pgx-main from prod added

pgx-main/stellar_parser.py

@@ -0,0 +1,51 @@
+# Generate a PharmCAT outside call file from a StellarPGx allele file
+from argparse import ArgumentParser
+from pathlib import Path
+import pandas as pd
+import shutil
+
+
+def parse_file(infile):
+    """
+    Generate a PharmCAT outside call file from a StellarPGx allele file
+    (also save input file to data/)
+
+    Args:
+        infile (str): StellarPGx allele file
+    """
+    assert infile.endswith(".alleles")
+    gene = infile.split("_")[-1][:-8].upper()
+    infile = Path(infile)
+    assert infile.exists()
+
+    stem =  infile.stem.replace(".deduped", "")
+
+    shutil.copy(infile, "data/" + stem + ".alleles")
+    outfile = "data/" + stem + ".tsv"
+
+    with open(infile, "r") as f:
+        lines = f.read().split("\n")
+    result = ""
+    likely = ""
+    for i, line in enumerate(lines):
+        if line.strip() == "Result:":
+            result = lines[i+1]
+        elif line.strip() == "Likely background alleles:":
+            likely = lines[i+1]
+    if result.startswith("Possible"):
+        diplotype = likely
+    else:
+        diplotype = result
+    pd.DataFrame([[gene, diplotype]]).to_csv(outfile, sep="\t", index=False, header=False)
+
+
+
+def main():
+    parser = ArgumentParser(description="StellarPGx Output Parser")
+    parser.add_argument('input_file', type=str, help="StellarPGx allele file")
+    args = parser.parse_args()
+    parse_file(args.input_file)
+
+
+if __name__ == '__main__':
+    main()