Updating a dictionary within a function

Question

I'm helping my girlfriend with an assignment. Part of this assignment is the calculation of the number of possible combinations in a DNA sequence that contains certain wildcard characters.

I'm using the following python script:

from Bio import Seq
from Bio import SeqIO

short = SeqIO.parse('short.fasta', 'fasta')
long = SeqIO.parse('long.fasta', 'fasta')

# IUPAC dictionary

IUPAC = {
    'R': 2,
    'Y': 2,
    'S': 2,
    'W': 2,
    'K': 2,
    'M': 2,
    'B': 3,
    'D': 3,
    'H': 3,
    'V': 3,
    'N': 4
}

# Define method to count number of possible sequences
def pos_seq(seqs):
    d = {}

    for record in seqs:
        pos = 1    
        name = record.id
        seq = record.seq

        for ltr in seq:
            if ltr in IUPAC.keys():
                pos = pos * IUPAC[ltr]

        d.update({name : pos})
        print(name + ": " + str(pos) + " possibilities")
        print("")

    print("end of file")
    print("")

    return d



print(pos_seq(short))
print(pos_seq(long))

The function pos_seq takes in a collection of sequences and returns the number of possibilities for each of sequence.

The script works fine and the function prints the correct answer on each iteration. However, I wanted to save the sequence's name and number of possibilities into a dictionary and return it.

Here is the problem: It always returns an empty dictionary (as defined at the start of the method).

Defining the dictionary globally (outside the function) works; the dictionary DOES get updated properly, so the problem may be that I defined the dictionary within the function. Maybe I need to change the .update line to specify the dictionary I want to update isn't a global dictionary?

Long story to ask a simple question: I can't seem to use a function to create a dictionary, update it several times and then return it. It stays empty.

I'm not very experienced in Python, but I couldn't find an answer to this question online.

Thanks for the help!

Answer 1

After a bit of research of the puzzling question that jez raised (no indentation error raised despite an indentation error), I found that the reason why your code works.

You were indenting with 8 spaces and tabs inconsistently. This is allowed in Python 2 but not allowed in Python 3. http://python3porting.com/differences.html#indentation

In Python 2 a tab will be equal to eight spaces as indentation, so you can indent one line with a tab, and the next line with eight spaces.

In Python 3 a tab is only equal to another tab. This means that each indentation level has to be consistent in its use of tabs and spaces.

Hence, if you try this code:

print("Hello world!")
def my_func(x):
        print(x)
    print(x)

It will work in Python 2 but will raise an indentation error in Python 3.

Another thing to note about StackOverflow that I also found out is that when you paste code with indents in them, it will show up as 4 spaces when displayed but when you go into edit mode, you will be able to copy and paste the tabs (try it).

And that is why, your code does not work even when there are still errors.