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annotate scripts/strike-ambigs.bf @ 0:f304c108aa1f draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
author iuc
date Wed, 09 Jun 2021 07:03:54 +0000
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f304c108aa1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
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1 RequireVersion ("2.5.20");
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3 LoadFunctionLibrary ("libv3/tasks/alignments.bf");
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4 LoadFunctionLibrary ("libv3/tasks/trees.bf");
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5 LoadFunctionLibrary ("libv3/UtilityFunctions.bf");
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6 LoadFunctionLibrary ("libv3/IOFunctions.bf");
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7 LoadFunctionLibrary ("libv3/convenience/math.bf");
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11 filter.analysis_description = {terms.io.info :
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12 "
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13 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
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14 ",
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15 terms.io.version : "0.1",
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16 terms.io.reference : "TBD",
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17 terms.io.authors : "Sergei L Kosakovsky Pond",
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18 terms.io.contact : "spond@temple.edu",
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19 terms.io.requirements : "An MSA"
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20 };
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23 io.DisplayAnalysisBanner (filter.analysis_description);
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25 utility.SetEnvVariable ("NORMALIZE_SEQUENCE_NAMES", FALSE);
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27 KeywordArgument ("code", "Which genetic code should be used", "Universal");
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28 KeywordArgument ("alignment", "An in-frame codon alignment in one of the formats supported by HyPhy");
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30 filter.in = alignments.PromptForGeneticCodeAndAlignment ("filter.dataset", "filter.input");
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32 KeywordArgument ("output", ".fasta for compressed data", None);
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33 filter.out = io.PromptUserForFilePath(".fasta for filtered data");
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34 fprintf (filter.out, CLEAR_FILE, KEEP_OPEN);
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35
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36 GetDataInfo (filter.site_patterns, filter.input);
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38 filter.patter2site = {};
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41 for (i,j,v; in; filter.site_patterns) {
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42 index = i+j;
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43 if (filter.patter2site / v == FALSE ) {
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44 filter.patter2site [v] = {};
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45 }
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46 filter.patter2site [v] + index;
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47 }
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48
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49 GET_DATA_INFO_RETURNS_ONLY_THE_INDEX = TRUE;
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50 COUNT_GAPS_IN_FREQUENCIES = FALSE;
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51 filter.unique_patterns = utility.Array1D (filter.input.site_freqs);
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52
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53 for (seq = 0; seq < filter.input.species; seq += 1) {
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54 io.ReportProgressBar ("filter","Processing sequence " + (1+seq));
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55 codons = {1, filter.input.sites};
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56 codons [0] = "";
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57 GetString (seq_name, filter.input, seq);
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58 GetDataInfo (seq_chars, filter.input, seq);
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60 filter.ambigs = 0;
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62 for (pattern = 0; pattern < filter.unique_patterns; pattern += 1) {
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63 GetDataInfo (pattern_info, filter.input, seq, pattern);
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64 if (pattern_info >= 0) {
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65 codon_start = (filter.patter2site[pattern])[0] * 3;
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66 codon = seq_chars [codon_start][codon_start+2];
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67 } else {
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68 codon = "---";
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69 filter.ambigs += Abs (filter.patter2site [pattern])
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70 }
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71 for (c; in; filter.patter2site [pattern] ) {
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72 codons[c] = codon;
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73 }
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74 }
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75 if (filter.ambigs > 0) {
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76 fprintf (stdout, "\nStriking ", filter.ambigs, " codons that are incompletely resolved from " + seq_name + "\n");
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77 }
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78 fprintf (filter.out,">",seq_name,"\n",Join ("", codons), "\n");
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79 }
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81 fprintf (filter.out,CLOSE_FILE);
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