Move old scripts

scripts_build/dbSnp/convert_to_chr.py

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+#!/usr/bin/env python3
+
+#
+# Convert chromosome IDs in a VCF file from NCBI to human-readable format
+#
+# Mapping file:
+#     Download the mapping file from:
+#       wget "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/001/405/GCF_000001405.40_GRCh38.p14/GCF_000001405.40_GRCh38.p14_assembly_report.txt"
+#     
+#     Then cut the relevant columns:
+#       cut -f 1,7 GCF_000001405.40_GRCh38.p14_assembly_report.txt | grep -v "^#" | tee chr2id.txt
+
+
+# Load the mapping file (assuming it's a TSV or space-separated file)
+mapping_file = "chr2id.txt"
+chrid2name = {}
+with open(mapping_file) as f:
+    for l in f.readlines():
+        chr_name, chr_id = l.strip().split("\t")
+        chrid2name[chr_id] = chr_name
+
+
+# Example: Translating IDs in a VCF file
+vcf_file = "GCF_000001405.38.vcf"
+with open(vcf_file, 'r') as file:
+    for line in file:
+        if not line.startswith("#"):  # Skip header lines
+            columns = line.strip().split('\t')
+            if columns[0] in chrid2name:
+                columns[0] = chrid2name[columns[0]]  # Replace chromosome ID
+            print('\t'.join(columns))  # Print or write to a new file
+        else:
+            print(line.strip())  # Print header lines as is