HWbash

Lecture on Perl, Lecture on command-line tools

• In this set of tasks, use command-line tools or one-liners in Perl, awk or sed. Do not write any scripts or programs.
• Your commands should work also for other input files with the same format (do not try to generalize them too much, but also do not use very specific properties of a particular input, such as the number of lines etc.)

Preparatory steps and submitting

# create a folder for this homework
mkdir bash
# move to the new folder
cd bash
# link input files to the current folder
ln -s /tasks/bash/known.fa /tasks/bash/yarLip.fa /tasks/bash/matches.tsv /tasks/bash/names.txt .
# copy protocol to the current folder
cp -i /tasks/bash/protocol.txt .

• Now you can open protocol.txt in your favorite editor and start working
• Command ln created symbolic links (shortcuts) to the input files, so you can use them under names such as known.fa rather than full paths such as /tasks/bash/known.fa.

When you are done, you can submit all required files as follows (substitute your username):

cp -ipv protocol.txt known.txt pairs.txt frequency.txt best.txt function.txt passwords.csv /submit/bash/your_username

# check what was submitted
ls -l /submit/bash/your_username

Introduction to tasks A-C

• In these tasks we will again process bioinformatics data. We have two files of sequences in the FASTA format. This time the sequences represent proteins, not DNA, and therefore they use 20 different letters representing different amino acids. Lines starting with '>' contain the identifier of a protein and potentially an additional description. This is followed by the sequence of this protein, which will not be needed in this task. This data comes from the Uniprot database.
• File /tasks/bash/yarLip.fa is a FASTA file with proteins from the yeast Yarrowia lipolytica. Each protein is identified in the FASTA file only by its ID such as Q6CFX1. We will call the proteins from yarLip.fa query proteins.
• File /tasks/bash/known.fa is a FASTA file with proteins from several yeast species. Each ID is followed by a description of the biological function of the protein. We will call the proteins from known.fa target proteins.
• These two sets of proteins were compared by the bioinformatics tool called BLAST, which finds proteins with similar sequences. The results of BLAST are in file /tasks/bash/matches.tsv. This file contains a section for each query protein. This section starts with several comments, i.e. lines starting with # symbol. This is followed by a table with the found matches in the TSV format, i.e., several values delimited by tab characters \t. We will be interested in the first two columns representing the IDs of the query and target proteins, respectively.

Task A (counting proteins)

Steps (1) and (2)

• Use files known.fa and yarLip.fa to find out how many proteins are in each. Each protein starts with a line starting with the > symbol, so it is sufficient to count those.
• Beware that > symbol means redirect in bash. Therefore you have to enclose it in single quotation marks '>' so that it is taken literally.
• For each file write a single command or a pipeline of several commands that will produce the number with the answer. Write the commands and the resulting protein counts to the appropriate sections of your protocol.

Step (3)

• Create file known.txt which contains sequence IDs and descriptions extracted from known.fa. This file will be used in Task C.
• Leading > should be removed. Any text after OS= in the description should be also removed.
• This file should be sorted alphabetically.
• The file should start as follows:

1433_CANAL 14-3-3 protein homolog 
1A1D_SCHPO Probable 1-aminocyclopropane-1-carboxylate deaminase 
2A5D_YEAST Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit delta isoform 
2AAA_SCHPO Protein phosphatase PP2A regulatory subunit A 
2AAA_YEAST Protein phosphatase PP2A regulatory subunit A 

• Submit file known.txt, write your commands to the protocol.

Task B (counting matches)

Step (1)

• From file matches.tsv extract pairs of similar proteins and store them in file pairs.txt.
• Each line of the file should contain a pair of protein IDs extracted from the first two columns of the matches.tsv file.
• These IDs should be separated by a single space and the file should be sorted alphabetically.
• Do not forget to omit lines with comments.
• Each pair from the input should be listed only once in the output.
• Commands grep, sort and uniq would be helpful. To select only some columns, you can use commands cut, awk or a Perl one-liner.
• The file pairs.txt should have 71834 lines (verify using command wc) and it should start as follows:

B5FVA8 PLB1_CANAL
B5FVA8 PLB1_SCHPO
B5FVA8 PLB1_YEAST

• Submit file pairs.txt and write your commands to the protocol.

Step (2)

• Find out how many query proteins (from yarLip.fa) have at least one similarity found in matches.tsv. This can be done by counting distinct values in the first column of your pairs.txt file from step (1).
• We suggest commands cut/awk/perl, sort, uniq, wc
• The result of your commands should be an output consisting of a single number (and the end-of-line character).
• Write your answer and commands to the protocol. Compare this number with the total number of query proteins found in Task A(2).

Step (3)

• For each query protein in the first column of pairs.txt file, count how many times it occurs in the file. The result should be a file named frequency.txt with pairs query protein ID, count separated by space, sorted from the proteins with the highest to the lowest count.
• To check you answer, look at lines 69 and 70 of the file as follows: head -n 70 frequency.txt | tail -n 2
• You should get the following two lines:

Q6CBP9 207
Q6C6A5 165

• This means that query protein Q6CBP9 occurs 207 times in the first column of pairs.txt, which means 207 target proteins are similar to it. Protein Q6C6A5 has 165 similar target proteins.
• Submit file frequency.txt, write your commands to the protocol. Also write to the protocol what is the highest and lowest count in the second column of your file.
• Note: The query proteins with zero matches are not listed in your file. Their number could be deduced from your results in step (2) and Task A(2) if needed.

Task C (joining information)

Step (1)

• For each query protein, the first (top) match in matches.tsv represents the strongest similarity.
• In this step, we want to extract such strongest match for each query protein which has at least one match.
• The result should be a file best.txt listing the two IDs separated by a space. The file should be sorted by the second column (target ID).
• The file should start as follows:

F2Z5Y1 1433_CANAL
F2Z6F8 1433_CANAL
Q6C7K1 2A5D_YEAST
Q6C3C5 2AAA_SCHPO

• This task can be done by printing the lines that are not comments but follow a comment line starting with #.
• In a Perl one-liner, you can create a state variable which will remember if the previous line was a comment and based on that you decide if you print the current line.
• Instead of using Perl, you can play with grep. Option -A 1 prints the matching lines as well as one line after each match.
• Submit file best.txt with the result and write your command to the protocol.

Step (2):

• Now we want to extend file best.txt with a description of each target protein.
• Since similar proteins often have similar functions, this will allow somebody studying query proteins from yarLip.fa to learn something about their possible functions based similarity to well-studied proteins from other species.
• To achieve this, we join together files best.txt and known.txt created in Task A(3). Conveniently, they are both sorted by the ID of the target protein.
• Use command join to join these files.
• Use option -1 2 to use the second column of best.txt as a key for joining
• The output of join may start as follows:

1433_CANAL F2Z5Y1 14-3-3 protein homolog 
1433_CANAL F2Z6F8 14-3-3 protein homolog 
2A5D_YEAST Q6C7K1 Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit delta isoform 

• Further reformat the output so that the query ID goes first (e.g. F2Z5Y1), followed by target ID (e.g. 1433_CANAL), followed by the rest of the text.
• Sort by query ID, store as function.txt
• The output should start as follows:

B5FVA8 Q5A7D5_CANAL Lysophospholipase
B5FVB0 Q59T91_CANAL Ubiquitin-conjugating enzyme E2 H
B5FVB1 RPAB5_SCHPO DNA-directed RNA polymerases I, II, and III subunit RPABC5

• Files best.txt and function.txt should have the same number of lines.
• Which target protein is the best match for the query protein Q6C7M8 and what its function?
• Submit file best.txt. Write your commands and the answer to the question above to your protocol.

Task D (passwords)

• The file /tasks/bash/names.txt contains data about several people, one per line.
• Each line consists of given name(s), surname and email separated by spaces.
• Each person can have multiple given names (at least 1), but exactly one surname and one email. Email is always of the form username@uniba.sk.
• The task is to generate file passwords.csv which contains a randomly generated password for each of these users
  • The output file has columns separated by commas ','
  • The first column contains username extracted from email address, the second column surname, the third column all given names and the fourth column the randomly generated password
• Submit file passwords.csv with the result of your commands. Write your commands to the protocol.

Example line from input:

Pavol Orszagh Hviezdoslav hviezdoslav32@uniba.sk

Example line from output (password will differ):

hviezdoslav32,Hviezdoslav,Pavol Orszagh,3T3Pu3un

Hints:

• Passwords can be generated using pwgen (e.g. pwgen -N 10 -1 prints 10 passwords, one per line)
• We also recommend using perl, wc, paste (check option -d in paste)
• In Perl, function pop may be useful for manipulating @F and function join for connecting strings with a separator.