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Presentation transcript:

(optional - but then again, all of these are optional)‏ Advanced Exercises (optional - but then again, all of these are optional)‏

FASTA format A FASTA file contains 0 or more records Each record starts with a header line The first character of the header is a “>” After that are a bunch of sequence lines After the sequence lines is a blanks line (In real FASTA files that line is optional. Don’t worry about that, since this version is easier to parse.)

Write a program to count the number of records in a FASTA file. Exercise #1 Write a program to count the number of records in a FASTA file. Once done, modify that program to print the total number of bases present and the total count of each base found.

Exercise #2 Write a program to print only the header lines in that FASTA file. It must not print the leading “>”.

Exercise #3 Write a program to find the record(s) where the header line contains a given text “XXX”. Print it out, in FASTA format. (That is, the output should not be changed.)‏

Command-line arguments In Python you can get the list of command-line arguments with sys.argv. This is a normal Python list. > cat print_args.py import sys print "Command-line arguments are:", sys.argv > python print_args.py Command-line arguments are: ['print_args.py'] > python print_args.py ls_orchid.fasta Command-line arguments are: ['print_args.py', 'ls_orchid.fasta'] > python print_args.py *.seq Command-line arguments are: ['print_args.py', '10_sequences.seq', 'ambiguous_sequences.seq', 'many_sequences.seq', 'sequences.seq'] >

Exercise #4 Write a program which gets two command line arguments, turns them into floats, and prints the sum. Note that sys.argv[0] is always the name of the Python program so you’ll need to use [1] and [2]

Exercise #5 Write a program to read a FASTA file and print the header line (without the leading “>”) if and only if the sequence ends with a C. Use a command-line argument to get the filename. Test it against both FASTA files in my directory.