fix bug in filter_sites

ktmeaton · Apr 27, 2021 · 2d5b754 · 2d5b754
1 parent 5dd79f8
commit 2d5b754
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Showing 3 changed files with 6 additions and 30 deletions.
diff --git a/workflow/rules/phylogeny.smk b/workflow/rules/phylogeny.smk
@@ -117,8 +117,8 @@ rule lsd:
             -s ${{constant_sites}} \
             -o {params.prefix} \
             -f 100 \
-						-l '-1' \
-						-q 0.2 \
+			-l '-1' \
+			-q 0.2 \
             -r k \
             -d {output.dates} \
             -g {output.outgroups} \

diff --git a/workflow/rules/targets.smk b/workflow/rules/targets.smk
@@ -69,27 +69,6 @@ rule snippy_pairwise_local:
 # Locus Coverage
 #------------------------------------------------------------------------------#
 
-locus_coverage_all_input      = results_dir + "/locus_coverage/all/snpden"
-locus_coverage_local_input    = [path.replace("all", "local") for path in locus_coverage_all_input]
-locus_coverage_assembly_input = [path.replace("all", "assembly") for path in locus_coverage_all_input]
-locus_coverage_sra_input      = [path.replace("all", "sra") for path in locus_coverage_all_input]
-
-rule locus_coverage_all:
-    input:
-        locus_coverage_all_input
-
-rule locus_coverage_assembly:
-    input:
-        locus_coverage_assembly_input
-
-rule locus_coverage_sra:
-    input:
-        locus_coverage_sra_input,
-
-rule locus_coverage_local:
-    input:
-        locus_coverage_local_input
-
 locus_coverage_collect_all_input = results_dir + "/locus_coverage_collect/all/locus_coverage.txt"
 locus_coverage_collect_local_input    = locus_coverage_collect_all_input.replace("all", "local")
 locus_coverage_collect_assembly_input    = locus_coverage_collect_all_input.replace("all", "assembly")
@@ -301,7 +280,6 @@ rule iqtree_all:
     input:
         iqtree_all_input
 
-#------------------------------------------------------------------------------#
 #------------------------------------------------------------------------------#
 # Remove outgroups
 iqtree_filter_all_input      = expand(results_dir + "/iqtree/all/{locus_name}/full/filter{missing_data}/filter-sites/snippy-multi.snps.aln",
@@ -311,15 +289,12 @@ rule iqtree_filter_all:
     input:
         iqtree_filter_all_input
 
-
-
-#------------------------------------------------------------------------------#
-iqtree_prune_all_input      = expand(results_dir + "/iqtree/all/{locus_name}/prune/filter{missing_data}/iqtree.nex",
+iqtree_filter_prune_all_input      = expand(results_dir + "/iqtree/all/{locus_name}/prune/filter{missing_data}/filter-sites/snippy-multi.snps.aln",
                                locus_name=config["reference_locus_name"],
                                missing_data = config["snippy_missing_data"])
-rule iqtree_prune_all:
+rule iqtree_filter_prune_all:
     input:
-        iqtree_prune_all_input
+        iqtree_filter_prune_all_input
 
 #------------------------------------------------------------------------------#
  # LSD Dating

diff --git a/workflow/scripts/filter_sites.py b/workflow/scripts/filter_sites.py
@@ -174,6 +174,7 @@
     # Constant site format [0,0,0,x]
     if count_list.count(0) == 3:
         constant_sites += 1
+        site_type = "constant"
     # Biallelic format [0,0,1,x]
     elif count_list.count(0) == 2 and count_list.count(1) >= 1:
         biallelic_singleton_sites += 1