如何解决这些错误：使用predORF，需要用唯一的名称填充x的插槽，或者下标包含越界索引？

问题描述

此功能predORF出现问题

  sqa <- c("CAGGGCACCTGGCCTTGGGATGCGCCTCCTGCCCGCTGAGCCCAGGGGCCGCTATGGCCCTTCTGGCCATGCTGGCGCTGCAGACAGCTCTCTACCTAGTAGGCTTCTTCTACCCGCCGGGAGGCATATGGCGCTGGATCACCCGGGAC") 
  print(sqa)   

首先，我将序列转换为输入格式

  dnastring = DNAString(sqa) 
  print(dnastring)

  dna <- DNAStringSet(sqa) 
  print(dna)

当我使用DNAstrings格式时：

    predORF(dnabase,n = 1,type = "grl",mode = "orf",strand = "sense",longest_disjoint=FALSE,startcodon = c("ATG"),stopcodon = c("TAA"))

我收到此错误

  Error in predORF(dnastring,: 
  Sequence name slot of x need be populated with unique names.
    

当我定义它的长度时，我得到了：

    predORF(dna[:149],stopcodon = c("TAA"))

  Error in predORF(dnastring[1:149],: 
  Sequence name slot of x need be populated with unique names.

当我使用DNAStringSet格式时：

    predORF(dna,stopcodon = c("TAA"))

我收到此错误

  Error in predORF(dna n = 1,stopcodon = c("TAA"))

  Error: subscript contains out-of-bounds indices

我该如何解决这个问题？

谢谢！

解决方法

问题在于predORF需要命名序列作为输入。见下文：

library(Biostrings)
library(systemPipeR)

sqa <- c("ATGTAA")
sqb <- c("ATGGCCTAA")
dna <- DNAStringSet(c(seq_a = sqa,seq_b = sqb),use.names = T) 
predORF(dna,n = 1,type = "grl",mode = "orf",strand = "sense",longest_disjoint=FALSE,startcodon = c("ATG"),stopcodon = c("TAA"))