change translation frame type description #58
Conversation
|
addressing the issue - #59 |
|
I understand this is the json output that is desired |
|
= is not a valid json character
|
|
|
|
also dictionaries are universally always written as key: value |
|
right, I recall that now. I guess my issue is not so much with |
| counts[ | ||
| 'Read length was shorter than 3 * peptide k-mer size'] += 1 | ||
| elif len(unique_categories) == 1: | ||
| counts[unique_categories[0]] += 1 |
There was a problem hiding this comment.
How does the index 0 work here?
There was a problem hiding this comment.
if there is only unique category writing incrementing for that
| read_id_category = coding_scores.filter(["read_id", "category"]) | ||
| read_ids = coding_scores.read_id.unique() | ||
|
|
||
| for read_id in read_ids: |
There was a problem hiding this comment.
For this I'd use pandas groupby to do:
for read_id, df in read_id_category.groupby('read_id'):
categories_for_read_id = df
There was a problem hiding this comment.
thanks, changed it
| @@ -95,29 +95,29 @@ def test_get_n_per_coding_classification( | |||
| peptide_bloom_filter_path, | |||
| alphabet, peptide_ksize, jaccard_threshold) | |||
| data = [ | |||
| ['read1', 'All translations shorter than peptide k-mer size + 1'], | |||
| ['read2', 'All translation frames have stop codons'], | |||
| ['read1', 'Translation is shorter than peptide k-mer size + 1'], | |||
There was a problem hiding this comment.
This data should get updated to have multiple results per read, so that we can test that e.g. if any result is coding, it is called coding
No description provided.