Mercurial > repos > ecology > aligned_to_consensus
annotate consensus_from_alignments.R @ 0:0ccbe1c20fc3 draft default tip
planemo upload for repository https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/consensus_from_alignments commit ecc21de8f368c6a95c57d4e6511ed42af9e72a66
author | ecology |
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date | Tue, 25 Apr 2023 10:05:29 +0000 |
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0ccbe1c20fc3
planemo upload for repository https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/consensus_from_alignments commit ecc21de8f368c6a95c57d4e6511ed42af9e72a66
ecology
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1 #Rscript |
0ccbe1c20fc3
planemo upload for repository https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/consensus_from_alignments commit ecc21de8f368c6a95c57d4e6511ed42af9e72a66
ecology
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2 |
0ccbe1c20fc3
planemo upload for repository https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/consensus_from_alignments commit ecc21de8f368c6a95c57d4e6511ed42af9e72a66
ecology
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3 ################################################################################ |
0ccbe1c20fc3
planemo upload for repository https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/consensus_from_alignments commit ecc21de8f368c6a95c57d4e6511ed42af9e72a66
ecology
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4 ## Extract consensus sequence from aligned forward and reverse fasta ## |
0ccbe1c20fc3
planemo upload for repository https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/consensus_from_alignments commit ecc21de8f368c6a95c57d4e6511ed42af9e72a66
ecology
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5 ################################################################################ |
0ccbe1c20fc3
planemo upload for repository https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/consensus_from_alignments commit ecc21de8f368c6a95c57d4e6511ed42af9e72a66
ecology
parents:
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6 |
0ccbe1c20fc3
planemo upload for repository https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/consensus_from_alignments commit ecc21de8f368c6a95c57d4e6511ed42af9e72a66
ecology
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7 #####Packages |
0ccbe1c20fc3
planemo upload for repository https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/consensus_from_alignments commit ecc21de8f368c6a95c57d4e6511ed42af9e72a66
ecology
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8 library(bioseq, quietly = TRUE) |
0ccbe1c20fc3
planemo upload for repository https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/consensus_from_alignments commit ecc21de8f368c6a95c57d4e6511ed42af9e72a66
ecology
parents:
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9 |
0ccbe1c20fc3
planemo upload for repository https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/consensus_from_alignments commit ecc21de8f368c6a95c57d4e6511ed42af9e72a66
ecology
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10 ##Load arguments |
0ccbe1c20fc3
planemo upload for repository https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/consensus_from_alignments commit ecc21de8f368c6a95c57d4e6511ed42af9e72a66
ecology
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11 args <- commandArgs(trailingOnly = TRUE) |
0ccbe1c20fc3
planemo upload for repository https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/consensus_from_alignments commit ecc21de8f368c6a95c57d4e6511ed42af9e72a66
ecology
parents:
diff
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12 |
0ccbe1c20fc3
planemo upload for repository https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/consensus_from_alignments commit ecc21de8f368c6a95c57d4e6511ed42af9e72a66
ecology
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13 if (length(args) == 0) { |
0ccbe1c20fc3
planemo upload for repository https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/consensus_from_alignments commit ecc21de8f368c6a95c57d4e6511ed42af9e72a66
ecology
parents:
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14 stop("This tool needs at least one argument") |
0ccbe1c20fc3
planemo upload for repository https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/consensus_from_alignments commit ecc21de8f368c6a95c57d4e6511ed42af9e72a66
ecology
parents:
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15 } else { |
0ccbe1c20fc3
planemo upload for repository https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/consensus_from_alignments commit ecc21de8f368c6a95c57d4e6511ed42af9e72a66
ecology
parents:
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16 fasta_f <- args[1] |
0ccbe1c20fc3
planemo upload for repository https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/consensus_from_alignments commit ecc21de8f368c6a95c57d4e6511ed42af9e72a66
ecology
parents:
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17 seq_type <- args[2] |
0ccbe1c20fc3
planemo upload for repository https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/consensus_from_alignments commit ecc21de8f368c6a95c57d4e6511ed42af9e72a66
ecology
parents:
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18 meth_choice <- args[3] |
0ccbe1c20fc3
planemo upload for repository https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/consensus_from_alignments commit ecc21de8f368c6a95c57d4e6511ed42af9e72a66
ecology
parents:
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19 gaps_tf <- as.logical(args[4]) |
0ccbe1c20fc3
planemo upload for repository https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/consensus_from_alignments commit ecc21de8f368c6a95c57d4e6511ed42af9e72a66
ecology
parents:
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20 out_og <- as.logical(args[5]) |
0ccbe1c20fc3
planemo upload for repository https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/consensus_from_alignments commit ecc21de8f368c6a95c57d4e6511ed42af9e72a66
ecology
parents:
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21 } |
0ccbe1c20fc3
planemo upload for repository https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/consensus_from_alignments commit ecc21de8f368c6a95c57d4e6511ed42af9e72a66
ecology
parents:
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22 |
0ccbe1c20fc3
planemo upload for repository https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/consensus_from_alignments commit ecc21de8f368c6a95c57d4e6511ed42af9e72a66
ecology
parents:
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23 ## Read input file |
0ccbe1c20fc3
planemo upload for repository https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/consensus_from_alignments commit ecc21de8f368c6a95c57d4e6511ed42af9e72a66
ecology
parents:
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24 seq_l <- bioseq::read_fasta(fasta_f, type = seq_type) |
0ccbe1c20fc3
planemo upload for repository https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/consensus_from_alignments commit ecc21de8f368c6a95c57d4e6511ed42af9e72a66
ecology
parents:
diff
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25 |
0ccbe1c20fc3
planemo upload for repository https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/consensus_from_alignments commit ecc21de8f368c6a95c57d4e6511ed42af9e72a66
ecology
parents:
diff
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26 if(bioseq::seq_nseq(seq_l) < 2){ |
0ccbe1c20fc3
planemo upload for repository https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/consensus_from_alignments commit ecc21de8f368c6a95c57d4e6511ed42af9e72a66
ecology
parents:
diff
changeset
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27 stop("Only one sequence in the file, at least two aligned sequences are needed to compute a consensus") |
0ccbe1c20fc3
planemo upload for repository https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/consensus_from_alignments commit ecc21de8f368c6a95c57d4e6511ed42af9e72a66
ecology
parents:
diff
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28 }else{ |
0ccbe1c20fc3
planemo upload for repository https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/consensus_from_alignments commit ecc21de8f368c6a95c57d4e6511ed42af9e72a66
ecology
parents:
diff
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29 if(length(unique(bioseq::seq_nchar(seq_l))) > 1) {stop("Sequences have different lengths, please provide aligned sequences")} |
0ccbe1c20fc3
planemo upload for repository https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/consensus_from_alignments commit ecc21de8f368c6a95c57d4e6511ed42af9e72a66
ecology
parents:
diff
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30 } |
0ccbe1c20fc3
planemo upload for repository https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/consensus_from_alignments commit ecc21de8f368c6a95c57d4e6511ed42af9e72a66
ecology
parents:
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31 |
0ccbe1c20fc3
planemo upload for repository https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/consensus_from_alignments commit ecc21de8f368c6a95c57d4e6511ed42af9e72a66
ecology
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32 ##Consensus sequence |
0ccbe1c20fc3
planemo upload for repository https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/consensus_from_alignments commit ecc21de8f368c6a95c57d4e6511ed42af9e72a66
ecology
parents:
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33 seq_con <- bioseq::seq_consensus(seq_l, method = meth_choice, gaps = gaps_tf) |
0ccbe1c20fc3
planemo upload for repository https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/consensus_from_alignments commit ecc21de8f368c6a95c57d4e6511ed42af9e72a66
ecology
parents:
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34 |
0ccbe1c20fc3
planemo upload for repository https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/consensus_from_alignments commit ecc21de8f368c6a95c57d4e6511ed42af9e72a66
ecology
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35 if(bioseq::seq_nseq(seq_con) > 1){stop("Consensus hasn't worked for an unknown reason, double-check your input file and the parameters you chose")} |
0ccbe1c20fc3
planemo upload for repository https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/consensus_from_alignments commit ecc21de8f368c6a95c57d4e6511ed42af9e72a66
ecology
parents:
diff
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36 |
0ccbe1c20fc3
planemo upload for repository https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/consensus_from_alignments commit ecc21de8f368c6a95c57d4e6511ed42af9e72a66
ecology
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37 names(seq_con) <- paste0("consensus_", Reduce(PTXQC::LCS, names(seq_l))) |
0ccbe1c20fc3
planemo upload for repository https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/consensus_from_alignments commit ecc21de8f368c6a95c57d4e6511ed42af9e72a66
ecology
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38 ##Create output |
0ccbe1c20fc3
planemo upload for repository https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/consensus_from_alignments commit ecc21de8f368c6a95c57d4e6511ed42af9e72a66
ecology
parents:
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39 if(out_og){ |
0ccbe1c20fc3
planemo upload for repository https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/consensus_from_alignments commit ecc21de8f368c6a95c57d4e6511ed42af9e72a66
ecology
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40 bioseq::write_fasta(c(seq_con, seq_l), file = "output.fasta", line_length = Inf, block_length = Inf) |
0ccbe1c20fc3
planemo upload for repository https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/consensus_from_alignments commit ecc21de8f368c6a95c57d4e6511ed42af9e72a66
ecology
parents:
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41 }else{ |
0ccbe1c20fc3
planemo upload for repository https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/consensus_from_alignments commit ecc21de8f368c6a95c57d4e6511ed42af9e72a66
ecology
parents:
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42 bioseq::write_fasta(seq_con, file = "output.fasta", line_length = Inf, block_length = Inf) |
0ccbe1c20fc3
planemo upload for repository https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/consensus_from_alignments commit ecc21de8f368c6a95c57d4e6511ed42af9e72a66
ecology
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43 } |