utilities.py

def colored(seq):
    bcolors = {
        'A': '\033[92m',
        'C': '\033[94m',
        'G': '\033[93m',
        'T': '\033[91m',
        'U': '\033[91m',
        'reset': '\033[0;0m'
    }

    tmpStr = ""

    for nuc in seq:
        if nuc in bcolors:
            tmpStr += bcolors[nuc] + nuc
        else:
            tmpStr += bcolors['reset'] + nuc

    return tmpStr + '\033[0;0m'


def read_file(file_path):
    '''Reading a file and returning a list of word line'''
    with open(file_path, 'r') as f:
        return [line.strip('\n') for line in f.readlines()]


def write_file(file_path, seq, mode='w'):
    '''Writing sequence in a file'''
    with open(file_path, mode) as f:
        f.write(seq + '\n')


def read_fasta(file_path):
    '''Reading fasta formatted file and returning into line'''
    with open(file_path, 'r') as f:
        # for storing the contents of the file into a list
        fasta_file = [line.strip('\n') for line in f.readlines()]

    # for storing labels and data
    fasta_dict = {}
    fasta_label = ''

    # for preparing data and taking into dictionary
    for line in fasta_file:
        if '>' in line:
            fasta_label = line
            fasta_dict[fasta_label] = ''
        else:
            fasta_dict[fasta_label] += line
    return fasta_dict