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Rely on reference prefix for NCBI protein database selection #22

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merged 2 commits into from
May 2, 2024
Merged

Rely on reference prefix for NCBI protein database selection #22

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caf96f2
Quick fix egquery down (#20)
mihailefter Apr 9, 2024
bf7a0da
Update protein prefixes
mihailefter May 2, 2024
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16 changes: 15 additions & 1 deletion mutalyzer_retriever/sources/ncbi.py
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Original file line number Diff line number Diff line change
Expand Up @@ -190,7 +190,21 @@ def fetch(reference_id, reference_type, size_on=True, timeout=1):

:returns tuple: raw annotations, type ("gff3" or "genbank")
"""
db = _get_database(reference_id)
db = "nuccore"
# https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4702849/
# https://support.nlm.nih.gov/knowledgebase/article/KA-03437/
# https://support.nlm.nih.gov/knowledgebase/article/KA-03434/
# https://support.nlm.nih.gov/knowledgebase/article/KA-03389/
# https://www.ncbi.nlm.nih.gov/books/NBK21091/table/ch18.T.refseq_accession_numbers_and_mole/
if (
reference_id.startswith("AP_")
or reference_id.startswith("NP_")
or reference_id.startswith("WP_")
or reference_id.startswith("XP_")
or reference_id.startswith("YP_")
or reference_id.startswith("ZP_")
):
db = "protein"
if reference_type in [None, "gff3"]:
return fetch_gff3(reference_id, db, timeout), "gff3"
elif reference_type == "fasta":
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