r - 在R中以记录格式打开txt文件

Question

我希望将 R 中记录格式的 txt 文件作为数据框读取，其中每一行对应一条记录。记录长短不一。知道我该怎么做吗？

这是第一条记录:

# C. elegans orthologs      
# WormBase version: WS241       
# Generated:        
# File is in record format with records separated by "=\n"      
#      Sample Record        
#      WBGeneID \t PublicName \n        
#      Species \t Ortholog \t MethodsUsedToAssignOrtholog \n        
# BEGIN CONTENTS        
=       
WBGene00000001  aap-1   
Ascaris suum    GS_11030    WormBase-Compara
Brugia malayi   WBGene00227541  WormBase-Compara
Bursephelenchus xylophilus  BUX.s00055.227  WormBase-Compara
Caenorhabditis angaria  Cang_2012_03_13_00205.g6964.t3  WormBase-Compara
Caenorhabditis brenneri WBGene00194098  TreeFam; WormBase-Compara
Caenorhabditis briggsae WBGene00032086  Hillier-set; OrthoMCL; Inparanoid_7; OMA;     WormBase-Compara
Caenorhabditis japonica WBGene00207613  WormBase-Compara
Caenorhabditis remanei  WBGene00069407  Inparanoid_7; OMA; TreeFam; WormBase-Compara
Caenorhabditis sp.11    Csp11.Scaffold542.g3421.t1  WormBase-Compara
Caenorhabditis sp.5 Csp5_scaffold_00676.g14307.t1   WormBase-Compara
Danio rerio ENSEMBL:ENSDARP00000056212  TreeFam
Dirofilaria immitis nDi.2.2.2.t01810    WormBase-Compara
Drosophila melanogaster ENSEMBL:FBpp0303635 EnsEMBL-Compara; TreeFam
Haemonchus contortus    HCOI02027400.t1 WormBase-Compara
Heterorhabditis bacteriophora   Hba_15363   WormBase-Compara
Homo sapiens    ENSEMBL:ENSP00000361075 Inparanoid_7; TreeFam
Loa loa EFO26046.2  WormBase-Compara
Meloidogyne hapla   MhA1_Contig1573.frz3.gene15 WormBase-Compara
Mus musculus    ENSEMBL:ENSMUSP00000034296  EnsEMBL-Compara; TreeFam
Onchocerca volvulus WBGene00241206  WormBase-Compara
Panagrellus redivivus   Pan_g2405.t1    WormBase-Compara
Pristionchus pacificus  WBGene00117228  Inparanoid_7; OMA; WormBase-Compara
Trichinella spiralis    EFV56516    WormBase-Compara
=       
WBGene00000002  aat-1   
Ascaris suum    GS_20881    WormBase-Compara

编辑:我真正需要的是每条记录中与“智人”对应的条目。所以，理想情况下，我在 R 中的 df 是:

WBGene00000001 aap-1 Homo sapiens ENSEMBL:ENSP00000361075 Inparanoid_7; TreeFam 
WBGene00000002 aat-1 etc etc

Answer 1

我建议使用 readLines 将数据读入 R。由于您在注释中给了我们文件路径，因此请先使用 file 打开与文件的连接，然后是 readLines。在我们读取数据并将数据存储到 R 之后，关闭 连接始终是一个好习惯。

> con <- file("../Input/c_elegans.PRJNA13758.current.best_blastp_hits.txt", 
              open = "r")
> XX <- readLines(con)
> close(con)

> record <- grep("^WBGene", XX, value = TRUE)
> sapien <- grep("Homo sapiens", XX, value = TRUE, fixed = TRUE)
> gsub("\\s+", " ", paste0(record[1], sapien))
## [1] "WBGene00000001 aap-1 Homo sapiens ENSEMBL:ENSP00000361075 Inparanoid_7; TreeFam"

样本数据的整个record 向量是

> record
## [1] "WBGene00000001  aap-1   " "WBGene00000002  aat-1   "

所以当我们找到记录 2 的智人时，它将被粘贴到记录 2，智人 3 到记录 3，依此类推

paste0(record, sapien)

值得注意OP的数据框最终是用

创建的

do.call(rbind, strsplit(paste0(record, sapien), split = "\\s+"))