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Add "--start" and "--end" arguments to newreference.py to allow for creating subgenic trees #58

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Add "--start" and "--end" arguments to newreference.py to allow for creating subgenic trees #58

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22 changes: 20 additions & 2 deletions scripts/newreference.py
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Original file line number Diff line number Diff line change
Expand Up @@ -5,7 +5,7 @@
import argparse
import sys

def new_reference(referencefile, outgenbank, outfasta, gene):
def new_reference(referencefile, outgenbank, outfasta, gene, start, end):
ref = SeqIO.read(referencefile, "genbank")
startofgene = None
endofgene = None
Expand All @@ -25,10 +25,20 @@ def new_reference(referencefile, outgenbank, outfasta, gene):
sys.exit(1)

record = ref[startofgene:endofgene]
# Allows for subgenic regions
if (gene is not None and start is not None and end is not None):
record = record[int(start):int(end)]

source_feature = SeqFeature(FeatureLocation(start=0, end=len(record)), type='source',
qualifiers=ref_source_feature.qualifiers)
record.features.append(source_feature)

# For subgenic regions, adds a CDS feature {gene}_{start}_{end}
if(gene is not None and start is not None and end is not None):
gene = gene + "_" + start + "_" + end
record.features.append(SeqFeature(FeatureLocation(start=0, end=len(record)), type='CDS',
qualifiers={'gene': gene}))

SeqIO.write(record, outgenbank, 'genbank')
SeqIO.write(record, outfasta, "fasta")

Expand All @@ -43,11 +53,19 @@ def new_reference(referencefile, outgenbank, outfasta, gene):
parser.add_argument("--output-fasta", required=True, help="GenBank new reference file")
parser.add_argument("--output-genbank", required=True, help="GenBank new reference file")
parser.add_argument("--gene", help="gene name or genome for entire genome")
parser.add_argument("--start", help="Start 0-based position relative to the gene (requires --gene argument)")
parser.add_argument("--end", help="End 0-based position relative to the gene (requires --gene argument)")
args = parser.parse_args()

if args.gene=='genome':
# Check if start and end are specified here
if (args.start is not None and args.end is not None):
print(f"ERROR: --start '{args.start}' --end '{args.end}' is not supported for full genome.", file=sys.stderr)
sys.exit(1)


shutil.copy(args.reference, args.output_genbank)
SeqIO.write(SeqIO.read(args.reference, 'genbank'), args.output_fasta, 'fasta')
else:
new_reference(args.reference, args.output_genbank, args.output_fasta, args.gene)
new_reference(args.reference, args.output_genbank, args.output_fasta, args.gene, args.start, args.end)