在 R 中加载 FASTA 文件比使用 seqinr 中的 read.fasta() 更快

问题描述

我目前正在使用 R 包 seqinr 中的函数 read.fasta().
我认为创建索引文件已经使读取速度更快，但我想知道是否已经有另一个函数可以更快地加载它?

I am currently using the function read.fasta() from the R package seqinr.
I think that creating an index file already make the reading faster but I was wondering if there was already another function to load it faster ?

我从 PopGenome 中寻找函数 read.big.fasta()，但该包已从 CRAN 和 Bioconductor 中删除，所以我不再那么确定了.有什么建议吗?

I looked for the function read.big.fasta() from PopGenome, but the package has been removed from CRAN and Bioconductor, so I am not so sure about it anymore.Any advices?

推荐答案

您可以使用 Biostrings 中的 readDNAStringSet.

You can use readDNAStringSet from Biostrings.

获取人类基因组:download.file("https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.fa.gz","../Downloads/test.fa.gz")

Get the human genome: download.file("https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.fa.gz","../Downloads/test.fa.gz")

使用 readDNAStringSet 或 read.fasta :

f1 = function(){readDNAStringSet("../Downloads/test.fa.gz")}
f2 = function(){read.fasta("../Downloads/test.fa.gz")}

library(Biostrings)
library(seqinr)

microbenchmark::microbenchmark(f1(),times=5)
Unit: seconds
 expr      min       lq     mean   median       uq      max neval
 f1() 42.82203 43.57036 45.10369 45.64206 46.37412 47.10987     5

microbenchmark::microbenchmark(f1(),times=5)
### did not finish running
### so definitely not the option for large fasta files

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