How to create a dataset using sequence file in python

Question

I have a protein sequence file looks like this:

>102L:A       MNIFEMLRIDEGLRLKIYKDTEGYYTIGIGHLLTKSPSLNAAAKSELDKAIGRNTNGVITKDEAEKLFNQDVDAAVRGILRNAKLKPVYDSLDAVRRAALINMVFQMGETGVAGFTNSLRMLQQKRWDEAAVNLAKSRWYNQTPNRAKRVITTFRTGTWDAYKNL       -------------------------------------------------------------------------------------------------------------------------------------------------------------------XX

The first one is the name of the sequence, the second one is the actual protein sequence, and the first one is the indicator that shows if there is any missing coordinates. In this case, notice that there is two "X" in the end. That means that the last two residue of the sequence witch are "NL" in this case are missing coordinates.

By coding in Python I would like to generate a table which should look like this:

1. name of the sequence
2. total number of missing coordinates (which is the number of X)
3. the range of these missing coordinates (which is the range of the position of those X) 4)the length of the sequence 5)the actual sequence

So the final results should looks like this:

>102L:A 2 163-164 164 MNIFEMLRIDEGLRLKIYKDTEGYYTIGIGHLLTKSPSLNAAAKSELDKAIGRNTNGVITKDEAEKLFNQDVDAAVRGILRNAKLKPVYDSLDAVRRAALINMVFQMGETGVAGFTNSLRMLQQKRWDEAAVNLAKSRWYNQTPNRAKRVITTFRTGTWDAYKNL

And my code looks like this so far:

total_seq = []
with open('sample.txt') as lines:
    for l in lines:
        split_list = l.split()

        # Assign the list number
        header = split_list[0]                                # 1
        seq = split_list[1]                                   # 5
        disorder = split_list[2]

        # count sequence length and total residue of missing coordinates
        sequence_length = len(seq)                            # 4

        for x in disorder:
            counts = 0
            if x == 'X':
                counts = counts + 1

        total_seq.append([header, seq, str(counts)])   # obviously I haven't finish coding 2 & 3

with open('new_sample.txt', 'a') as f:
    for lol in total_seq:
        f.write('\n'.join(lol))

I'm new in python, would anyone help please?

Answer 1

Here's your modified code. It now produces your desired output.

with open("sample.txt") as infile:
    matrix  = [line.split() for line in infile.readlines()]

    header_list  = [row[0] for row in matrix]
    seq_list = [str(row[1]) for row in matrix]
    disorder_list = [str(row[2]) for row in matrix]

f = open('new_sample.txt', 'a')

for i in range(len(header_list)):
    header = header_list[i]
    seq = seq_list[i]
    disorder = disorder_list[i]

    # count sequence length and total residue of missing coordinates
    sequence_length = len(seq)                            

    # get total number of missing coordinates
    num_missing = disorder.count('X')             

    # get the range of these missing coordinates
    first_X_pos = disorder.find('X')
    last_X_pos = disorder.rfind('X')
    range_missing = '-'.join([str(first_X_pos), str(last_X_pos)])

    reformat_seq=" ".join([header, str(num_missing), range_missing, str(sequence_length), seq, '\n'])  
    f.write(reformat_seq)

f.close()

---

Some more tips:

Don't forget about python's string functions. They will solve a lot of your problems automatically. The documentation is very good.

If you searched for how to do just part 2 or just part 3 in your question, you would find the results elsewhere.