OPTbash

This is an optional set of exercises for lecture on command-line tools (Lbash). They use a bioinformatics input file with annotation of the yeas genome.

Task A (yeast genome)

The input file:

• /tasks/optional/bash/saccharomyces_cerevisiae.gff contains annotation of the yeast genome
  • Downloaded from http://yeastgenome.org/ on 2016-03-09, in particular from [1].
  • It was further processed to omit DNA sequences from the end of file.
  • The size of the file is 5.6M.
• For easier work, link the file to your directory by ln -s /tasks/optional/bash/saccharomyces_cerevisiae.gff yeast.gff
• The file is in GFF3 format
• The lines starting with # are comments, other lines contain tab-separated data about one interval of some chromosome in the yeast genome
• Meaning of the first 5 columns:
  • column 0 chromosome name
  • column 1 source (can be ignored)
  • column 2 type of interval
  • column 3 start of interval (1-based coordinates)
  • column 4 end of interval (1-based coordinates)
• You can assume that these first 5 columns do not contain whitespace

Task:

• Print for each type of interval (column 2), how many times it occurs in the file.
• Sort from the most common to the least common interval types.
• Hint: commands sort and uniq will be useful. Do not forget to skip comments, for example using grep -v '^#'
• The result should be a file types.txt formatted as follows:

   7058 CDS
   6600 mRNA
...
...
      1 telomerase_RNA_gene
      1 mating_type_region
      1 intein_encoding_region

Task B (chromosomes)

• Continue processing file from task A.
• For each chromosome, the file contains a line which has in column 2 string chromosome, and the interval is the whole chromosome.
• To file chrosomes.txt, print a tab-separated list of chromosome names and sizes in the same order as in the input
• The last line of chromosomes.txt should list the total size of all chromosomes combined.
• Hints:
  • The total size can be computed by a perl one-liner.
  • Example from the lecture: compute the sum of interval sizes if each line of the file contains start and end of one interval: perl -lane'$sum += $F[1]-$F[0]; END { print $sum; }'
  • Grepping for word chromosome does not check if this word is indeed in the second column
  • Tab character is written in Perl as "\t".
• Your output should start and end as follows:

chrI    230218
chrII   813184
...
...
chrXVI  948066
chrmt   85779
total   12157105