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.
• Each task can be split into several stages and intermediate files written to disk, but you can also use pipelines to reduce the number of temporary files.
• 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.)
• Include all relevant used commands in your protocol and add a short description of your approach.
• Submit the protocol and required output files.
• Outline of the protocol is in /tasks/bash/protocol.txt, submit to directory /submit/bash/yourname

Preparatory steps

We will not include such detailed steps in future homeworks, you will have to adjust these as needed.

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

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

===Introduction to tasks A-C===
* In these tasks we will again process bioinformatics data. We have two files in the FASTA format, which you have seen in [[HWperl]]. Unlike before, this time the sequences represent proteins, not DNA, and therefore they use 20 different letters representing different amino acids. Lines starting with '>' contain identifier of a protein and potentially additional description. This is followed by the sequence of this protein, which will not be needed in this task. This data comes from the [https://www.uniprot.org/ Uniprot] database.
* File <tt>/tasks/bash/yarLip.fa</tt> is a FASTA file with proteins from the yeast ''Yarrowia lipolytica''. We will pretend that nothing is known about the function of these proteins and indeed, each protein is identified in the FASTA file only by its identifier such as <tt>Q6CFX1</tt>.
* File <tt>/tasks/bash/known.fa</tt> is a FASTA file with proteins from several yeast species. Each identifier is followed by a description of its biological function. 
* These two sets of proteins were compared by a bioinformatics tool called BLAST which finds proteins or their parts with similar sequences. The results of BLAST are in file <tt>/tasks/bash/pairs.tsv</tt>. This file contains a section for each protein in <tt>yarLip.fa</tt> which starts with several comments, i.e. lines starting with <tt>#</tt> symbol. 
This is followed by a table with found matches in <tt>TSV</tt> format, i.e., several values delimited by tab characters <tt>\t</tt>. We will be most interested in the first two columns representing the ID of a protein from <tt>yarLip.fa</tt> and from the <tt>known.fa</tt>, respectively. 

===Task A===

'''Steps (1) and (2)'''
* Use files <tt>yarLip.fa</tt> and <tt>known.fa</tt> to find put how many proteins are in each. Each protein starts with a line starting with <tt>></tt> symbol, so it is sufficient to count those.
* Beware that <tt>></tt> symbol means redirect, therefore you have to enclose it in single quotation marks <tt>'>'</tt> 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 both the command and corresponding number to the appropriate section of your protocol. 

'''Step 3'''
* Create file <tt>known.tsv</tt> which contains sequence names and descriptions extracted from <tt>known.fa</tt>
* Leading <tt>></tt> should be removed. Any text after  <tt>OS=</tt> should be also removed.
* This file should be sorted alphabetically.
* The file should start as follows (lines are trimmed below):
<pre>
sp|A0A023PXA5|YA19A_YEAST Putative uncharacterized protein YAL019W-A
sp|A0A023PXB0|YA019_YEAST Putative uncharacterized protein YAR019W-A

• Submit file known.tsv, write your command(s) to the protocol.

Task B

• From file pairs.tsv extract pairs of similar proteins

• Get the first (strongest) match for each query from known.blast.
• This 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
• Print only the first two columns separated by tab (name of query, name of target), sort the file by the second column.
• Store the result in file best.tsv. The file should start as follows:

Q6CBS2  sp|B5BP46|YP52_SCHPO
Q6C8R4  sp|B5BP48|YP54_SCHPO
Q6CG80  sp|B5BP48|YP54_SCHPO
Q6CH56  sp|B5BP48|YP54_SCHPO

• Submit file best.tsv with the result

Step 2:

• Create file known.tsv which contains sequence names extracted from known.fa with leading > removed
• This file should be sorted alphabetically.
• The file should start as follows (lines are trimmed below):

sp|A0A023PXA5|YA19A_YEAST Putative uncharacterized protein YAL019W-A OS=Saccharomyces...
sp|A0A023PXB0|YA019_YEAST Putative uncharacterized protein YAR019W-A OS=Saccharomyces...

• Submit file known.tsv

Step 3:

• For each Y.lipolytica protein, we have found similar proteins from other yeasts
• Now we want to extract for each protein in Y.lipolytica its closest match among all known proteins and see what is its function. This will give a clue about the potential function of the Y.lipolytica protein.

• Use command join to join the files best.tsv and known.tsv so that each line of best.tsv is extended with the text describing the corresponding target in known.tsv
• Use option -1 2 to use the second column of best.tsv as a key for joining
• The output of join may look as follows:

sp|B5BP46|YP52_SCHPO Q6CBS2 Putative glutathione S-transferase C1183.02 OS=Schizosaccharomyces...
sp|B5BP48|YP54_SCHPO Q6C8R4 Putative alpha-ketoglutarate-dependent sulfonate dioxygenase OS=...

• Further reformat the output so that the query name goes first (e.g. Q6CBS2), followed by target name (e.g. sp|B5BP46|YP52_SCHPO), followed by the rest of the text, but remove all text after OS=
• Sort by query name, store as best.txt
• The output should start as follows:

B5FVA8  tr|Q5A7D5|Q5A7D5_CANAL  Lysophospholipase
B5FVB0  sp|O74810|UBC1_SCHPO    Ubiquitin-conjugating enzyme E2 1
B5FVB1  sp|O13877|RPAB5_SCHPO   DNA-directed RNA polymerases I, II, and III subunit RPABC5

• Submit file best.txt

Note:

• Not all Y.lipolytica proteins are necessarily included in your final output (some proteins do not have blast match).
  • You can think how to find the list of such proteins, but this is not part of the task.
• Files best.txt and best.tsv should have the same number of lines.

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.

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.