Skip to content

Fix sequence validation to handle NaN values in DRAMP database download #538

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

Merged
jfy133 merged 4 commits into from
Jul 3, 2026
Merged

Fix sequence validation to handle NaN values in DRAMP database download #538

Changes from 2 commits
Commits
Show all changes
4 commits
Select commit Hold shift + click to select a range
aee3dc9
Merge pull request #533 from nf-core/dev
jfy133 Jun 27, 2026
23f3890
Fix sequence validation to handle NaN values in DRAMP database download
hindrek Jul 1, 2026
43edf7b
Add fix details to CHANGELOG.md
hindrek Jul 3, 2026
19e0581
Merge branch 'dev' into fix/dramp-missing-sequences
jfy133 Jul 3, 2026
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
2 changes: 1 addition & 1 deletion bin/ampcombi_download.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -58,7 +58,7 @@ def download_ref_db(database, threads):
valid_sequence_pattern = re.compile("^[ACDEFGHIKLMNPQRSTVWY]+$")
for index, row in db_df.iterrows():
sequence = row['Sequence']
if valid_sequence_pattern.match(sequence):
if pd.notna(sequence) and valid_sequence_pattern.match(sequence):
record = SeqRecord(Seq(sequence), id=str(row['DRAMP_ID']), description="")
records.append(record)
output_file = f'{db}/general_amps_{date}.fasta'
Expand Down
Loading