search

cstubben / trinotateR

Trinotate annotation report summaries in R
12 stars 6 forks source link

Error in fred (read_trinotate) problem. trinotateR #5

Open berumeng opened 3 years ago

berumeng commented 3 years ago

Dear all: I used Trinotate to annotate a transcriptome and I am trying to use trinotateR to manipulate the final product of Trinotate. I have a Trinotate.xls file report (I used the .xls file, the .docx file is just to show the columns of the .xls file) Trinity_example.docx

However when i used the read_trinotate function: x <- read_trinotate("Trinotate.xls")

I get the following error:

Error in fread(file, sep = "\t", na.strings = ".", ...) : embedded nul in string: '\xd0\xcf\021\u0871\032\xe1\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0>\0\003\0\xfe\xff'

Could you please help me solve this?

Thanks in advance!!

cstubben commented 3 years ago

read_trinotate runs fread(file, sep="\t", na.strings=".") and a few extra steps. It requires a tab-delimited file as input and when I wrote this five years ago, the Trinotate.xls output was a text file with a .xls ending. That may have changed, so please check the file type - the null string seems like something Excel would add.

head -1 Trinotate_report.xls
#gene_id    transcript_id   sprot_Top_BLASTX_hit ...
berumeng commented 3 years ago

Thanks, this help me a lot!