Assignment 4

INPUT:

The program will read data from standard input using fgets. The data will be the contents of a DNA sequence file which will be in the FASTA format:

• A line beginning with a ">" is the header line for the next sequence
• All other lines contain sequence data.
• There may be any number of sequences per file.
• A sequence may be split over several lines.
• Sequence data may be upper or lower case.
• Sequence data may contain white space which should be ignored.

OUTPUT:

• The number of sequences in the input file
• The total length of all sequences
• The average length of the sequences
• The maximum length of any sequence
• The minimum length of any sequence
• The overall percent of the letters A, T, C, and G in the sequences (ignoring the case of the input).
• The overall percent of other letters in the sequences

Hints

• Don't save the lines. Read in one line at a time, process it, and throw it away.

• To have your program read the contents of a file through standard input, redirect the contents of the file into the program. From the command line either of the following should work

  ./hw4 < test1.fsa
cat test1.fsa | ./hw4

Input Data Files

• test1.fsa and the expected output should look like test1.out
• test2.fsa and the expected output should look like test2.out
• test3.fsa and the expected output should look like test3.out
• H_influenzae.fsa and the expected output should look like H_influenzae.out