23 24 25 26
27 28
<202|0>bioskill:~> cal 2005
2005
January February March
Su Mo Tu We Th Fr Sa Su Mo Tu We Th Fr Sa Su Mo Tu We Th Fr Sa
1 1 2 3 4 5 1 2 3 4 5
2 3 4 5 6 7 8 6 7 8 9 10 11 12 6 7 8 9 10 11 12
9 10 11 12 13 14 15 13 14 15 16 17 18 19 13 14 15 16 17 18 19
16 17 18 19 20 21 22 20 21 22 23 24 25 26 20 21 22 23 24 25 26
23 24 25 26 27 28 29 27 28 27 28 29 30 31
30 31
April May June
Su Mo Tu We Th Fr Sa Su Mo Tu We Th Fr Sa Su Mo Tu We Th Fr Sa
1 2 1 2 3 4 5 6 7 1 2 3 4
3 4 5 6 7 8 9 8 9 10 11 12 13 14 5 6 7 8 9 10 11
10 11 12 13 14 15 16 15 16 17 18 19 20 21 12 13 14 15 16 17 18
17 18 19 20 21 22 23 22 23 24 25 26 27 28 19 20 21 22 23 24 25
24 25 26 27 28 29 30 29 30 31 26 27 28 29 30
July August September
Su Mo Tu We Th Fr Sa Su Mo Tu We Th Fr Sa Su Mo Tu We Th Fr Sa
1 2 1 2 3 4 5 6 1 2 3
3 4 5 6 7 8 9 7 8 9 10 11 12 13 4 5 6 7 8 9 10
10 11 12 13 14 15 16 14 15 16 17 18 19 20 11 12 13 14 15 16 17
17 18 19 20 21 22 23 21 22 23 24 25 26 27 18 19 20 21 22 23 24
24 25 26 27 28 29 30 28 29 30 31 25 26 27 28 29 30
31
October November December
Su Mo Tu We Th Fr Sa Su Mo Tu We Th Fr Sa Su Mo Tu We Th Fr Sa
1 1 2 3 4 5 1 2 3
2 3 4 5 6 7 8 6 7 8 9 10 11 12 4 5 6 7 8 9 10
9 10 11 12 13 14 15 13 14 15 16 17 18 19 11 12 13 14 15 16 17
16 17 18 19 20 21 22 20 21 22 23 24 25 26 18 19 20 21 22 23 24
23 24 25 26 27 28 29 27 28 29 30 25 26 27 28 29 30 31
30 31
<204|0>bioskill:~> cal 2005 | cat -n
1 2005
2
3 January February March
4 Su Mo Tu We Th Fr Sa Su Mo Tu We Th Fr Sa Su Mo Tu We Th Fr Sa
5 1 1 2 3 4 5 1 2 3 4 5
6 2 3 4 5 6 7 8 6 7 8 9 10 11 12 6 7 8 9 10 11 12
7 9 10 11 12 13 14 15 13 14 15 16 17 18 19 13 14 15 16 17 18 19
8 16 17 18 19 20 21 22 20 21 22 23 24 25 26 20 21 22 23 24 25 26
9 23 24 25 26 27 28 29 27 28 27 28 29 30 31
10 30 31
11 April May June
12 Su Mo Tu We Th Fr Sa Su Mo Tu We Th Fr Sa Su Mo Tu We Th Fr Sa
13 1 2 1 2 3 4 5 6 7 1 2 3 4
14 3 4 5 6 7 8 9 8 9 10 11 12 13 14 5 6 7 8 9 10 11
15 10 11 12 13 14 15 16 15 16 17 18 19 20 21 12 13 14 15 16 17 18
16 17 18 19 20 21 22 23 22 23 24 25 26 27 28 19 20 21 22 23 24 25
17 24 25 26 27 28 29 30 29 30 31 26 27 28 29 30
18
19 July August September
20 Su Mo Tu We Th Fr Sa Su Mo Tu We Th Fr Sa Su Mo Tu We Th Fr Sa
21 1 2 1 2 3 4 5 6 1 2 3
22 3 4 5 6 7 8 9 7 8 9 10 11 12 13 4 5 6 7 8 9 10
23 10 11 12 13 14 15 16 14 15 16 17 18 19 20 11 12 13 14 15 16 17
24 17 18 19 20 21 22 23 21 22 23 24 25 26 27 18 19 20 21 22 23 24
25 24 25 26 27 28 29 30 28 29 30 31 25 26 27 28 29 30
26 31
27 October November December
28 Su Mo Tu We Th Fr Sa Su Mo Tu We Th Fr Sa Su Mo Tu We Th Fr Sa
29 1 1 2 3 4 5 1 2 3
30 2 3 4 5 6 7 8 6 7 8 9 10 11 12 4 5 6 7 8 9 10
31 9 10 11 12 13 14 15 13 14 15 16 17 18 19 11 12 13 14 15 16 17
32 16 17 18 19 20 21 22 20 21 22 23 24 25 26 18 19 20 21 22 23 24
33 23 24 25 26 27 28 29 27 28 29 30 25 26 27 28 29 30 31
34 30 31
<205|0>bioskill:~> cal 2005 | head -10
2005
January February March
Su Mo Tu We Th Fr Sa Su Mo Tu We Th Fr Sa Su Mo Tu We Th Fr Sa
1 1 2 3 4 5 1 2 3 4 5
2 3 4 5 6 7 8 6 7 8 9 10 11 12 6 7 8 9 10 11 12
9 10 11 12 13 14 15 13 14 15 16 17 18 19 13 14 15 16 17 18 19
16 17 18 19 20 21 22 20 21 22 23 24 25 26 20 21 22 23 24 25 26
23 24 25 26 27 28 29 27 28 27 28 29 30 31
30 31
<206|0>bioskill:~> cal 2005 | cat -n | head -10
1 2005
2
3 January February March
4 Su Mo Tu We Th Fr Sa Su Mo Tu We Th Fr Sa Su Mo Tu We Th Fr Sa
5 1 1 2 3 4 5 1 2 3 4 5
6 2 3 4 5 6 7 8 6 7 8 9 10 11 12 6 7 8 9 10 11 12
7 9 10 11 12 13 14 15 13 14 15 16 17 18 19 13 14 15 16 17 18 19
8 16 17 18 19 20 21 22 20 21 22 23 24 25 26 20 21 22 23 24 25 26
9 23 24 25 26 27 28 29 27 28 27 28 29 30 31
10 30 31
<207|0>bioskill:~> cal 2005 | cat -n | tail -10
25 24 25 26 27 28 29 30 28 29 30 31 25 26 27 28 29 30
26 31
27 October November December
28 Su Mo Tu We Th Fr Sa Su Mo Tu We Th Fr Sa Su Mo Tu We Th Fr Sa
29 1 1 2 3 4 5 1 2 3
30 2 3 4 5 6 7 8 6 7 8 9 10 11 12 4 5 6 7 8 9 10
31 9 10 11 12 13 14 15 13 14 15 16 17 18 19 11 12 13 14 15 16 17
32 16 17 18 19 20 21 22 20 21 22 23 24 25 26 18 19 20 21 22 23 24
33 23 24 25 26 27 28 29 27 28 29 30 25 26 27 28 29 30 31
34 30 31
<208|0>bioskill
:~> cal 2005 | cat -n | tail -n +20
20 Su Mo Tu We Th Fr Sa Su Mo Tu We Th Fr Sa Su Mo Tu We Th Fr Sa
21 1 2 1 2 3 4 5 6 1 2 3
22 3 4 5 6 7 8 9 7 8 9 10 11 12 13 4 5 6 7 8 9 10
23 10 11 12 13 14 15 16 14 15 16 17 18 19 20 11 12 13 14 15 16 17
24 17 18 19 20 21 22 23 21 22 23 24 25 26 27 18 19 20 21 22 23 24
25 24 25 26 27 28 29 30 28 29 30 31 25 26 27 28 29 30
26 31
27 October November December
28 Su Mo Tu We Th Fr Sa Su Mo Tu We Th Fr Sa Su Mo Tu We Th Fr Sa
29 1 1 2 3 4 5 1 2 3
30 2 3 4 5 6 7 8 6 7 8 9 10 11 12 4 5 6 7 8 9 10
31 9 10 11 12 13 14 15 13 14 15 16 17 18 19 11 12 13 14 15 16 17
32 16 17 18 19 20 21 22 20 21 22 23 24 25 26 18 19 20 21 22 23 24
33 23 24 25 26 27 28 29 27 28 29 30 25 26 27 28 29 30 31
34 30 31
<203|0>bioskill:~> man grep !?! What is the meaning of the flags -i,-v,-A,-B in the grep command?<203|0>bioskill:~> cal 2005 | grep 30 23 24 25 26 27 28 29 27 28 27 28 29 30 31 30 31 24 25 26 27 28 29 30 29 30 31 26 27 28 29 30 24 25 26 27 28 29 30 28 29 30 31 25 26 27 28 29 30 23 24 25 26 27 28 29 27 28 29 30 25 26 27 28 29 30 31 30 31<209|0>bioskill:~> cal 2005 | tr 'A-Z' 'a-z' 2005 january february march su mo tu we th fr sa su mo tu we th fr sa su mo tu we th fr sa 1 1 2 3 4 5 1 2 3 4 5 2 3 4 5 6 7 8 6 7 8 9 10 11 12 6 7 8 9 10 11 12 9 10 11 12 13 14 15 13 14 15 16 17 18 19 13 14 15 16 17 18 19 16 17 18 19 20 21 22 20 21 22 23 24 25 26 20 21 22 23 24 25 26 23 24 25 26 27 28 29 27 28 27 28 29 30 31 30 31 april may june su mo tu we th fr sa su mo tu we th fr sa su mo tu we th fr sa 1 2 1 2 3 4 5 6 7 1 2 3 4 3 4 5 6 7 8 9 8 9 10 11 12 13 14 5 6 7 8 9 10 11 10 11 12 13 14 15 16 15 16 17 18 19 20 21 12 13 14 15 16 17 18 17 18 19 20 21 22 23 22 23 24 25 26 27 28 19 20 21 22 23 24 25 24 25 26 27 28 29 30 29 30 31 26 27 28 29 30 july august september su mo tu we th fr sa su mo tu we th fr sa su mo tu we th fr sa 1 2 1 2 3 4 5 6 1 2 3 3 4 5 6 7 8 9 7 8 9 10 11 12 13 4 5 6 7 8 9 10 10 11 12 13 14 15 16 14 15 16 17 18 19 20 11 12 13 14 15 16 17 17 18 19 20 21 22 23 21 22 23 24 25 26 27 18 19 20 21 22 23 24 24 25 26 27 28 29 30 28 29 30 31 25 26 27 28 29 30 31 october november december su mo tu we th fr sa su mo tu we th fr sa su mo tu we th fr sa 1 1 2 3 4 5 1 2 3 2 3 4 5 6 7 8 6 7 8 9 10 11 12 4 5 6 7 8 9 10 9 10 11 12 13 14 15 13 14 15 16 17 18 19 11 12 13 14 15 16 17 16 17 18 19 20 21 22 20 21 22 23 24 25 26 18 19 20 21 22 23 24 23 24 25 26 27 28 29 27 28 29 30 25 26 27 28 29 30 31 30 31<210|0>bioskill:~> cal | sed 's/february/bioskill/' February 2005 Su Mo Tu We Th Fr Sa 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28<211|0>bioskill:~> cal | sed 's/february/bioskill/i' bioskill 2005 Su Mo Tu We Th Fr Sa 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28!?! What is the flag -g in the sed command?<212|0>bioskill:~> cal | fold -w 7 Febr uary 20 05 Su Mo T u We Th Fr Sa 1 2 3 4 5 6 7 8 9 10 11 12 13 14 1 5 16 17 18 19 20 21 2 2 23 24 25 26 27 28!?! Instead of using cat for viewing a file, try more or less (Look at the MAN pages)Part II - Primitive motif search - E.Coli sigma70 sites
<201|0>bioskill:~> cd Data/EColi/Promoters/
<202|0>bioskill:Promoters> cat50-TSS.tfa | head -10
>ORF83.1 GCATAAAAAACTCTGCTGGCATTCACAAATGCGCAGGGGTAAAACGTTTC >ORF83.2 AATGCGCAGGGGTAAAACGTTTCCTGTAGCACCGTGAGTTATACTTTGTA >accA TATGCTCGCGGGCTTGCTATCTCGCTGACGGACAGGCAAATTGATGACCA >accB TTACATGTTAGCTGTTGATTATCTTCCCTGATAAGACCAGTATTTAGCTG >accD TCGACCACTTTTTTATCCAAAGTTTCGGGCTGTTATGTTTTAATGTGCAA!?! Do you know what is the Fasta format ?<203|141>bioskill:Promoters> cat 50-TSS.tfa | FASTA2line.pl | head -10
>ORF83.1 GCATAAAAAACTCTGCTGGCATTCACAAATGCGCAGGGGTAAAACGTTTC >ORF83.2 AATGCGCAGGGGTAAAACGTTTCCTGTAGCACCGTGAGTTATACTTTGTA >accA TATGCTCGCGGGCTTGCTATCTCGCTGACGGACAGGCAAATTGATGACCA >accB TTACATGTTAGCTGTTGATTATCTTCCCTGATAAGACCAGTATTTAGCTG >accD TCGACCACTTTTTTATCCAAAGTTTCGGGCTGTTATGTTTTAATGTGCAA >aceBAK TAAAATGGAAATTGTTTTTGATTTTGCATTTTAAATGAGTAGTCTTAGTT >aceE ACTAAACGTAGAACCTGTCTTATTGAGCTTTCCGGCGAGAGTTCAATGGG >acnAP1 CGTTATTCCAGACGACTGGCAACTAACATCGCAGCAGCAAGCCTTTATAG >acnAP2 ATTTGGGTTGTTATCAAATCGTTACGCGATGTTTGTGTTATCTTTAATAT >acnB TTTTTTGTAAACAGATTAACACCTCGTCAAAATCCTGCTATTCTGCCCGT<204|141>bioskill:Promoters> cat 50-TSS.tfa | FASTA2line.pl | grep -v ORF | head -10
>accA TATGCTCGCGGGCTTGCTATCTCGCTGACGGACAGGCAAATTGATGACCA >accB TTACATGTTAGCTGTTGATTATCTTCCCTGATAAGACCAGTATTTAGCTG >accD TCGACCACTTTTTTATCCAAAGTTTCGGGCTGTTATGTTTTAATGTGCAA >aceBAK TAAAATGGAAATTGTTTTTGATTTTGCATTTTAAATGAGTAGTCTTAGTT >aceE ACTAAACGTAGAACCTGTCTTATTGAGCTTTCCGGCGAGAGTTCAATGGG >acnAP1 CGTTATTCCAGACGACTGGCAACTAACATCGCAGCAGCAAGCCTTTATAG >acnAP2 ATTTGGGTTGTTATCAAATCGTTACGCGATGTTTGTGTTATCTTTAATAT >acnB TTTTTTGTAAACAGATTAACACCTCGTCAAAATCCTGCTATTCTGCCCGT >ada GCGCAAGATTGTTGGTTTTTGCGTGATGGTGACCGGGCAGCCTAAAGGCT >adhE GTTGTGCAAAACATGCTAATGTAGCCACCAAATCATACTACAATTTATTA<205|141>bioskill:Promoters> cat 50-TSS.tfa | FASTA2line.pl | grep -v ORF | FASTAfromline.pl > 50-TSS.no-ORF.tfa
<206|141>bioskill:Promoters> head -7 50-TSS.no-ORF.tfa
>accA TATGCTCGCGGGCTTGCTATCTCGCTGACGGACAGGCAAATTGATGACCA >accB TTACATGTTAGCTGTTGATTATCTTCCCTGATAAGACCAGTATTTAGCTG >accD TCGACCACTTTTTTATCCAAAGTTTCGGGCTGTTATGTTTTAATGTGCAA >aceBAK<207|0>bioskill:Promoters> FASTA2line.pl 50-TSS.tfa | wc -l
447<208|0>bioskill:Promoters> FASTA2line.pl 50-TSS.tfa | grep TATAAT | wc -l
25<209|1>bioskill:Promoters> FASTA2line.pl 50-TSS.tfa | grep TTGACA | wc -l
18<210|0>bioskill:Promoters> FASTA2line.pl 50-TSS.tfa | grep TATAAT | grep TTGACA | wc -l
0Part III - Statistics on E.Coli genes' length
<201|0>bioskill:~> cd Data/EColi/
<202|0>bioskill:EColi> head -10 Colibri_Gene.list
Colibri name Gene length SWISS-PROT Location (kb) Description aarF 1641 P27854 4017.80 Regulator of 2'-N-acetyltransferase; involved in respiratory cofactor ubiquinone production aas 2160 P31119 2974.00 2-Acyl-glycerophosphoethanolamine acyltransferase; acyl-ACP synthetase; salvage pathway for reacylation; inner membrane; bifunctional for turnover/incorporation aat 705 P23885 926.70 Aminoacyl-tRNA-protein-transferase abc 1032 P30750 222.60 ABC protein family homolog abgA 1311 P77357 1402.60 Gene in putative abgABT operon; function unknown abgB 1446 P76052 1401.30 Gene in putative abgABT operon; function unknown abgR 909 P77744 1402.80 Putative regulator of abgABT operon abgT 1533 P46133 1399.80 Para-aminobenzoyl-glutamate utilization; cryptic gene abrB 1047 P75747 747.00 Possible regulator of aidB expression!?! Are you familiar with the awk pattern scanning and processing language?
AWK scans each input file for lines that match a set of patterns. With each pattern there can be an associated action. Such a statement has the form: (pattern){ action }<203|141>bioskill:EColi> cat Colibri_Gene.list | awk -F '\t' '{print $2}' | head -10
Gene length 1641 2160 705 1032 1311 1446 909 1533 1047<204|141>bioskill:EColi> cat Colibri_Gene.list | awk -F'\t' '(FNR>1){print $2}' | head -10
1641 2160 705 1032 1311 1446 909 1533 1047 960!?! What will be the result of: awk -F'\t' '(FNR>1){print $0}' and awk -F'\t' '(FNR>1)'<205|141>bioskill:EColi> cat Colibri_Gene.list | awk -F'\t' '(FNR>1){print NF}'|uniq
5!?! What will be the result of the same command when omitting the -F'\t'?<205|141>bioskill:EColi> cat Colibri_Gene.list | awk -F'\t' '(FNR>1){sum+=$2;n++}END{print sum/n}'
948.826<206|141>bioskill:EColi> tail +2 Colibri_Gene.list | cut -f 2 | stats.pl
Average : 948.826452064381 Sum : 4067619 Sum Sqrs: 5631951129 Variance: 413552.642295925 Std dev.: 643.080587715043 N : 4287<207|0>bioskill:EColi> tail +2 Colibri_Gene.list | awk '{a[int($2/100)]++}END{for (i in a){print 100*i,a[i]}}' | sort -g > tmp
<208|0>bioskill:EColi> gnuplot
gnuplot> plot 'tmp' with lines gnuplot> exit!?! We will learn more about gnuplot and other graphical tools in Lesson 10Part IV - Whole genomes nucleotide composition
Can we find the nucleotide composition by using simple shell commands?<201|0>bioskill:~> cd Data/Bacteria
<202|0>bioskill:Bacteria> ls -l
total 1954 -rw-r--r-- 1 bioskill users 923807 Mar 10 19:48 Borrelia_Burgdorferi.tfa -rw-r--r-- 1 bioskill users 828126 Mar 10 19:44 Mycoplasma_Pneumonia.tfa<203|0>bioskill:Bacteria> grep -v '^>' Borrelia_Burgdorferi.tfa | head -10
TAAATATAATTTAATAGTATAAAAAAAATTAAATCAAATTAATAATAGTTTAAAAAACTGTTTGTATAAT ATAATATTATTATATATAATATTAAGCAACTACTATGATACTAATGAAGTATAGTGCTATTTTATTAATA TGTAGCGTTAATTTATTTTGTTTTCAAAATAAATTAACTACTTCTCGATGGGAATTCCCTAAAGAAGATT TAATTAAAAAAAAAATAAAAATAGGCATAATTTACCATAATTACATAAATTCTATCTTTTACAATGAAAA TTATAAATACATTGCCTTTATCGGAATATTGACATCTTATAATGAATGGATTGAAATACAATTTAGCCCC ATAAATTTTTTTACTATCCCAACAAATAAAGATTTTATTTCAAATACTTATTTCAATTTAGCTTTCACTA TTTACATTACCAAGTATTCAATTTTAACTGATACACTTGCTATAAAATTTTTTATTGGAACCCAAATCGA TTTAACTCTGAGAACTACTATATTTACAGGAAAAACAACTCATGCATTTCTCTATCCAATTCTTCCCATA ATTACCTTCAAATTTGAAATTGATTTCATACCTAATAACTATAGTATTTACTATAAATTATCGACTTCTT TTAAAGAATTTATCCTTTTAGATCTAGGAATTTCTATATTTATATAATCCTTTTTTTATTATAGAACTTT<204|0>bioskill:Bacteria> grep -v '^>' Borrelia_Burgdorferi.tfa | tr 'acgt' 'ACGT' | tr -cd 'ACGT' | fold -w 1 | sort | uniq -c
323079 A 130760 C 129646 G 327196 T<205|0>bioskill:Bacteria> grep -v '^>' Mycoplasma_Pneumonia.tfa | tr 'acgt' 'ACGT' | tr -cd 'ACGT' | fold -w 1 | sort | uniq -c
249211 A 162920 C 163703 G 240560 T<205|0>bioskill:Bacteria> grep -v '^>' Mycoplasma_Pneumonia.tfa | fold -w 1 | awk '{a[$1]++}END{for (i in a){print i,a[i]}}'
A 249211 C 162920 G 163703 T 240560<206|0>bioskill:Bacteria> cd ../Virus
<207|0>bioskill:Virus> ls -l
total 242 -rw-r--r-- 1 bioskill users 235788 Mar 10 19:59 Amsacta_Moorei_Entomopoxvirus.tfa -rw-r--r-- 1 bioskill users 10589 Mar 10 19:48 Human_Immunodeficiency_Virus.tfa<208|0>bioskill:Virus> grep -v '^>' Amsacta_Moorei_Entomopoxvirus.tfa | head -10
ATTTTTTTAAAATGAAAAAAAAAAATATCATAACTACTAACTATGGATTTACCTATAGAAATTTTAGAAA TTATATTTAATTATACAGATACATACATAAAATTATAATTTATATATTTAAAATATTTAGAATTTATTGA AAATTAGTAAAATTAGATTGTTCTAAAACATATATTGATTCTCTAAAAGGAATACATTATCTTACTAATT TACAAAAATTAATTCTTTAAAAGAAATATGTTGCCTTAATAATATTAAAAAAATAAATTGTTCATATACA ATCATTGATTCTCTAAAAGGAATAAGTCTTAATAATTTAGAAGAATTATATTGTTATAATATAAAAATTT ATTCTTTAAATATAATAATAAAAAATCTGCTTATTAAAAATATTAAATGGTTATAAATACATAAATTAAT TATTTTATATAAATTATTGTTAAACATTTATATTAATATTCTAATATTAAAAATTGAAAAAAAAAATAAT TATGTTAAAATGGAGTTACCTGTAGAAATGTTAGAAATTATATTTAATTATTTAGATAATGATACTAAAT TACAATTTATAGATTCAAAATGTATTATATCAAAACTTATATATAAATTAAAATATAATTCTTGTTTAAA AGAAATAAAGAATTTTATTAATTTAAAAGAATTAATATATAATAATTATTATATAAAATCTTTAGAAGGT<209|0>bioskill:Virus> grep -v '^>' Amsacta_Moorei_Entomopoxvirus.tfa | tr 'acgt' 'ACGT' | tr -cd 'ACGT' | fold -w 1 | awk '{a[$1]++}END{for (i in a){print i,a[i]}}'
A 94121 C 20868 G 20454 T 96949<210|0>bioskill:Virus> grep -v '^>' Human_Immunodeficiency_Virus.tfa | tr 'acgt' 'ACGT' | tr -cd 'ACGT' | fold -w 1 | awk '{a[$1]++}END{for (i in a){print i,a[i]}}'
A 3506 C 2132 G 2598 T 2123
Text: cat, sort, uniq, grep, echo head, tail, wc tr, cut, fold awk, sed paste, join Web: lynx, wget Math: bc Control: if, foreach, while, jobs, kill, ctrl-D, ctrl-S, ctrl-Q, bg, fg [or in general: tcsh manual, (ba)sh manual] Files: File redirections (<, >, >>, >&, >!, >&!), tee