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channen1221
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@channen1221-14311
Last seen 7.2 years ago
Hi there
I am terrible in R - its my worst nightmare. And i only post this because I am desperate.
I have a .biom file (json version; format: Biological Observation Matrix 1.0.0). However when trying to import to RStudio I get an error message:
Error in read_biom(biom_file = BIOMfilename) : Both attempts to read input file: either as JSON (BIOM-v1) or HDF5 (BIOM-v2). Check file path, file name, file itself, then try again.
I'm not entirely certain what I need to change or if i'm not using the correct packages.
Thanks
Hi all,
I have the same error.
I have my otu_table.biom constructed by Qiime 1.9 and my metadata file and I tried to import in Phyloseq and until now I have not couldn't; I changed my otu_table.biom to json with this command
biom convert -i otu_table.biom -o otu_table_json.biom --table-type="OTU table" --to-json
However, with this file, I have not couldn't,
jsonbiomfile = "C/Users/metagenomic/Desktop/otu_table_json.biom"
jsonbiomfile = "C/Users/metagenomic/Desktop/metadata_ITS.txt"
biom_file <- paste(jsonbiomfile, "otu_table_json.biom", sep = "")
map_file <- paste(jsonbiomfile, "metadata_ITS.txt", sep = "")
read_biom(biom_file)
then I got this message
Error in read_biom(biom_file) : Both attempts to read input file:
C/Users/metagenomic/Desktop,otu_table_json.biom
either as JSON (BIOM-v1) or HDF5 (BIOM-v2).
Check file path, file name, file itself, then try again.
Please if you have any advice, I appreciate that, thanks in advance
Dear voteroj,
without looking at the read_biom() code, I guess it is trying to tell you that there is a problem with your
filename. These look like Windows paths and I'd suggest to simply add a colon to the drive letter, as in
jsonbiomfile = "C:/Users/metagenomic/Desktop/otu_table_json.biom"
(untested, I'm on linux)
Hope this helps.
Thanks Axel,
I tried, but again I got the same message
jsonbiomfile = "C:/Users/metagenomic/Desktop"
jsonbiomfi = "C:/Users/metagenomic/Desktop/metadata_ITS.txt"
biom_file <- paste(jsonbiomfile, "otu_table_json.biom", sep = "")
map_file <- paste(jsonbiomfi, "metadata_ITS.txt", sep = "")
biom_file
read_biom(biom_file)
Error in read_biom(biom_file) : Both attempts to read input file:
C:/Users/metagenomic/Desktopotu_table_json.biom
either as JSON (BIOM-v1) or HDF5 (BIOM-v2).
Check file path, file name, file itself, then try again.
:(
use
file.path()instead ofpaste(), orbiom_file <- file.choose(); but instead of typing stuff and hoping that it works, check that it makes sense, for instance, do you actually have a file at C/Users/metagenomic/Desktop,otu_table_json.biom ?Hi Martin, Thanks for your answer,
I tested your recommendation and the error is the same.
and well after I reviewed some post in github, and I red phyloseq manual for import .biom table, I have couldn't understand what is the problem, I have my file in the desktop as you see in the first part of my script
jsonbiomfile = "C:/Users/metagenomic/Desktop"
But then it appears
C:/Users/metagenomic/Desktopotu_table_json.biom
I don't know why; please if you have another text or place to visit please don't hesitate to tell me, I want to learn and is my first time,
Thanks in advance,
HI Martin,
I tried this
#####Input .biom
jsonbiomfile = "C:/Users/metagenomic/Desktop/otu_table_json.biom"
read_biom(jsonbiomfile)
x = read_biom(jsonbiomfile)
header(x)
biom_shape(x)
nrow(x)
ncol(x)
rownames(x)
colnames(x)
matrix_element_type(x)
biom_data(x)
and it's works!!!!
Ouch, apologies for providing misleading help by posting a quick reply when I was about to leave my office... I had completely overlooked your paste() call...
In your call to paste(), you're explicitly asking for no (empty) separator between file path and filename by setting argument sep = "". It would have worked if you had used sep = "/" (and "C:").
?paste
However, as Martin has told you, it is much better to use file.path() instead of paste() because it will pick the right path separator for your OS by default.
?file.path