Linux Practice

Troubleshooting

100

How many instances of the flu are there?

grep -c "flu" pandemics.csv

This will give you a count of zero because grep is case sensitive. You need to either:

1) use the -i flag to ignore case or

2) capitalize the first f in flu.

200

Log onto logrus

ssh [e-mail]

This is missing the port (44111).

ssh -p 44111 [e-mail]

300

Look at the top part of a file that you loaded into the variable dns in R.

head dns

That is linux syntax. In R you have to use parentheses:

1) head(dns)

If you want to see 10 lines

2) head(dns,n=10) or head(dns,n=10L)

400

Print the pathogen column

awk '{print $2}' pandemics.csv

1) You need to change the delimiter to a comma.

2) Alternatively, you could use:

cut -d, -f2 pandemics.csv

500

Find the unique pathogens.

awk -F, '{print $2}' sort.pandemics.csv | uniq

You need to sort it first. If you run it like this it will only collapse duplicates that are on adjacent rows. You will get: virus, unknown, virus, bacteria, virus, bacteria.

1) awk -F, '{print $2}' sort.pandemics.csv | sort | uniq

1) awk -F, '{print $2}' sort.pandemics.csv | sort -u

Pandemic Movies

100

How many movies are there?

wc -l some_pandemic_movies.txt

cut -f 1 some_pandemic_movies.txt | wc -l

awk -F "\t" some_pandemic_movies.txt | wc -l

200

Print only the year (column 2).

cut -f 2 some_pandemic_movies.txt

awk '{print $2}' some_pandemic_movies.txt

awk -F "\t" '{print $2}' some_pandemic_movies.txt

300

Grab all lines ith pandemic movies that were made before 1980 (column 2)

awk '$2<1980{print}'

awk '$2<=1979{print}'

awk -F "\t" '$2<1980{print}'

awk -F "\t" '$2<=1979{print}'

400

Print only the movie column (1st column).

cut -f 1 some_pandemic_movies.txt

awk -F "\t" '{print $1}' some_pandemic_movies.txt

500

Grab all lines with pandemic movies that were made between 1980 and 2000 (column 2).

awk '$2>=1980&&<=2000{print}'

awk '$2>1979&&<2001{print}'

awk -F "\t" '$2>=1980&&<=2000{print}'

etc

Pandemic Movies 2

100

How many movies were released in 2023?

grep -c 2023 some_pandemic_movies.txt

grep 2023 some_pandemic_movies.txt|wc -l

200

Sort the file by year (second column)

sort -nk2 some_pandemic_movies.txt

sort -k2 some_pandemic_movies.txt (because all the years are 4 numbers, this will give you the same answer but best practice is to use -n regardless).

300

How many unique movie titles are there?

cut -f 1 some_pandemic_movies.txt | sort -u | wc -l

cut -f 1 some_pandemic_movies.txt | sort | uniq | wc -l

awk -F "\t" some_pandemic_movies.txt | sort -u | wc -l

etc

400

How many of each pathogen (column 3) are there?

cut -f 3 some_pandemic_movies.txt | sort | uniq -c

cut -f 3 some_pandemic_movies.txt | sort -u | wc -l

awk -F "\t" '{print $3}' some_pandemic_movies.txt | sort | uniq -c

etc

500

How many movies start with "Virus"?

grep -c "^Virus" some_pandemic_movies.txt

cut -f 1 some_pandemic_movies.txt | grep -c "^Virus$"

awk -F 1 some_pandemic_movies.txt | grep -c "^Virus$"

Influenza A Sequences

100

How many sequences are there in the file?

grep -c '>' flu_sequences.fa

grep '>' flu_sequences.fa | wc -l

200

What is the earliest (field 6) flu sequence in the file? Make sure you remove blank lines.

grep '>' influenzaA_sequences.fa | awk -F'|' '{print $6}'|grep -v '^$'|sort -n|head -1

grep '>' influenzaA_sequences.fa | cut -f 6 -d '|' |grep -v '^$'|sort -n|head -1

etc

300

How many countries (field 5) are represented in this file? Note that some samples will have a blank entry in the country field and shouldn't be counted.

grep '>' influenzaA_sequences.fa | awk -F'|' '{print $5}'|sort -u| grep -v '^$' | wc -l

grep '>' influenzaA_sequences.fa | cut -f 5 -d '|' |sort -u| grep -v '^$' | wc -l

etc

400

How many H1N1 sequences from 2009 are there?

grep H1N1 influenzaA_sequences.fa | grep 2009

grep '>' influenzaA_sequences.fa | grep H1N1 | awk -F '|' '$6~/2009/{print}'|wc -l

Note that there are 8 that have an empty collection date but say 2009 elsewhere in the header so you will get two different counts.

etc

500

Figure out how many of each host (field 7) there are and sort them from the host with the fewest to the most sequences.

grep '>' influenzaA_sequences.fa | cut -f 7 -d'|' | sort |uniq -c |sort -n

grep '>' influenzaA_sequences.fa | awk -F'|' '{print $7}' | sort |uniq -c |sort -n

etc