Mercurial > repos > iuc > hyphy_bgm

comparison scripts/annotator.bf @ 23:ede53272264e draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
author iuc
date Tue, 20 Apr 2021 10:33:00 +0000
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22:373afb209788 23:ede53272264e
1 LoadFunctionLibrary ("libv3/tasks/trees.bf");
2 LoadFunctionLibrary ("libv3/tasks/alignments.bf");
3 LoadFunctionLibrary ("libv3/convenience/regexp.bf");
4 LoadFunctionLibrary ("libv3/IOFunctions.bf");
5
6 tags = {
7 "^Node" : "Internal"
8 };
9
10
11
12
13 tree = trees.LoadAnnotatedTopology (TRUE);
14 ts = tree[^"terms.trees.newick_with_lengths"];
15 root_node = io.PromptUserForString ("Root on this node");
16
17
18
19 Topology T = ts;
20 ts = RerootTree (T, root_node);
21 ACCEPT_ROOTED_TREES = FALSE;
22 Topology T = ts;
23 ACCEPT_ROOTED_TREES = TRUE;
24 Topology TR = ts;
25
26
27 NORMALIZE_SEQUENCE_NAMES = FALSE;
28 SetDialogPrompt ("File with the sequences to label as the in-clade");
29 DataSet query = ReadDataFile (PROMPT_FOR_FILE);
30 GetString (seqNames,query,-1);
31
32 label = io.PromptUserForString ("Use this label");
33
34
35 for (s;in;seqNames) {
36 tags [s && 6] = label;
37 }
38
39 reg_exp = Rows (tags);
40
41
42 node_labels = {};
43 for (_regexp_, _leaves_; in; regexp.PartitionByRegularExpressions (BranchName (T,-1), reg_exp)) {
44 tag = tags[_regexp_];
45
46 if (tag != "Internal") {
47
48 if (Abs (tag) == 0) {
49 tag = "Reference";
50 }
51
52 for (l; in; _leaves_) {
53 node_labels[l] = tag;
54 }
55 }
56 }
57
58 node_labelsR = {};
59 for (_regexp_, _leaves_; in; regexp.PartitionByRegularExpressions (BranchName (TR,-1), reg_exp)) {
60 tag = tags[_regexp_];
61
62 if (tag != "Internal") {
63
64 if (Abs (tag) == 0) {
65 tag = "Reference";
66 }
67
68 for (l; in; _leaves_) {
69 node_labelsR[l] = tag;
70 }
71 }
72 }
73
74
75 leaf_labels = node_labels;
76 node_labelsF = node_labels;
77 node_labels * ((trees.ParsimonyLabel ("T", node_labels))["labels"]);
78 node_labelsR * ((trees.ParsimonyLabel ("T", node_labelsR))["labels"]);
79 node_labelsF * ((trees.ParsimonyLabel ("T", node_labelsF))["labels"]);
80
81 output_to = io.PromptUserForString ("Write output to this prefix");
82
83 fprintf (output_to + "labels.json", CLEAR_FILE, leaf_labels);
84 fprintf (output_to + "int.nwk", CLEAR_FILE, tree.Annotate ("T", "relabel_and_annotate", "{}", FALSE));
85 fprintf (output_to + "clade.nwk", CLEAR_FILE, tree.Annotate ("TR", "relabel_and_annotate_full", "{}", FALSE));
86 fprintf (output_to + "full.nwk", CLEAR_FILE, tree.Annotate ("T", "relabel_and_annotate_full", "{}", FALSE));
87
88 function relabel_and_annotate (node_name) {
89 _label = "";
90 if (node_labels / node_name && leaf_labels / node_name == FALSE) {
91 _label = "{" + node_labels[node_name] + "}";
92 }
93 return node_name + _label;
94 }
95
96 function relabel_and_annotate_full (node_name) {
97 _label = "";
98 if (node_labelsR / node_name) {
99 _label = "{" + node_labelsR[node_name] + "}";
100 }
101 return node_name + _label;
102 }