Hiring_task

Hiring task 2023@Malay Basu

Table of contents:-

  1 Task 
  
  2 Data
  
  3 Specification
  
  4 Rules

Task 1

You need to write a computer program that takes a GMT file as an input and replace the gene names (or symbol) in the file with Entrez Ids that effectively creates another GMT file with Entrez ID. Entrez ID (or gene ID) is a unique number that is given to any gene in the NCBI Entrez database. A GMT file is a tab-delimited text file (columns are separated by tabs). These files are used in pathway analysis. The file format is described in the data section below.

Task 2

E. coli MG1655 is the standard reference strain of E. coli. The protein FASTA file for this strain can be downloaded from https://ftp.ncbi.nlm.nih.gov/genomes/archive/old_refseq/Bacteria/Escherichia_coli_K_12_substr__MG1655_uid57779/NC_000913.faa Using just bash commands can you find out what is the average length of protein in this strain? You may use as many commands as you may wish.

Task 3

Use R and ggplot2 package draw a a plot of number of genes per chromosome in human genomes. This task requires the data file Homo_sapiens.gene.info.gz. You need to use columns 3 and 7 indicating Symbol and chromosome respectively. You script should create a plot exactly as shown below. Save the plot to PDF file.
Data- for task 1

There are two files you need to complete this task. The files may have been compressed using gzip software. Preferably, you should not unzip these files at all. Most modern computer languages should be able to read these files as it is.
1. Homo_sapiens.gene_info.gz . This is a tab-delimited text file that contains information about all the genes in the human genome. The file contains a lot of information, but we are interested in only the following columns: 2, 3, 5. These are GeneID (Entrez Id), Symbol and Synonyms. Create a mapping of Symbol to GeneId. You have to be particularly careful about the Synonym column which may have multiple Symbol names separated by |. Like this AACT|ACT|GIG24|GIG25. You need to extract the individual gene names from this column add them to the Symbol to GeneId map. If you are interested in more about this file format check here: https://ftp.ncbi.nih.gov/gene/DATA/README.
2. h.all.v2023.1.Hs.symbols.gmt. This is a gene matrix transposed file. This is a tab-delimited text file. This type of file is used for pathway analysis. It is a very simple file format, however, each line can be of different lengths. This file, therefore, should be read line by line, not by columns. If you split each line on tab, it will create a number of values (or fields). The first two values are “pathway name" and”pathway description". All subsequent values are gene names that belong to the particular pathway. Your goal is to replace the gene names with Entrez ID extracted from the first “gene_info” file.
  
  Data-for task 2
  
  NC_000913.faa.gz is a amino acid FASTA file compressed using gzip. You download the same file from here: https://ftp.ncbi.nlm.nih.gov/genomes/archive/old_refseq/Bacteria/Escherichia_coli_K_12_substr__MG1655_uid57779/NC_000913.faa
  
  Note:
  1. You must use only bash commands. No other programming language is allowed. If you are using Mac or Linux, then bash automatically comes along with the machine. For windows you need to install bash. Follow the instructions here:https://superuser.com/questions/608106/how-can-i-use-a-bash-like-shell-on-windows
  2. You can either provide a single command line or a bash script.
  3. You may need the following commands in bash to complete this task: wget, zcat, wc, tr, bc, and grep. You are not restricted to any of these commands. You can use any or all or any other bash commands in your script or command line.
  4. Save your command or bash script as task2.sh.
  5. Hint: you need to count the number of sequences in the file and the total number of amino acids then divide the latter with the former. The answer is 316
  Data for task 3
  
  Homo_sapiens.gene_info.gz . This is a tab-delimited text file that contains information about all the genes in the human genome. If you are interested in more about this file format check here:https://ftp.ncbi.nih.gov/gene/DATA/README
  
  Note:
  1. The figure should exactly look like the above figure.
  2. There are some data in the chromosome column that are ambiguous and look like this: 10|19|3. You need to discard all rows where the chromosome value contains a |
Specification for task 1-
1. Your program should read the gene_info file and create a unique mapping of all gene (symbol) names to their corresponding Entrez ID. You need to be comprehensive to include all symbols both including those in the Synonyms and Symbol columns.
2. Read GMT file and proceed to the next step.
3. Write a file (or print in the terminal) a new GMT file where symbols have been replaced with Entrez IDs.
Rules-
1. You have 48 hours to finish the task.
2. You can use any computer language of your choice. However, you get bonus points for finishing this task in R.
3. Strictly follow the submission instruction. The only way your submission is accepted is through a GitHub link. No other way of submission is admissible.
4. All program must be a stand-alone script, runnable from the command line. No Jupyter, iPython notebook, or Rmarkdown allowed.
5. Strictly follow the submission instruction. The only way your submission is accepted is through a GitHub link. No other way of submission is admissible.

pratyusha-code/Hiring_task

Hiring_task