Completed gene finder #1
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SeunginLyu
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SeunginLyu
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It looks really good in general! I like your clean syntax practices and the code is really well documented with appropriate docstings. I added a few comments that are mostly stylistic guides.
| from load import load_seq | ||
| dna = load_seq("./data/X73525.fa") | ||
| import doctest | ||
| from pickle import dump, load |
| import random | ||
| from amino_acids import aa, codons, aa_table # you may find these useful | ||
| from load import load_seq | ||
| dna = load_seq("./data/X73525.fa") |
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you usually want to separate any function calls from these import statements. It would make more sense to put it under if name == "main":
| elif nucleotide == 'T': | ||
| return 'A' | ||
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| #doctest.run_docstring_examples(get_complement, globals(), verbose=True) |
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please remove comments in your final upload
| I added two more doctests because each complementary nucleotide is in | ||
| its own if/else if branch. If one branch doesn't work and there is no | ||
| doctest for that branch, the mistake will not be caught. In fact, I | ||
| found out that I spelled nucleotide wrong in the G branch. |
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great practice that you are adding your own tests
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| return comp_str | ||
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| #doctest.run_docstring_examples(get_reverse_complement, globals(), verbose=True) |
| for nuc in range(0, len(reversed_dna)): | ||
| comp_nuc = get_complement(reversed_dna[nuc]) | ||
| comp_list.append(comp_nuc) | ||
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if you wanna get fancy with just one line of code :
return ''.join([get_complement(reversed_dna[nuc]) for nuc in dna[::-1]])
| I added two more doctests: one in which the frame stop codon is TAA and | ||
| another in which there is no frame stop codon. This way, all the | ||
| branches are tested for error. | ||
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| return dna | ||
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| #doctest.run_docstring_examples(rest_of_ORF, globals(), verbose=True) |
| frame1 = find_all_ORFs_oneframe(dna) | ||
| frame2 = find_all_ORFs_oneframe(dna[1:]) | ||
| frame3 = find_all_ORFs_oneframe(dna[2:]) | ||
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you could also use a for loop here
[find_all_ORFs_oneframe(dna[i:]) for i in range 3]
| humongest = longest_ORF(dna_shuffles[i+1]) | ||
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| return len(humongest) | ||
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it would be more memory efficient to just save the max_length of longest_ORF than to save the actual longest_ORF
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I finally understood the purpose of if name == "main": and moved the gene_finder(dna) portion under that branch.