Merge pull request #38 from cov-lineages/dev

Dev
cov-lineages · Dec 8, 2021 · d1d63bf · d1d63bf
2 parents c0db12f + 1dfb55a
commit d1d63bf
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Showing 6 changed files with 28 additions and 12 deletions.
diff --git a/scorpio/__init__.py b/scorpio/__init__.py
@@ -1,2 +1,2 @@
 _program = "scorpio"
-__version__ = "0.3.14"
+__version__ = "0.3.15"
diff --git a/scorpio/__main__.py b/scorpio/__main__.py
@@ -113,6 +113,10 @@ def main(sysargs = sys.argv[1:]):
         "--combination", dest="combination", action="store_true",
         help="Combines the mutations for the specified constellations, and outputs a string across them all, with counts per found constellation"
     )
+    subparser_haplotype.add_argument(
+        "--interspersion", dest="interspersion", action="store_true",
+        help="Evaluates an interspersion score"
+    )
     subparser_haplotype.set_defaults(func=scorpio.subcommands.haplotype.run)
 
     # _______________________________  report  __________________________________#

diff --git a/scorpio/scripts/type_constellations.py b/scorpio/scripts/type_constellations.py
@@ -133,9 +133,14 @@ def variant_to_variant_record(l, refseq, features_dict, ignore_fails=False):
     to a dict
     """
     #print("Parsing variant %s" %l)
-    lsplit = l.split(":")
     info = {}
 
+    if "#" in l:
+        l = l.split("#")[0].strip()
+        if l == "":
+            return info
+    lsplit = l.split(":")
+
     if "+" in l:
         m = re.match(r'[aa:]*(?P<cds>\w+):(?P<pos>\d+)\+(?P<alt_allele>[a-zA-Z]+)', l)
         if not m:
@@ -479,7 +484,7 @@ def call_variant_from_fasta(record_seq, var, ins_char="?", oth_char=None, codon=
     elif var["type"] == "aa":
         try:
             query = record_seq.upper()[var["ref_start"] - 1:var["ref_start"] - 1 + 3 * len(var["ref_allele"])]
-            query_allele = query.translate()
+            query_allele = query.translate(gap = "-")
             #query_allele_minus = record_seq.upper()[var["ref_start"] - 2:var["ref_start"] + 1].translate()
             #query_allele_plus = record_seq.upper()[var["ref_start"]:var["ref_start"] + 3].translate()
             #print("Found", query_allele, query_allele_minus, query_allele_plus)
@@ -532,15 +537,15 @@ def call_variant_from_fasta(record_seq, var, ins_char="?", oth_char=None, codon=
         if query_allele == var["ref_allele"]:
             call = 'ref'
             query_allele = 0
+        elif query_allele == "-" * var["length"] or query_allele == "N" * var["length"]:
+            call = 'alt'
+            query_allele = max(int(var["length"] / 3), 1)
         elif "N" in query_allele:
             call = 'ambig'
             if not oth_char:
                 query_allele = "X"
             else:
                 query_allele = "N"
-        elif query_allele == "-" * var["length"]:
-            call = 'alt'
-            query_allele = int(var["length"] / 3)
         else:
             call = 'oth'
             if not oth_char:

diff --git a/scorpio/subcommands/haplotype.py b/scorpio/subcommands/haplotype.py
@@ -15,4 +15,5 @@ def run(options):
                         options.append_genotypes,
                         options.mutations,
                         options.dry_run,
-                        options.combination)
+                        options.combination,
+                        options.interspersion)
diff --git a/scorpio/tests/data/type_constellations/lineage_X.json b/scorpio/tests/data/type_constellations/lineage_X.json
@@ -20,7 +20,7 @@
 		"s:Y144-",
 		"s:E484K",
 		"s:N501Y",
-		"s:A570D",
+		"s:A570D # spike ",
 		"s:P681H",
 		"s:T716I",
 		"s:S982A",
@@ -29,11 +29,12 @@
 		"8:R52I",
 		"8:Y73C",
 		"N:D3L",
-		"N:S235F"
+		"N:S235F",
+                "#s:T777I"
 	],
 	"rules": {
 		"min_alt": 4,
 		"max_ref": 6,
 		"s:E484K": "alt"
 	}
-}
+}
diff --git a/scorpio/tests/type_constellations_test.py b/scorpio/tests/type_constellations_test.py
@@ -217,8 +217,13 @@ def test_call_variant_from_fasta():
 
     for var in variants:
         call, query_allele = call_variant_from_fasta(Seq(ambig_string), var)
-        assert call == "ambig"
-        assert query_allele in ["X", "N", "NN", "--"]
+        print(var, call, query_allele)
+        if var["type"] == "del":
+            assert call == "alt" or call == "ambig"
+            assert query_allele in [2, "X"]
+        else:
+            assert call == "ambig" or call == "alt"
+            assert query_allele in ["X", "N", "NN", "--"]
 
     for var in variants:
         call, query_allele = call_variant_from_fasta(Seq(oth_string), var, oth_char="X")