From 92db969e270b830583234938f900730a771a8fae Mon Sep 17 00:00:00 2001
From: Jennifer Chang <jennifer.chang.bioinform@gmail.com>
Date: Tue, 4 Jun 2024 13:07:05 -0700
Subject: [PATCH] Copy newreference script from RSV

https://github.com/nextstrain/rsv/blob/335c7f596c516f832691d70122fec5bfeeb25df8/scripts/newreference.py
---
 phylogenetic/scripts/newreference.py | 53 ++++++++++++++++++++++++++++
 1 file changed, 53 insertions(+)
 create mode 100644 phylogenetic/scripts/newreference.py

diff --git a/phylogenetic/scripts/newreference.py b/phylogenetic/scripts/newreference.py
new file mode 100644
index 0000000..a89c819
--- /dev/null
+++ b/phylogenetic/scripts/newreference.py
@@ -0,0 +1,53 @@
+from Bio import SeqIO
+from Bio.SeqRecord import SeqRecord
+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' or feature.type == 'CDS':
+            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' that is not found, error out as this may indicate that
+    # the gene name is misspelled or the user may be using the wrong GenBank file.
+    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)
+    record.features.append(source_feature)
+
+    SeqIO.write(record, outgenbank, 'genbank')
+    SeqIO.write(record, outfasta, "fasta")
+
+
+
+if __name__ == '__main__':
+    parser = argparse.ArgumentParser(
+        description="make new reference depending on whether the entire genome or only part is to be used for the tree",
+        formatter_class=argparse.ArgumentDefaultsHelpFormatter
+    )
+    parser.add_argument("--reference", required=True, help="GenBank file with reference sequences")
+    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")
+    args = parser.parse_args()
+
+    if args.gene=='genome':
+        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)
+