Mercurial > repos > iuc > hyphy_meme

annotate scripts/annotator.bf @ 23:2f07f5b4e47b 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 10:24:10 +0000
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2f07f5b4e47b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
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diff changeset
1 LoadFunctionLibrary ("libv3/tasks/trees.bf");
2f07f5b4e47b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
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2 LoadFunctionLibrary ("libv3/tasks/alignments.bf");
2f07f5b4e47b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
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3 LoadFunctionLibrary ("libv3/convenience/regexp.bf");
2f07f5b4e47b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
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4 LoadFunctionLibrary ("libv3/IOFunctions.bf");
2f07f5b4e47b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
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2f07f5b4e47b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
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6 tags = {
2f07f5b4e47b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
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7 "^Node" : "Internal"
2f07f5b4e47b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
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8 };
2f07f5b4e47b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
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2f07f5b4e47b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
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2f07f5b4e47b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
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13 tree = trees.LoadAnnotatedTopology (TRUE);
2f07f5b4e47b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
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14 ts = tree[^"terms.trees.newick_with_lengths"];
2f07f5b4e47b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
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15 root_node = io.PromptUserForString ("Root on this node");
2f07f5b4e47b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
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19 Topology T = ts;
2f07f5b4e47b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
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20 ts = RerootTree (T, root_node);
2f07f5b4e47b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
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21 ACCEPT_ROOTED_TREES = FALSE;
2f07f5b4e47b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
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22 Topology T = ts;
2f07f5b4e47b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
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23 ACCEPT_ROOTED_TREES = TRUE;
2f07f5b4e47b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
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24 Topology TR = ts;
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27 NORMALIZE_SEQUENCE_NAMES = FALSE;
2f07f5b4e47b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
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28 SetDialogPrompt ("File with the sequences to label as the in-clade");
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iuc
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29 DataSet query = ReadDataFile (PROMPT_FOR_FILE);
2f07f5b4e47b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
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30 GetString (seqNames,query,-1);
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32 label = io.PromptUserForString ("Use this label");
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35 for (s;in;seqNames) {
2f07f5b4e47b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
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36 tags [s && 6] = label;
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37 }
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39 reg_exp = Rows (tags);
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42 node_labels = {};
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43 for (_regexp_, _leaves_; in; regexp.PartitionByRegularExpressions (BranchName (T,-1), reg_exp)) {
2f07f5b4e47b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
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44 tag = tags[_regexp_];
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46 if (tag != "Internal") {
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48 if (Abs (tag) == 0) {
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49 tag = "Reference";
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50 }
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52 for (l; in; _leaves_) {
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53 node_labels[l] = tag;
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54 }
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55 }
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56 }
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58 node_labelsR = {};
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59 for (_regexp_, _leaves_; in; regexp.PartitionByRegularExpressions (BranchName (TR,-1), reg_exp)) {
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60 tag = tags[_regexp_];
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62 if (tag != "Internal") {
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64 if (Abs (tag) == 0) {
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65 tag = "Reference";
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66 }
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68 for (l; in; _leaves_) {
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69 node_labelsR[l] = tag;
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70 }
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71 }
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72 }
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75 leaf_labels = node_labels;
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76 node_labelsF = node_labels;
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77 node_labels * ((trees.ParsimonyLabel ("T", node_labels))["labels"]);
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78 node_labelsR * ((trees.ParsimonyLabel ("T", node_labelsR))["labels"]);
2f07f5b4e47b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
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79 node_labelsF * ((trees.ParsimonyLabel ("T", node_labelsF))["labels"]);
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81 output_to = io.PromptUserForString ("Write output to this prefix");
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83 fprintf (output_to + "labels.json", CLEAR_FILE, leaf_labels);
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84 fprintf (output_to + "int.nwk", CLEAR_FILE, tree.Annotate ("T", "relabel_and_annotate", "{}", FALSE));
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85 fprintf (output_to + "clade.nwk", CLEAR_FILE, tree.Annotate ("TR", "relabel_and_annotate_full", "{}", FALSE));
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86 fprintf (output_to + "full.nwk", CLEAR_FILE, tree.Annotate ("T", "relabel_and_annotate_full", "{}", FALSE));
2f07f5b4e47b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
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87
2f07f5b4e47b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
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88 function relabel_and_annotate (node_name) {
2f07f5b4e47b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
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89 _label = "";
2f07f5b4e47b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
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90 if (node_labels / node_name && leaf_labels / node_name == FALSE) {
2f07f5b4e47b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
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91 _label = "{" + node_labels[node_name] + "}";
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92 }
2f07f5b4e47b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
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93 return node_name + _label;
2f07f5b4e47b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
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94 }
2f07f5b4e47b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
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95
2f07f5b4e47b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
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96 function relabel_and_annotate_full (node_name) {
2f07f5b4e47b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
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97 _label = "";
2f07f5b4e47b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
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98 if (node_labelsR / node_name) {
2f07f5b4e47b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
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99 _label = "{" + node_labelsR[node_name] + "}";
2f07f5b4e47b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
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100 }
2f07f5b4e47b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
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101 return node_name + _label;
2f07f5b4e47b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
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102 }