Question: fasta file loading error
0
gravatar for tcf.hcdg
4.6 years ago by
tcf.hcdg60
European Union
tcf.hcdg60 wrote:

Hello

I hava a sequence file containing 10,22,058 entries in fasta format. I wanted to load this file in the R using "seqinr" package. 

I have installed the seqinr and ade4 package. 

when I run the command it gives the error and only around 10,000 sequences out of 10,22,058 are showed in the consol window.

the code I tried to load the file id 

 

getwd()
library(seqinr)
library(ade4)

read.fasta(file="Z:/R/07072015/CSANX.fasta", seqtype ="AA", as.string = TRUE, set.attributes = FALSE, legacy.mode = TRUE, strip.desc = FALSE)

after executing it gives the error

" [ reached getOption("max.print") -- omitted 1012058 entries ]"

 

Could you please guide what could be the possible reason for this.

 

Thanks in advance

 

read.fasta • 1.7k views
ADD COMMENTlink modified 4.6 years ago by royefendymarbun30 • written 4.6 years ago by tcf.hcdg60
0
gravatar for Devon Ryan
4.6 years ago by
Devon Ryan94k
Freiburg, Germany
Devon Ryan94k wrote:

You need to assign that to a variable. As is, you're reading it in and printing the output to the screen. BTW, that's not an error, just a warning.

fa <- read.fasta(file="Z:/R/07072015/CSANX.fasta", seqtype ="AA", as.string = TRUE, set.attributes = FALSE, legacy.mode = TRUE, strip.desc = FALSE)
ADD COMMENTlink written 4.6 years ago by Devon Ryan94k

Thanks for correction.

this command works in this warning.

options(max.print=1.5E6)

ADD REPLYlink written 4.6 years ago by tcf.hcdg60

If you just wanted to view a fasta file it'd be simpler to just use cat.

ADD REPLYlink written 4.6 years ago by Devon Ryan94k
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