Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Update RKI data processing #476

Merged
merged 5 commits into from
Sep 13, 2024
Merged

Update RKI data processing #476

Changes from 1 commit
Commits
Show all changes
5 commits
Select commit Hold shift + click to select a range
a587f18
Update RKI_INDEX_COL since SEQUENCE.ID renamed to igs_id
j23414 Sep 12, 2024
f86c4fa
Update COLUMN_MAP for RKI data
j23414 Sep 12, 2024
2df0af9
Add new RKI date format %Y-%m-%dT%H:%M:%S to expected date_formats
j23414 Sep 12, 2024
7767c76
Parse new RKI JSON blob for pango_lineage
j23414 Sep 12, 2024
e57f3c0
fixup: Parse new RKI JSON blob for pango_lineage
j23414 Sep 13, 2024
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
3 changes: 3 additions & 0 deletions lib/utils/transformpipeline/transforms.py
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,6 +1,7 @@
import csv
import re
import unicodedata
import json
from collections import defaultdict
from typing import Any, Collection, List, MutableMapping, Sequence, Tuple , Dict , Union
import pandas as pd
Expand Down Expand Up @@ -287,6 +288,8 @@ def __init__(self):
def transform_value(self, entry: dict) -> dict:
entry['sequence'] = entry['sequence'].replace('\n', '')
entry['length'] = len(entry['sequence'])
lineage_dict = json.loads(entry['pango_lineage'])
entry['pango_lineage'] = lineage_dict[0]['lineage']
Copy link
Member

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Out of interest, what does entry['pango_lineage'] look like?

Copy link
Contributor Author

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Sure thing! From here, the original format looks like

[{'method': 'PANGOLIN_LATEST', 'classification_version': 'PUSHER-v1.28.1', 'tool_version': '4.3', 'lineage': 'BA.2', '@qc_notes': 'Ambiguous_content:0.02', '@is_designated': False, '@qc_status': 'pass', '@conflict': 0.0, '@note': 'Usher placements: BA.2(1/1)'}]

Or a few examples from the data:

pango_lineages
[{"classification_version": "PUSHER-v1.29", "lineage": "BA.2", "tool_version": "4.3", "method": "PANGOLIN_LATEST", "@is_designated": false, "@qc_status": "pass", "@conflict": 0.0, "@qc_notes": "Ambiguous_content:0.02", "@note": "Usher placements: BA.2(1/1)"}]
[{"classification_version": "PUSHER-v1.29", "lineage": "BA.2.9", "tool_version": "4.3", "method": "PANGOLIN_LATEST", "@is_designated": false, "@qc_status": "pass", "@conflict": 0.0, "@qc_notes": "Ambiguous_content:0.02", "@note": "Usher placements: BA.2.9(1/1)"}]
[{"classification_version": "PUSHER-v1.29", "lineage": "BA.2", "tool_version": "4.3", "method": "PANGOLIN_LATEST", "@is_designated": false, "@qc_status": "pass", "@conflict": 0.0, "@qc_notes": "Ambiguous_content:0.02", "@note": "Usher placements: BA.2(2/2)"}]

which, after the change, get corrected to:

pango_lineages
"BA.2"
"BA.2.9"
"BA.2"

Copy link
Member

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Thanks! My only suggestion would be to do something like

assert len(lineage_dict)==1, f"RKI pango_lineage unexpectedly had more than one entry. Strain: {entry['name']}"
# (not sure if "name" is the correct key to use)

(also, perhaps lineage_dict isn't the best name if it's a list)

Copy link
Contributor Author

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

I might rename lineage_dict to "lineage_json_blob" based on their own description (JSON-Blob).

Instead of erroring out on multiple entries, I would move to looping through the entries to find the one with "method": "PANGOLIN_LATEST". We're not sure if they're setting this up to historical past pangolin lineage assignments, as lineage systems get updated.

Copy link
Contributor Author

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Heh, in the end, I went with your assert statement to at least flag when multiple entries start showing up (e57f3c0). This will help us double-check the purpose of the multiple entries, if they do eventually occur.

I double-checked entry.keys(), and the entry['rki_accession'] is the strain ID.

Copy link

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Hi, I just stumbled upon this issue, and we intend always to use PANGOLIN_LATEST for the latest assignment. So, you can filter the JSON array this way. I am sorry for not being more specific in our README. I will change that in our documentation. Please feel free to write us an email if you have questions igs-developers(at)rki.de .

Copy link
Contributor

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Thanks for chiming in @TheBready!

Tracking in #478


# Normalize all string data to Unicode Normalization Form C, for
# consistent, predictable string comparisons.
Expand Down