Add ingest script to link GISAID records #211
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Links records downloaded from GISAID EpiFlu to output NDJSON that can be processed in a `augur curate` pipeline. Each record represents a single GISAID record with metadata and 10 segment sequences. From what I've seen, the "HE" and "P3" segments are empty but they are kept for a complete representation of the downloaded data.
There was an unexpected number of GISAID records that could not link to their segment sequences in my testing. Turns out the metadata can still have a segment accession even though the sequence itself has been removed from GISAID. This commit changes to output warnings per record rather than per segment sequence so that it's easier to read through the logs.
Fail loudly to guard against potential data issues: 1. If not all segment columns are not present, then GISAID might have changed the format of the Excel file and the expected `SEGMENTS` or `SEGMENT_COLUMNS` need to be updated. 2. If all records are missing segment accessions, then GISAID might have changed the format of the segment ids and the `SEGMENT_ACCESSION_PATTERN` needs to be updated. 3. If all records are missing segment sequences, then the GISAID Excel file and FASTA file might be from different downloads and therefore do not contain matching records.
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Running on a fresh download from GISAID.
python3 ./ingest/scripts/link-gisaid-metadata-and-fasta.py \
--metadata data/gisaid_epiflu_isolates.xls \
--sequences data/gisaid_epiflu_sequence.fasta \
> data/linked-gisaid.ndjson \
2> data/link-warnings.txt |
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Description of proposed changes
Links records downloaded from GISAID EpiFlu to output NDJSON that can be processed in a
augur curatepipeline. Each record represents a single GISAID record with metadata and 10 segment sequences. From what I've seen, the "HE" and "P3" segments are empty but they are kept for a complete representation of the downloaded data.Related issue(s)
Related to nextstrain/fauna#162
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