Tag: extract

To name

I have two problems with your name:

First, do not use underscores to separate words. Instead of uniquepatternuse unique_pattern.

Second, your names don't really tell me anything! Functions, particularly non-method functions, must include a verb unless the verb is implicitly get or is. And implicit is should be used with some caution.

Then instead of unique_pattern, the name must be a phrase that reflects what its function does. As you mention "scaffolding names", maybe that function should be group_scaffold_names_by_unique_pattern?

Or maybe the unique pattern has another name? I like it prefix? (See my question in the comments.) Then maybe it should be group_scaffold_names_by_prefix?

Is that long? Yes. Does it say what's up? Furthermore, if. Clarity for victory!

Redundancy. Repetition. Duplication. Multiple copies

In coding, if you find yourself writing something a second time, STOP! Whatever it is, it must be stored once and referenced from different places. Write a function. Store text in a variable. Create a class Do what is necessary, but DO NOT REPEAT. (This is called the "DRY" principle).

This code is repeated:

    pattern_name = re.search(r"(A-Z){1}(a-z){2}", name)

What does? Well, it seems to be used to extract the first matching pattern as the "key" for each name in the list.

So, let's write a function for this:

def extract_key(name):
    """ Extract unique pattern from a scaffold name. 
        Apparently, patterns are just the first three characters,
        so don't use regexes, just grab the substring.
    """        
    return name(:3)

Use the standard library

It has a separate function that extracts the keys (unique patterns) from the names, and returns a list of them without specifying, which it apparently only uses to initialize the keys of a dictionary.

Instead of doing that, just use collections.defaultdict To create a dictionary that starts with empty lists:

import collections

groups = collections.defaultdict(list)

With that code, you can be sure that groups(key) it is a list (unless you explicitly cancel it with any value that is not from the list). So let's rewrite your function:

import collections
from typing import Dictionary, Iterable, List

def group_scaffold_names_by_prefix(names: Iterable(str)) -> Dictionary(str, List(str)):
    """ Given a list of scaffold names, return a dictionary that
        groups them together by their prefix.
    """
    groups = collections.defaultdict(list)

    for name in names:
        groups(extract_key(name)).append(name)

    return groups