将文本文件作为字典读入程序

Question

Using Python 3.

I have to write a function that take one argument (a string), and must return a dictionary from a txt-file that contains names of the sequences (keys) and the sequences (values). Both keys and values must be strings.

The text-file:

Read1 GGCTCCCCACGGGGTACCCATAACTTGACAGTAGATCTCGTCCAGACCCCTAGC
Read2 CTTTACCCGGAAGAGCGGGACGCTGCCCTGCGCGATTCCAGGCTCCCCACGGG
Read4 TGCGAGGGAAGTGAAGTATTTGACCCTTTACCCGGAAGAGCG
Read3 GTCTTCAGTAGAAAATTGTTTTTTTCTTCCAAGAGGTCGGAGTCGTGAACACATCAGT
Read5 CGATTCCAGGCTCCCCACGGGGTACCCATAACTTGACAGTAGATCTC
Read6 TGACAGTAGATCTCGTCCAGACCCCTAGCTGGTACGTCTTCAGTAGAAAATTGTTTTTTTCTTCCAAGAGGTCGGAGT

I've come this far, but I think I am missing something and I don't know if what my work here is correct. I've marked the lines (with #) where I'm in doubt whether it is correct or not.

def read_data(file_name):
    input_file=open(sequencing_reads.txt)
    #sequence_dict={}
    for line in input_file:
        #x=line.split(",")
    #return sequence_dict
    input_file.close()

I know it must return the dictionary with the following content:

{'Read1': 'GGCTCCCCACGGGGTACCCATAACTTGACAGTAGATCTCGTCCAGACCCCTAGC',
 'Read2': 'CTTTACCCGGAAGAGCGGGACGCTGCCCTGCGCGATTCCAGGCTCCCCACGGG',
 'Read4': 'TGCGAGGGAAGTGAAGTATTTGACCCTTTACCCGGAAGAGCG',
 'Read3': 'GTCTTCAGTAGAAAATTGTTTTTTTCTTCCAAGAGGTCGGAGTCGTGAACACATCAGT',
 'Read5': 'CGATTCCAGGCTCCCCACGGGGTACCCATAACTTGACAGTAGATCTC',
 'Read6': 'TGACAGTAGATCTCGTCCAGACCCCTAGCTGGTACGTCTTCAGTAGAAAATTGTTTTTTTCTTCCAAGAGGTCGGAGT'}

Can you help me fill out the gaps?

EDIT: I need to keep it simple so please no imports of packages and smart tricks :-)

EDIT 2:

I've tried this too:

with open('sequencing_reads.txt', 'r') as document:
    answer = {}
    for line in document:
        line = line.split()
        if not line:  
            continue
        answer[line[0]] = line[1:]
print(answer)

The output is:

{'Read1': ['GGCTCCCCACGGGGTACCCATAACTTGACAGTAGATCTCGTCCAGACCCCTAGC'], 'Read2': ['CTTTACCCGGAAGAGCGGGACGCTGCCCTGCGCGATTCCAGGCTCCCCACGGG'], 'Read4': ['TGCGAGGGAAGTGAAGTATTTGACCCTTTACCCGGAAGAGCG'], 'Read3': ['GTCTTCAGTAGAAAATTGTTTTTTTCTTCCAAGAGGTCGGAGTCGTGAACACATCAGT'], 'Read5': ['CGATTCCAGGCTCCCCACGGGGTACCCATAACTTGACAGTAGATCTC'], 'Read6': ['TGACAGTAGATCTCGTCCAGACCCCTAGCTGGTACGTCTTCAGTAGAAAATTGTTTTTTTCTTCCAAGAGGTCGGAGT']}

How do I get rid of the "[ ]" around my sequences?

EDIT4:

def read_data(file_name):
    with open("sequencing_reads.txt", "r") as document:
        answer = {}
        for line in document:
            line = line.split()
            if not line:
                continue
                answer[line[0]] = line[1:]
                final_answer = {a:b[0] for a, b in answer.items()}
final_answer = read_data("sequencing_reads.txt")
print(final_answer)

prints:

None

Answer 1

You can try this:

import re
def read_data(file_name):
   data = open(file_name).read()
   keys = [filter(lambda x:bool(x), i)[0][1:-1] for i in re.findall("{(.*?)\:|(?<=,\n\s)(.*?)\:", data)]
   values = [filter(lambda x:bool(x), i)[0][1:-1] for i in re.findall('(?<=:\s)(.*?)(?=,\n)|(?<=\s)(.*?)(?=})', data)]
   final_data = {a:b for a, b in zip(keys, values)}
   return final_data

Output:

{'Read1': 'GGCTCCCCACGGGGTACCCATAACTTGACAGTAGATCTCGTCCAGACCCCTAGC', 'Read3': 'GTCTTCAGTAGAAAATTGTTTTTTTCTTCCAAGAGGTCGGAGTCGTGAACACATCAGT', 'Read2': 'CTTTACCCGGAAGAGCGGGACGCTGCCCTGCGCGATTCCAGGCTCCCCACGGG', 'Read5': 'CGATTCCAGGCTCCCCACGGGGTACCCATAACTTGACAGTAGATCTC', 'Read4': 'TGCGAGGGAAGTGAAGTATTTGACCCTTTACCCGGAAGAGCG', 'Read6': "'Read6': 'TGACAGTAGATCTCGTCCAGACCCCTAGCTGGTACGTCTTCAGTAGAAAATTGTTTTTTTCTTCCAAGAGGTCGGAGT"}

Edit:

import ast 
def read_data(file_name):
   final_data = ast.literal_eval(open(file_name).read())
   return final_data

Edit 1: Regarding the removal of the brackets, just access the value by indexing:

final_answer = {a:b[0] for a, b in answer.items()}
print(final_answer)

If you are having issues printing the value returned from read_data , you can try this:

answer = read_data("the_file.txt")
print(answer)

Edit 3:

def read_data(file_name):
   with open(file_name, "r") as document:
      answer = {}
      for line in document:
         line = line.split()
         if line:
            answer[line[0]] = line[1:]
      return {a:b[0] for a, b in answer.items()}

print(read_data("sequencing_reads.txt"))

Answer 2

Your file "sequencing_reads.txt" is in json format. You can use the json module in the python standard library to load your content into a dictionary quite easily.

import json

with open("sequencing_reads.txt") as f:
    sequence_dict = json.load(f)

Answer 3

Firstly, if your file is in json format and in separate lines, you should read it into a single line, maybe like this:

def read_data(file_name):
    lines = open(file_name).readlines()
    merged_line = " ".join([line.strip() for line in lines])

Secondly, The json.loads requires double quotes for the string(eg: {"a":"a"}). If you are using single quote(as in your example), there may be errors. So you can do like this:

# 1,use json.loads, but replace first
import json
merged_line = merged_line.replace("'", '"')
data = json.loads(merged_line)

# 2,use ast
import ast
data = ast.literal_eval(merged_line)