70 lines
2.3 KiB
R
70 lines
2.3 KiB
R
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#!/usr/bin/env Rscript
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# parse parameter ---------------------------------------------------------
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Sys.setenv(PATH = paste("/home/userlab/bin", Sys.getenv("PATH"), sep = ":"))
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library(argparser, quietly=TRUE)
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# Create a parser
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p <- arg_parser("draw Multiple sequence alignment for proteins")
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# Add command line arguments
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p <- add_argument(p, "fasta", help="input: protein sequences in fasta format", type="character")
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p <- add_argument(p, "output", help="output prefix", type="character")
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# Parse the command line arguments
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argv <- parse_args(p)
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fasta <- argv$fasta
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output <- argv$output
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library(msa)
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library(Biostrings)
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pdf.options(useDingbats = FALSE, family = "Helvetica")
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mySequenceFile <- fasta
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mySequences <- readAAStringSet(mySequenceFile)
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# 使用系统命令调用 MAFFT
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# 创建临时文件
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temp_input <- tempfile(fileext = ".fasta")
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temp_output <- tempfile(fileext = ".fasta")
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# 写入序列到临时文件
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writeXStringSet(mySequences, temp_input)
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# 调用 MAFFT
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# --auto 让 MAFFT 自动选择最佳参数
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# --reorder 按照输入顺序输出
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# --thread -1 使用所有可用CPU核心
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mafft_cmd <- sprintf("mafft --auto --reorder --thread -1 %s > %s",
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temp_input, temp_output)
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# 执行 MAFFT 命令
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system(mafft_cmd)
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# 读取 MAFFT 比对结果
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mafft_alignment <- readAAStringSet(temp_output)
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# 将比对结果转换为 msa 对象（通过 as.MSA 函数）
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# 注意：msaPrettyPrint 需要 MSA 对象，而不是 AAStringSet
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# 我们需要创建一个 MSA 对象
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myFirstAlignment <- msa(mafft_alignment, type = "protein")
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# 或者，如果你需要保持原始顺序，可以使用：
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# 先创建一个空的 MSA 对象，然后用比对序列填充
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# 但 msa() 需要原始的未比对序列
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# 所以更好的方法是直接使用系统命令得到比对，然后创建 MSA 对象
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msaPrettyPrint(myFirstAlignment,
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output = "pdf",
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file = paste(output, "msa_seqlogo.pdf", sep = "."),
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alFile = paste(output, "msa_seqlogo.fasta", sep = "."),
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showNames = "left",
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showLogo = "top",
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logoColors = "chemical",
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shadingMode = "similar",
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showLegend = FALSE,
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askForOverwrite = FALSE)
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# 清理临时文件
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unlink(c(temp_input, temp_output))
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