fasta file loading error
1
0
Entering edit mode
7.4 years ago
tcf.hcdg ▴ 70

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 • 2.6k views
ADD COMMENT
0
Entering edit mode
7.4 years ago

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 COMMENT
0
Entering edit mode

Thanks for correction.

this command works in this warning.

options(max.print=1.5E6)

ADD REPLY
0
Entering edit mode

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

ADD REPLY

Login before adding your answer.

Traffic: 1756 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6