Searches through given peptide sequences to generate unique fragments and their counts.

uniqe_fragments.py

#  Copyright (c) 2020
#  Author: Rohit Suratekar
#
#  This program finds unique peptides and their frequency in given peptide
#  fragment data.
#
# IMPORTANT NOTE:
# This assumes there are NO Gaps in your peptide sequence
# Every peptide sequence has to be sequential without any gap.
# Your INPUT peptide data.
# Remember in python range(1,4) => 1,2,3
peptides = [
    range(1, 11),
    range(6, 14),
    range(9, 12),
    range(11, 17)
]


# Use "count_fragments" function to get unique fragments and their counts
def get_points(data):
    """
    Converts peptides into their range
    """
    return [(min(x), max(x)) for x in data]


def get_first_fragment(data):
    """
    Generates fragment based on given range
    """
    all_starts = [x[0] for x in data]
    all_ends = [x[1] for x in data]
    start = min(all_starts)  # This is easy
    # First check with other start points
    end = [x for x in all_starts if x > start]
    if len(end) == 0:
        end = start - 1
    else:
        end = min(end) - 1
    if end < start:
        # All starts with same
        # So Now check with all end points
        end_extra = [x for x in all_ends if x > end]
        if len(end_extra) != 0:
            end = min(end_extra)
        else:
            end = start

    return start, end


def remove_fragment(data, fragment):
    """
    Removes Fragment from the point range
    """
    new_data = []
    for d in data:
        start, end = d
        if d[0] <= fragment[1] < d[1]:
            start = fragment[1] + 1
            if start > end:
                start = fragment[1]

        if (start, end) != fragment:
            new_data.append((start, end))
    return new_data


def extract_fragments(data):
    """
    Extracts all fragment from given range
    """
    all_fragments = []
    points = get_points(data)
    while len(points) != 0:
        fg = get_first_fragment(points)
        points = remove_fragment(points, fg)
        all_fragments.append(fg)
    return all_fragments


def count_fragments(data):
    """
    Counts all fragments
    :param data: Peptide sequence list
    """
    fms = {x: 0 for x in extract_fragments(data)}
    for d in get_points(data):
        for x in fms:
            start, end = x
            if d[0] <= start and d[1] >= end:
                fms[x] += 1
    print("Range ==> Count")
    for x in fms:
        print(f"{x[0]} to {x[1]} ==> {fms[x]}")


# Here is the main function to run
if __name__ == "__main__":
    count_fragments(peptides)