Homework 1

Create a hw1 repository on github and make it within the biodataprog organization

Write a bash / shell script to accomplish the following tasks. Remeber you can make a shell script as a series of commands just as you would type on the command line.

1. Getting data

   • Use a cmdline downloading program (e.g. curl) to download this BLAST report from the web: Ecoli-vs-Yersinia.BLASTP.tab.gz or https://biodataprog.github.io/2018_programming-intro/data/Ecoli-vs-Yersinia.BLASTP.tab.gz
   • Print out how big this file is (in kilobytes)?

2. Compressing and uncompressing

   • Uncmpress this file with gunzip.
   • How big is the uncompressed file (in kilobases)?

3. Counting and viewing (Using the same BLAST report)

   • Print out the first 25 lines of the file
   • Print out the last 3 lines of the file
   • Print the total number lines in the file

4. Sorting

   • Obtain the data file Nc3H.expr.tab. This file contains gene expression value assigned to each gene in the Neurospora crassa (a fungus) genome. https://biodataprog.github.io/2018_programming-intro/data/Nc3H.expr.tab
   • Sort the file based on the FPKM column (which is the gene expression) (write out to a new file called Nc3H.expr.sorted.tab). Remember the in-class introduction to sorting which ignores the header. Note your sorting will be more complicated than what is depicted here.

    (head -n 1 <filename> && tail -n +2 <filename> | sort) > newfile

   • Print out a list of the top 10 most highly expressed genes based on FPKM.

5. Finding and Counting

   • Report the number of CDS features in this genbank file - see for example this explanation of a genbank file if you are not familiar. https://biodataprog.github.io/2018_programming-intro/data/D_mel.63B12.gbk
   • Print how many sequence alignments are 100% identical in the previously downloaded file Ecoli-vs-Yersinia.BLASTP.tab.
   • Print how many sequence alignments are 90% identical or better in the previously downloaded file Ecoli-vs-Yersinia.BLASTP.tab. (Hint, review the options in awk for filtering or processing column delimited data).

6. Sort and Uniq

   • Obtain the file listing the standard codons and amino acids translations. codon_table.txt. Column 1 is the codon, Column 2 is the amino acid, and Column 3 is the Amino acid written out. https://biodataprog.github.io/2018_programming-intro/data/codon_table.txt
   • Print out the name or symbol of each amino acid and how many codons encode that amino acid. (e.g. Lysine/K is encoded by 2 codons)