Nechaeva #1
Open
Nechaeva #1
Conversation
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Comment on lines
+15
to
+16
| if (set(seq).issubset(DNA_ALPHABET)) or (set(seq).issubset(RNA_ALPHABET)): | ||
| if ('u' in seq) or ('U' in seq): |
| return sum(quality_phred_33) / len(quality_phred_33) | ||
|
|
||
|
|
||
| def create_report_about_filt(seqs: dict[str, tuple[str, str]], filter_seq: dict[str, tuple[str, str]]) -> str: |
There was a problem hiding this comment.
filt? 0_0
create_filtration_report можно, например
| :return: int | ||
| """ | ||
| sequence_upper = sequence.upper() | ||
| molecular_weight = sum(AMINO_ACID_WEIGHTS.get(aa, 0) for aa in sequence_upper) |
Comment on lines
+100
to
+110
| if percent: | ||
| result_dict = {"Percentage of positively charged amino acids": | ||
| (round((amount_positive * 100) / len(amino_seq))), | ||
| "Percentage of neutrally charged amino acids": | ||
| (round((amount_neutral * 100) / len(amino_seq))), | ||
| "Percentage of negatively charged amino acids": | ||
| (round((amount_negative * 100) / len(amino_seq)))} | ||
| else: | ||
| result_dict = {"Number of positively charged amino acids": amount_positive, | ||
| "Number of neutrally charged amino acids": amount_neutral, | ||
| "Number of negatively charged amino acids": amount_negative} |
There was a problem hiding this comment.
Не оч хорошо, что возвращается словарь с разными ключами. Ты же скорее всего эту функцию будешь вызывать не только для отображения. Соответственно, в другой функции тебе нужно будет доставать значение по ключу
Comment on lines
+135
to
+142
| if percent: | ||
| result_dict = {'Percentage of hydrophilic amino acids': | ||
| (round((amount_hydrophilic * 100) / len(amino_seq), 2)), | ||
| 'Percentage of hydrophobic amino acids': | ||
| (round((amount_hydrophobic * 100) / len(amino_seq), 2))} | ||
| else: | ||
| result_dict = {'Number of hydrophilic amino acids': amount_hydrophilic, | ||
| 'Number of hydrophobic amino acids': amount_hydrophobic} |
There was a problem hiding this comment.
Та же история и тут, что ключи различаются
Comment on lines
+2
to
+4
| import additional_modules.for_filter_read as ffr | ||
| import additional_modules.dna_rna_tools as drt | ||
| import additional_modules.run_aminoacid_seq as amino |
|
|
||
| filter_seqs = {} | ||
|
|
||
| if type(gc_bounds) != tuple: |
|
|
||
| if type(gc_bounds) != tuple: | ||
| gc_bounds = (0, gc_bounds) | ||
| if type(length_bounds) != tuple: |
Comment on lines
+98
to
+100
| if gc_bounds[0] <= ffr.determine_gc_content(read) <= gc_bounds[1]: | ||
| if length_bounds[0] <= ffr.determine_lenght(read) <= length_bounds[1]: | ||
| if ffr.determine_quality(quality) > quality_threshold: |
There was a problem hiding this comment.
Это все можно было бы сделать в одном ифе через and ))
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
2 participants
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
No description provided.