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In today exercise you are asked to make a simple converter between two frequently used bioinformatics formats:

GeneBank format (.gp) -->  Fasta format (.fas)

Go to: http://gp2fasta.netmark.pl

a) You need some files for testing:
from https://www.ncbi.nlm.nih.gov/protein/ download some proteins in GenPept format (after making query you can
download the results via "Send to:" button

b) a task: do CLI version of the tool with similar functionalities i.e. converting the names, extracting species and
shortening it, etc.

Note: the tool should be able to process multiple records in one gp file

Expected result: gp2fasta.py script that takes as an input (from CLI) *.gp and returns *.fas file.

In this particular exercise do not use bioinformatics libraries like biopython or cogent. Write the whole parser
using pure python from scratch.

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The python script plus some files for testing should be added to the project folder.
All files should be sent until Sunday 02.03.2025 via email to lukaskoz@mimuw.edu.pl
with the email subject: 'ADP25_lab1_hw_Surname_Name' without email text body
and with 'ADP25_lab1_hw_Surname_Name.7z' (without Polish letters) attachment containing the project.

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						EXTRA TASK 
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For HPC part that we will do in few weeks we need to get acces to Entropy cluster:

Go to and register:
https://entropy.mimuw.edu.pl/register/

GPU types: Titan V, Titan X, RTX 2080 Ti
Required GPUs: 4
Estimated enqueued job time in days: 8 hours
Comment: Access to Entropy for ADP classes
Preferred login: see section below


DOCUMENTATION:
https://entropy-doc.mimuw.edu.pl

Please review the "Time limit" section of the documentation.
Properly estimating and setting jobs time limit ("--time" flag)
should improve overall scheduling efficiency.
https://entropy-doc.mimuw.edu.pl/submittingjobs.html#time-limit

The "GPUMinutes" parameter is the limit of total computation time
set for your account. After depleting this resource, running new
jobs won't be possible.
https://entropy-doc.mimuw.edu.pl/queuesresources.html#gpuminutes

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You will need to provide generate SSH keys and state public SSH key URL
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For instructions how to generate the SSH key see for instance:
- https://www.ssh.com/academy/ssh/keygen
- https://cloud.ibm.com/docs/ssh-keys?topic=ssh-keys-generating-and-using-ssh-keys-for-remote-host-authentication
- "Generate your SSH keys" section from https://docs.lumi-supercomputer.eu/firststeps/SSH-keys/
- https://docs.acquia.com/acquia-cloud-platform/manage-apps/command-line/ssh/getting-started/generate
	
Type command: ssh-keygen -t rsa -b 4096
The key is stored usually in /home/username/.ssh/
id_rsa.pub - public key (this the file you are looking for)
id_rsa     - private key (never show/send it to anyone) 

If you work from 'student' then you place the public key file to ~/public_html/ directory
and cutomize URL https://students.mimuw.edu.pl/~username/username.keys
 
e.g. https://students.mimuw.edu.pl/~ag2232823/id_rsa.pub (the file is id_rsa.pub and the user is ag2232823)
     https://duch.mimuw.edu.pl/~lukaskoz/lukaskoz.keys   (the file is lukaskoz.keys and the user is lukaskoz)
     etc.
 
After obtaining the email that the account is created you log in by typing (from student)
ssh ag2232823@entropy.mimuw.edu.pl (adjust as needed) - NO PASSWORD NEEDED

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