Fixed --knownFunction function

Illumina · May 15, 2020 · 064a0fd · 064a0fd
1 parent e1a29fa
commit 064a0fd
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Showing 2 changed files with 33 additions and 27 deletions.
diff --git a/caller/construct_star_table.py b/caller/construct_star_table.py
@@ -183,33 +183,37 @@ def get_hap_table(hap_table):
     dhap_exon9_x2 = {}
     for star1 in EXON9GC_ALLELES:
         for star2 in EXON9GC_ALLELES:
-            for star3 in dstar:
-                for star4 in dstar:
-                    variant_list = sorted(
-                        dstar[star1].split("_")
-                        + dstar[star2].split("_")
-                        + dstar[star3].split("_")
-                        + dstar[star4].split("_")
-                    )
-                    star_set = "_".join(sorted([star1, star2, star3, star4]))
-                    make_hap_dic(variant_list, star_set, dhap_exon9_x2)
-
-    # exon9hybx3. limit the search to EXON9GC_ALLELES
-    dhap_exon9_x3 = {}
-    for star1 in EXON9GC_ALLELES:
-        for star2 in EXON9GC_ALLELES:
-            for star3 in EXON9GC_ALLELES:
-                for star4 in dstar:
-                    for star5 in dstar:
+            if star1 in dstar and star2 in dstar:
+                for star3 in dstar:
+                    for star4 in dstar:
                         variant_list = sorted(
                             dstar[star1].split("_")
                             + dstar[star2].split("_")
                             + dstar[star3].split("_")
                             + dstar[star4].split("_")
-                            + dstar[star5].split("_")
                         )
-                        star_set = "_".join(sorted([star1, star2, star3, star4, star5]))
-                        make_hap_dic(variant_list, star_set, dhap_exon9_x3)
+                        star_set = "_".join(sorted([star1, star2, star3, star4]))
+                        make_hap_dic(variant_list, star_set, dhap_exon9_x2)
+
+    # exon9hybx3. limit the search to EXON9GC_ALLELES
+    dhap_exon9_x3 = {}
+    for star1 in EXON9GC_ALLELES:
+        for star2 in EXON9GC_ALLELES:
+            for star3 in EXON9GC_ALLELES:
+                if star1 in dstar and star2 in dstar and star3 in dstar:
+                    for star4 in dstar:
+                        for star5 in dstar:
+                            variant_list = sorted(
+                                dstar[star1].split("_")
+                                + dstar[star2].split("_")
+                                + dstar[star3].split("_")
+                                + dstar[star4].split("_")
+                                + dstar[star5].split("_")
+                            )
+                            star_set = "_".join(
+                                sorted([star1, star2, star3, star4, star5])
+                            )
+                            make_hap_dic(variant_list, star_set, dhap_exon9_x3)
 
     # exon9hybx4. limit the search to *10 and *36
     dhap_exon9_x4 = {}

diff --git a/star_caller.py b/star_caller.py
@@ -246,12 +246,14 @@ def d6_star_caller(
     ref_read, long_ins_read, short_ins_read = get_allele_counts_42128936(
         bamfile, call_parameters.genome
     )
-    long_ins_index = var_list.index("g.42128936-42128937insGGGGCGAAAGGGGCGAAA")
-    short_ins_index = var_list.index("g.42128936-42128937insGGGGCGAAA")
-    var_alt[long_ins_index] = long_ins_read
-    var_ref[long_ins_index] = short_ins_read + ref_read
-    var_alt[short_ins_index] = short_ins_read
-    var_ref[short_ins_index] = long_ins_read + ref_read
+    if "g.42128936-42128937insGGGGCGAAAGGGGCGAAA" in var_list:
+        long_ins_index = var_list.index("g.42128936-42128937insGGGGCGAAAGGGGCGAAA")
+        var_alt[long_ins_index] = long_ins_read
+        var_ref[long_ins_index] = short_ins_read + ref_read
+    if "g.42128936-42128937insGGGGCGAAA" in var_list:
+        short_ins_index = var_list.index("g.42128936-42128937insGGGGCGAAA")
+        var_alt[short_ins_index] = short_ins_read
+        var_ref[short_ins_index] = long_ins_read + ref_read
     # Variants in homology regions. Get read counts at both D6/D7 positions.
     var_homo_db = call_parameters.var_homo_db
     var_homo_alt, var_homo_ref = get_supporting_reads(