Mercurial > repos > iuc > hyphy_bgm
view scripts/strike-ambigs.bf @ 28:0286ee7cc27d draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2063bc1f8f9cb97de147b86dbe9189fc496b206a"
author | iuc |
---|---|
date | Wed, 09 Jun 2021 17:34:51 +0000 |
parents | ede53272264e |
children |
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RequireVersion ("2.5.20"); LoadFunctionLibrary ("libv3/tasks/alignments.bf"); LoadFunctionLibrary ("libv3/tasks/trees.bf"); LoadFunctionLibrary ("libv3/UtilityFunctions.bf"); LoadFunctionLibrary ("libv3/IOFunctions.bf"); LoadFunctionLibrary ("libv3/convenience/math.bf"); filter.analysis_description = {terms.io.info : " 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 ", terms.io.version : "0.1", terms.io.reference : "TBD", terms.io.authors : "Sergei L Kosakovsky Pond", terms.io.contact : "spond@temple.edu", terms.io.requirements : "An MSA" }; io.DisplayAnalysisBanner (filter.analysis_description); utility.SetEnvVariable ("NORMALIZE_SEQUENCE_NAMES", FALSE); KeywordArgument ("code", "Which genetic code should be used", "Universal"); KeywordArgument ("alignment", "An in-frame codon alignment in one of the formats supported by HyPhy"); filter.in = alignments.PromptForGeneticCodeAndAlignment ("filter.dataset", "filter.input"); KeywordArgument ("output", ".fasta for compressed data", None); filter.out = io.PromptUserForFilePath(".fasta for filtered data"); fprintf (filter.out, CLEAR_FILE, KEEP_OPEN); GetDataInfo (filter.site_patterns, filter.input); filter.patter2site = {}; for (i,j,v; in; filter.site_patterns) { index = i+j; if (filter.patter2site / v == FALSE ) { filter.patter2site [v] = {}; } filter.patter2site [v] + index; } GET_DATA_INFO_RETURNS_ONLY_THE_INDEX = TRUE; COUNT_GAPS_IN_FREQUENCIES = FALSE; filter.unique_patterns = utility.Array1D (filter.input.site_freqs); for (seq = 0; seq < filter.input.species; seq += 1) { io.ReportProgressBar ("filter","Processing sequence " + (1+seq)); codons = {1, filter.input.sites}; codons [0] = ""; GetString (seq_name, filter.input, seq); GetDataInfo (seq_chars, filter.input, seq); filter.ambigs = 0; for (pattern = 0; pattern < filter.unique_patterns; pattern += 1) { GetDataInfo (pattern_info, filter.input, seq, pattern); if (pattern_info >= 0) { codon_start = (filter.patter2site[pattern])[0] * 3; codon = seq_chars [codon_start][codon_start+2]; } else { codon = "---"; filter.ambigs += Abs (filter.patter2site [pattern]) } for (c; in; filter.patter2site [pattern] ) { codons[c] = codon; } } if (filter.ambigs > 0) { fprintf (stdout, "\nStriking ", filter.ambigs, " codons that are incompletely resolved from " + seq_name + "\n"); } fprintf (filter.out,">",seq_name,"\n",Join ("", codons), "\n"); } fprintf (filter.out,CLOSE_FILE);