Mercurial > repos > iuc > hyphy_cfel
view scripts/annotator.bf @ 9:5b63871000c9 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 4bb2092ac089e709bdc0ec3c3680f47e17be509a"
author | iuc |
---|---|
date | Wed, 30 Mar 2022 00:24:23 +0000 |
parents | 3d4ea0544af1 |
children |
line wrap: on
line source
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; }