--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/scripts/strike-ambigs.bf	Tue Apr 20 10:32:25 2021 +0000
@@ -0,0 +1,83 @@
+RequireVersion ("2.5.20");
+
+LoadFunctionLibrary     ("libv3/tasks/alignments.bf");
+LoadFunctionLibrary     ("libv3/tasks/trees.bf");
+LoadFunctionLibrary     ("libv3/UtilityFunctions.bf");
+LoadFunctionLibrary     ("libv3/IOFunctions.bf");
+LoadFunctionLibrary     ("libv3/convenience/math.bf");
+
+
+
+filter.analysis_description = {terms.io.info :
+                            "
+                            Read an alignment of coding sequences and replace any ambiguous codons with ---. Write results to a new file in FASTA format, and report changed sequences to stdout
+                            ",
+                            terms.io.version :          "0.1",
+                            terms.io.reference :        "TBD",
+                            terms.io.authors :          "Sergei L Kosakovsky Pond",
+                            terms.io.contact :          "spond@temple.edu",
+                            terms.io.requirements :     "An MSA"
+                          };
+
+
+io.DisplayAnalysisBanner (filter.analysis_description);
+
+utility.SetEnvVariable ("NORMALIZE_SEQUENCE_NAMES", FALSE);
+
+KeywordArgument ("code",      "Which genetic code should be used", "Universal");
+KeywordArgument ("alignment", "An in-frame codon alignment in one of the formats supported by HyPhy");
+
+filter.in =  alignments.PromptForGeneticCodeAndAlignment ("filter.dataset", "filter.input");
+
+KeywordArgument     ("output", ".fasta for compressed data", None);
+filter.out = io.PromptUserForFilePath(".fasta for filtered data");
+fprintf (filter.out, CLEAR_FILE, KEEP_OPEN);
+
+GetDataInfo (filter.site_patterns, filter.input);
+
+filter.patter2site = {};
+
+
+for (i,j,v; in; filter.site_patterns) {
+    index = i+j;
+    if (filter.patter2site / v == FALSE ) {
+        filter.patter2site [v] = {};
+    }  
+    filter.patter2site [v] + index;
+}
+
+GET_DATA_INFO_RETURNS_ONLY_THE_INDEX = TRUE;
+COUNT_GAPS_IN_FREQUENCIES = FALSE;
+filter.unique_patterns = utility.Array1D (filter.input.site_freqs);
+
+for (seq = 0; seq < filter.input.species; seq += 1) {
+     io.ReportProgressBar ("filter","Processing sequence " + (1+seq));
+     codons = {1, filter.input.sites};
+     codons [0] = "";
+     GetString (seq_name, filter.input, seq);
+     GetDataInfo (seq_chars, filter.input, seq);
+
+     filter.ambigs = 0;
+
+     for (pattern = 0; pattern < filter.unique_patterns; pattern += 1) {
+        GetDataInfo (pattern_info, filter.input, seq, pattern); 
+        if (pattern_info >= 0) {
+            codon_start = (filter.patter2site[pattern])[0] * 3;
+            codon = seq_chars [codon_start][codon_start+2];
+        } else {
+            codon = "---";
+            filter.ambigs += Abs (filter.patter2site [pattern])
+        }
+        for (c; in; filter.patter2site [pattern] ) {
+            codons[c] = codon;
+        }
+     }
+     if (filter.ambigs > 0) {
+        fprintf (stdout, "\nStriking ", filter.ambigs, " codons that are incompletely resolved from " + seq_name + "\n");
+     }
+     fprintf (filter.out,">",seq_name,"\n",Join ("", codons), "\n");
+}
+
+fprintf (filter.out,CLOSE_FILE);
+
+