Bioinformatics Data Skills

Assignment 6

1. Read through Chapter 7 at least twice

2. It’s a big chapter which is why we’ve got 2 weeks with it, but pay attention to things like grep, sed, awk, etc…

3. Here’s a fasta file (Assignment_6_File_1.fasta.gz) you should download into an appropriate place in your Assignment_6 project directory and uncompress it.

4. I need you to convert that file into tabular format using some combination of the tools you’ve learned. Tabular format looks like the following:

OTU8      TACGGAGGGTGCAAGC...
OTU11     TGGCAGACTAGAGTAT...

The first column is just the OTUID, the second column is just the sequence; one line per sequence

5. Keep track of any steps you take to convert from fasta to that tabular (with two columns) format, and save the new version of the data file as “Assignment_6_File_1.tsv

6. Now, starting from that new tabular file, use paste/awk/sed/etc. to convert it back to standard fasta format. Record all your commands that got the job done.

7. Okay, now download this other fasta file (Assignment_6_File_2.fasta.gz) … get it uncompressed. This file is essentially the same as the first file, but the fasta headers contain taxonomic assignments for each sequence in the format: Kingdom;Phylum;Class;Order;Family;Genus

8. Write a short pipeline to extract an alphabetical list of the unique genera that were identified in the Enterobacteriaceae family

9. Create a tab-separated list consisting of 2 columns:

Column 1 = full taxonomy of all genera found in the Enterobacteriaceae family

Column 2 = the number of times that genus was observed in this file

Example output:  
    >Bacteria;Proteobacteria;Gammaproteobacteria;Enterobacteriales;Enterobacteriaceae;Proteus;  5
    >Bacteria;Proteobacteria;Gammaproteobacteria;Enterobacteriales;Enterobacteriaceae;Tatumella;    6
    >Bacteria;Proteobacteria;Gammaproteobacteria;Enterobacteriales;Enterobacteriaceae;Buttiauxella; 7
    >Bacteria;Proteobacteria;Gammaproteobacteria;Enterobacteriales;Enterobacteriaceae;Escherichia/Shigella; 7

10. Export that list to a new file named “Enterobacteriaceae_Genus_Counts.tsv”

What to turn in:

  • Store a cleaned-up plain-text file that documents the code you used for tasks 3-10
  • Be sure to include comments explaining what is going on in your code

Upload that plain-text file to Canvas. You’ll be graded on completeness, documentation, and readability.