diff application.py @ 0:6b226c5907a1 draft default tip

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fastg2protlib commit e777bdb1d28b1ffee75cb1a8ad782a50c10a5358"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/application.py	Fri Aug 07 06:17:31 2020 -0400
@@ -0,0 +1,88 @@
+import argparse
+
+import fastg2protlib.fastg2protlib as fg
+
+expasy_rules = [
+    "arg-c",
+    "asp-n",
+    "bnps-skatole",
+    "caspase 1",
+    "caspase 2",
+    "caspase 3",
+    "caspase 4",
+    "caspase 5",
+    "caspase 6",
+    "caspase 7",
+    "caspase 8",
+    "caspase 9",
+    "caspase 10",
+    "chymotrypsin high specificity",
+    "chymotrypsin low specificity",
+    "clostripain",
+    "cnbr",
+    "enterokinase",
+    "factor xa",
+    "formic acid",
+    "glutamyl endopeptidase",
+    "granzyme b",
+    "hydroxylamine",
+    "iodosobenzoic acid",
+    "lysc",
+    "ntcb",
+    "pepsin ph1.3",
+    "pepsin ph2.0",
+    "proline endopeptidase",
+    "proteinase k",
+    "staphylococcal peptidase i",
+    "thermolysin",
+    "thrombin",
+    "trypsin",
+    "trypsin_exception",
+]
+
+
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser(description="Run peptides for fastg")
+    parser.add_argument("fastg", help="Path to Spades formatted FASTG.")
+    parser.add_argument(
+        "-d",
+        "--dbname",
+        default="results.db",
+        help="Name for the results database. Defaults to results.db",
+    )
+    parser.add_argument(
+        "-c",
+        "--cleavage",
+        default="trypsin",
+        help="Cleavage rule from ExPASy cleavage rules. Defaults to trypsin.",
+    )
+    parser.add_argument(
+        "-p",
+        "--min_protein_length",
+        default=55,
+        type=int,
+        help="Minimum protein length in number of amino acids. Defaults to 55.",
+    )
+    parser.add_argument(
+        "-m",
+        "--min_peptide_length",
+        default=8,
+        type=int,
+        help="Minimum peptide length in amino acids. Defaults to eight.",
+    )
+    parser.add_argument(
+        "-l", "--plots", default=True, type=bool, help="Generate diagnostic plots.",
+    )
+
+    args = parser.parse_args()
+
+    print(args)
+
+    fg.peptides_for_fastg(
+        fastg_filename=args.fastg,
+        db_name=args.dbname,
+        cleavage=args.cleavage,
+        min_protein_length=(args.min_protein_length * 3),
+        min_peptide_length=args.min_peptide_length,
+        create_plots=args.plots,
+    )