Mercurial > repos > iuc > hyphy_prime
diff scripts/annotator.bf @ 15:296f6bc03fa6 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
author | iuc |
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date | Tue, 20 Apr 2021 10:30:38 +0000 (2021-04-20) |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/scripts/annotator.bf Tue Apr 20 10:30:38 2021 +0000 @@ -0,0 +1,102 @@ +LoadFunctionLibrary ("libv3/tasks/trees.bf"); +LoadFunctionLibrary ("libv3/tasks/alignments.bf"); +LoadFunctionLibrary ("libv3/convenience/regexp.bf"); +LoadFunctionLibrary ("libv3/IOFunctions.bf"); + +tags = { + "^Node" : "Internal" +}; + + + + +tree = trees.LoadAnnotatedTopology (TRUE); +ts = tree[^"terms.trees.newick_with_lengths"]; +root_node = io.PromptUserForString ("Root on this node"); + + + +Topology T = ts; +ts = RerootTree (T, root_node); +ACCEPT_ROOTED_TREES = FALSE; +Topology T = ts; +ACCEPT_ROOTED_TREES = TRUE; +Topology TR = ts; + + +NORMALIZE_SEQUENCE_NAMES = FALSE; +SetDialogPrompt ("File with the sequences to label as the in-clade"); +DataSet query = ReadDataFile (PROMPT_FOR_FILE); +GetString (seqNames,query,-1); + +label = io.PromptUserForString ("Use this label"); + + +for (s;in;seqNames) { + tags [s && 6] = label; +} + +reg_exp = Rows (tags); + + +node_labels = {}; +for (_regexp_, _leaves_; in; regexp.PartitionByRegularExpressions (BranchName (T,-1), reg_exp)) { + tag = tags[_regexp_]; + + if (tag != "Internal") { + + if (Abs (tag) == 0) { + tag = "Reference"; + } + + for (l; in; _leaves_) { + node_labels[l] = tag; + } + } +} + +node_labelsR = {}; +for (_regexp_, _leaves_; in; regexp.PartitionByRegularExpressions (BranchName (TR,-1), reg_exp)) { + tag = tags[_regexp_]; + + if (tag != "Internal") { + + if (Abs (tag) == 0) { + tag = "Reference"; + } + + for (l; in; _leaves_) { + node_labelsR[l] = tag; + } + } +} + + +leaf_labels = node_labels; +node_labelsF = node_labels; +node_labels * ((trees.ParsimonyLabel ("T", node_labels))["labels"]); +node_labelsR * ((trees.ParsimonyLabel ("T", node_labelsR))["labels"]); +node_labelsF * ((trees.ParsimonyLabel ("T", node_labelsF))["labels"]); + +output_to = io.PromptUserForString ("Write output to this prefix"); + +fprintf (output_to + "labels.json", CLEAR_FILE, leaf_labels); +fprintf (output_to + "int.nwk", CLEAR_FILE, tree.Annotate ("T", "relabel_and_annotate", "{}", FALSE)); +fprintf (output_to + "clade.nwk", CLEAR_FILE, tree.Annotate ("TR", "relabel_and_annotate_full", "{}", FALSE)); +fprintf (output_to + "full.nwk", CLEAR_FILE, tree.Annotate ("T", "relabel_and_annotate_full", "{}", FALSE)); + +function relabel_and_annotate (node_name) { + _label = ""; + if (node_labels / node_name && leaf_labels / node_name == FALSE) { + _label = "{" + node_labels[node_name] + "}"; + } + return node_name + _label; +} + +function relabel_and_annotate_full (node_name) { + _label = ""; + if (node_labelsR / node_name) { + _label = "{" + node_labelsR[node_name] + "}"; + } + return node_name + _label; +}