Upload New File with basic functions

# -*- coding: utf-8 -*-

import json

def open_annotation(annotation_file):

    """Open anotation file.

    Parameters

    ----------

    annotation_file : string

        Annotation file name.

    Returns

    -------

    genes : List

        List containing genes.

    """

    # open file

    file = open(annotation_file, 'r')

    data = json.load(file)

    file.close()

    # List of genes

    genes = []

    for geneID in data:

        # get gene data

        gene_dictionary = data[geneID]

        seq_range = gene_dictionary['seq_range']

        seq_type = 'gene'

        orientation = gene_dictionary['orientation']

        gene = Gene(seq_type, seq_range, orientation, geneID)

        genes.append(gene)

    return genes

def open_repeats(repeat_file, orientation):

    """Open repeat data file.

    Parameters

    ----------

    repeat_file : String

        Repeats data file.

    orientation : String

        Repeat sequence orientation, it can be '+' or '-'.

    Returns

    -------

    repeats : List

        List of repeats sequences.

    """

    # Open data file

    file = open(repeat_file, 'r')

    lines = file.readlines()

    file.close()

    # repeats list

    repeats = []

    for index in range(1, len(lines)):

        line = lines[index].split()

        start = int(line[0])

        end = int(line[1])

        repeat = Sequence('repeat', (start, end), orientation)

        repeats.append(repeat)

    return repeats