Mercurial > repos > ecology > aligned_to_consensus
comparison 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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-1:000000000000 | 0:0ccbe1c20fc3 |
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1 #Rscript | |
2 | |
3 ################################################################################ | |
4 ## Extract consensus sequence from aligned forward and reverse fasta ## | |
5 ################################################################################ | |
6 | |
7 #####Packages | |
8 library(bioseq, quietly = TRUE) | |
9 | |
10 ##Load arguments | |
11 args <- commandArgs(trailingOnly = TRUE) | |
12 | |
13 if (length(args) == 0) { | |
14 stop("This tool needs at least one argument") | |
15 } else { | |
16 fasta_f <- args[1] | |
17 seq_type <- args[2] | |
18 meth_choice <- args[3] | |
19 gaps_tf <- as.logical(args[4]) | |
20 out_og <- as.logical(args[5]) | |
21 } | |
22 | |
23 ## Read input file | |
24 seq_l <- bioseq::read_fasta(fasta_f, type = seq_type) | |
25 | |
26 if(bioseq::seq_nseq(seq_l) < 2){ | |
27 stop("Only one sequence in the file, at least two aligned sequences are needed to compute a consensus") | |
28 }else{ | |
29 if(length(unique(bioseq::seq_nchar(seq_l))) > 1) {stop("Sequences have different lengths, please provide aligned sequences")} | |
30 } | |
31 | |
32 ##Consensus sequence | |
33 seq_con <- bioseq::seq_consensus(seq_l, method = meth_choice, gaps = gaps_tf) | |
34 | |
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")} | |
36 | |
37 names(seq_con) <- paste0("consensus_", Reduce(PTXQC::LCS, names(seq_l))) | |
38 ##Create output | |
39 if(out_og){ | |
40 bioseq::write_fasta(c(seq_con, seq_l), file = "output.fasta", line_length = Inf, block_length = Inf) | |
41 }else{ | |
42 bioseq::write_fasta(seq_con, file = "output.fasta", line_length = Inf, block_length = Inf) | |
43 } |