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Allows for CDS (as well as gene) features to generate a new gene reference #55

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j23414 merged 2 commits into from
Mar 12, 2024
Merged

Allows for CDS (as well as gene) features to generate a new gene reference #55

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Allows for CDS (as well as gene) features to generate a new gene refe…
j23414 Mar 8, 2024
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newreference: If gene is given but not found in genbank, error out
j23414 Mar 8, 2024
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11 changes: 10 additions & 1 deletion scripts/newreference.py
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Original file line number Diff line number Diff line change
Expand Up @@ -3,18 +3,27 @@
from Bio.SeqFeature import SeqFeature, FeatureLocation, Seq
import shutil
import argparse
import sys

def new_reference(referencefile, outgenbank, outfasta, gene):
ref = SeqIO.read(referencefile, "genbank")
startofgene = None
endofgene = None
for feature in ref.features:
if feature.type == 'source':
ref_source_feature = feature
if feature.type =='gene':
if feature.type =='gene' or feature.type == 'CDS':
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@jameshadfield jameshadfield Mar 8, 2024

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Ideally we'd use a centralised GenBank parser, such as augur.utils.load_features. It seem like our parser only considers CDS feature types at the moment, but that could be easily extended.

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@j23414 j23414 Mar 8, 2024

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Ohh, I'm open to using augur.utils.load_features. Ah, is there an example script that can be easily referenced?

For extending to "gene feature types" is this basically adding a duplicate code block like the following?

if feat.type=='gene':
    # ... copy internal code from "if feat.type=='CDS'"

I assume if both a "gene" and a "CDS" feature are named "E", one won't overwrite the nucleotide coordinates of the other (although hopefully they match)?

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@jameshadfield jameshadfield Mar 10, 2024

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Thanks for nextstrain/augur#1435! Upon review, and in order to not hold up progress here (and measles), I'd suggest using the code as it stands and then we can move to using a util function once we're happy with the changes there.

a = list(feature.qualifiers.items())[0][-1][0]
if a == gene:
startofgene = int(list(feature.location)[0])
endofgene = int(list(feature.location)[-1])+1

# If user provides a --gene 'some name' is not found, print a warning and use the entire genome.
# Otherwise do not print a warning.
if(gene is not None and startofgene is None and endofgene is None):
print(f"ERROR: No '{gene}' was found under 'gene' or 'CDS' features in the GenBank file.", file=sys.stderr)
sys.exit(1)

record = ref[startofgene:endofgene]
source_feature = SeqFeature(FeatureLocation(start=0, end=len(record)), type='source',
qualifiers=ref_source_feature.qualifiers)
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