read_fasta.py

def read_fasta(fasta_filename):
    '''Function to parse a fasta sequence file'''

    # Initialize dictionary
    fasta_dict = {}

    # Open file and iterate over lines
    for line in open(fasta_filename): 

        # Remove newline and other whitespace from end of line
        line = line.rstrip()  

        # Test if line starts with '>'
        if line[0] == '>':

            # If so, save name in variable
            name = line[1:]

            # Register name in dictionary - with empty sequence
            fasta_dict[name] = ""

        else:
            # Add partial sequence to the entry in the dictionary
            fasta_dict[name] += line
  

    # Return result
    return fasta_dict