Get all rows matching to list

Question

[Bioinfonext]

Hi,

I have got a large tab-delimited data file like this;

OTU     Sample  Abundance   Kingdom      Phylum         Class         Order           Family
OTU1    1D_M2   0.000233111 Bacteria    Bacteroidetes   Bacteroidia Bacteroidales   Marinilabiliaceae
OTU1    1D_M1   9.96E-05    Bacteria    Bacteroidetes   Bacteroidia Bacteroidales   Marinilabiliaceae
OTU1    1D_R1   8.82E-05    Bacteria    Bacteroidetes   Bacteroidia Bacteroidales   Marinilabiliaceae   
OTU2    2W_R2   8.41E-06    Bacteria    Proteobacteria  Deltaproteobacteria Desulfobacterales   Desulfobulbaceae
OTU2    2W_M1   8.37E-06    Bacteria    Proteobacteria  Deltaproteobacteria Desulfobacterales   Desulfobulbaceae
OTU2    1D_R1   5.21E-06    Bacteria    Proteobacteria  Deltaproteobacteria Desulfobacterales   Desulfobulbaceae

I want to get all rows that match to list of OTU that in the separated file like this

OTU1
OTU2
OTU3..........

Like if I want to get OUT1 then it should give me output like this;

    OTU   Sample    Abundance   Kingdom      Phylum         Class         Order           Family
    OTU1    1D_M2   0.000233111 Bacteria    Bacteroidetes   Bacteroidia Bacteroidales   Marinilabiliaceae
    OTU1    1D_M1   9.96E-05    Bacteria    Bacteroidetes   Bacteroidia Bacteroidales   Marinilabiliaceae
    OTU1    1D_R1   8.82E-05    Bacteria    Bacteroidetes   Bacteroidia Bacteroidales   Marinilabiliaceae

Many thanks

[cpad0112]

try df[df$OTU==list,] or subset(df, OTU %in% list)

[Bioinfonext]

thank you so much, this code is working perfectly;

## read your data.frame in
df <- read.delim('soil.new.genus.relative.count.txt',sep='\t')

## create your list for matching
##your.list <- unique(df$OTU)
list <- list("ab3feea76dbe8d5688328e879961352c","16c306238059e7942361b356cb1fe8e0","4d4ee91e5bbea2b2ac79903df95ac919","418da7c18e8ca5e4fef06abbdbd2a55c","8e60d301122d7aa359eb6b0b00f37f62","fb991c397395f953464de888e90cfa9c","d71c327f54f6d2e4a6ecf5850a8d059f","d8e9b1d7677e9679bd818655c7fdd9cd","471688174511fedf079b2ce447e8fe6d","adc782d5c4173d56e0d5a74abadb73e3","29ba2f1a4ed84c982f33a8dd96cb2707","339ad5ba4905ffd4a692bd4430766cf4","a691c59fede09b1b48dbfa629ad8b0a1","bd2302ce018f3c596a4ccdbb47dbf2a0","df37cff8946279336357981f544316f5","42c64327f413a7e956921ead9e6cd50c","aed2016cb5b34512ababa75ee4f0f951","f3209372727b47240d46b5c23ca66059","1d4da1099aa9bf25526311cb611bb148","b657956cb832931182f6acf4e0f7e455","359e93139648e7b077316c58160a3a08","d8bc5de7908695c52ec4f75425f1ff5e","01add9ed426ff8519b767caef56d0942","b2137100989578bf9c643d4835076389","9f63daa5c7dbbf68c5f554a35059f2a4","f47757d1267b4d34e903a8c0ee82fe34","91bf6f1720f3875b5bc34550cbd12fa4","fd88fed64df1f69a1d179796193f727a","f1623ead3e6340f23f732988d40ff9f0","bfad6370d28182cc6304844e9bec7fb6","fc67529355587119c01c02a63f43fe9b","5ec8c16ff26835b40c4c5764369d51a2","13f195c7ed592a10db09c876e153b6e4","f7ff11244ec62b05834cb1c585dd3ecb","28628b5969f6f9e53e9684aa7411251b
")

df1<-subset(df, OTU %in% list)

write.table(df1,"soil.top.genera.txt")

[zx8754]

Split your data into list, each list item will have data for 1 OTU, something like

d_split <- split(d, d$OTU)

Answer 1

[benformatics]

## read your data.frame in
df <- read.delim('large_tab_delimited_data_file_like_this.tsv',sep='\t')

## create your list for matching
##your.list <- unique(df$OTU)
your.list <- list("OTU1","OTU2","OTU3")

## subset your df object by the OTU values in your list
df.subsets.list <- lapply(your.list,function(x){
subset(df,OTU %in% x)
##write.table(x,file=paste0('subset_',x,'.tsv),sep='\t',quote=FALSE,row.names=FALSE)
})

df.subsets.list

Not sure what you want to do with your output but if you uncomment that it will make new files with each subset

[Bioinfonext]

thanks so much, I am using above code but getting this error;

<0 rows> (or 0-length row.names)

Error in (function (..., row.names = NULL, check.rows = FALSE, check.names = TRUE,  :
  arguments imply differing number of rows: 12, 0
Calls: write.table ... as.data.frame -> as.data.frame.list -> do.call -> <Anonymous>
Execution halted

Code that used;

## read your data.frame in
df <- read.delim('soil.new.genus.relative.count.txt',sep='\t')

## create your list for matching
##your.list <- unique(df$OTU)
your.list <- list("ab3feea76dbe8d5688328e879961352c","16c306238059e7942361b356cb1fe8e0","4d4ee91e5bbea2b2ac79903df95ac919","418da7c18e8ca5e4fef06abbdbd2a55c","8e60d301122d7aa359eb6b0b00f37f62","fb991c397395f953464de888e90cfa9c","d71c327f54f6d2e4a6ecf5850a8d059f","d8e9b1d7677e9679bd818655c7fdd9cd","471688174511fedf079b2ce447e8fe6d","adc782d5c4173d56e0d5a74abadb73e3","29ba2f1a4ed84c982f33a8dd96cb2707","339ad5ba4905ffd4a692bd4430766cf4","a691c59fede09b1b48dbfa629ad8b0a1","bd2302ce018f3c596a4ccdbb47dbf2a0","df37cff8946279336357981f544316f5","42c64327f413a7e956921ead9e6cd50c","aed2016cb5b34512ababa75ee4f0f951","f3209372727b47240d46b5c23ca66059","1d4da1099aa9bf25526311cb611bb148","b657956cb832931182f6acf4e0f7e455","359e93139648e7b077316c58160a3a08","d8bc5de7908695c52ec4f75425f1ff5e","01add9ed426ff8519b767caef56d0942","b2137100989578bf9c643d4835076389","9f63daa5c7dbbf68c5f554a35059f2a4","f47757d1267b4d34e903a8c0ee82fe34","91bf6f1720f3875b5bc34550cbd12fa4","fd88fed64df1f69a1d179796193f727a","f1623ead3e6340f23f732988d40ff9f0","bfad6370d28182cc6304844e9bec7fb6","fc67529355587119c01c02a63f43fe9b","5ec8c16ff26835b40c4c5764369d51a2","13f195c7ed592a10db09c876e153b6e4","f7ff11244ec62b05834cb1c585dd3ecb","28628b5969f6f9e53e9684aa7411251b
")

## subset your df object by the OTU values in your list
df.subsets.list <- lapply(your.list,function(x){
subset(df,OTU %in% x)
##write.table(x,file=paste0('subset_',x,'.tsv),sep='\t',quote=FALSE,row.names=FALSE)
})

df.subsets.list


write.table(df.subsets.list,"soil.top.genera.txt")

[benformatics]

Can you do head(df) and include what is shown. It could be that the file isn't importing correctly. Also your write.table command wont work you need to uncomment (i.e. remove ##) from the part of my code. It will then create files named:

ab3feea76dbe8d5688328e879961352c.txt

16c306238059e7942361b356cb1fe8e0.txt

etc...

Which will contain the subsets that match those OTUs.