rap_fasta from phyloseq object

[koutnymarek]

Please,

Can I make rap_fasta object, that I want to use for Tax4Fun2 function, easily out of my phyloseq object which contains DNA sequences?
I have realized file2meco does not add rap_fasta automatically into microtable from phyloseq.

Thanks.

MK

[ChiLiubio]

Hi. Which version of file2meco are you using? Current v0.5.0 in CRAN support the sequences conversion. I test the steps again.

library(file2meco)
packageVersion("file2meco")
# see the help document
?qiime1meco
# Let's run the examples
# use the raw data files stored inside the package
otu_file_path <- system.file("extdata", "otu_table_raw.txt", package="file2meco")
sample_file_path <- system.file("extdata", "sample_info.csv", package="file2meco")
phylo_file_path <- system.file("extdata", "rep_phylo.tre", package="file2meco")
# if you want to use Tax4Fun2 approach, you need read the representative sequences and add it to the microtable object.
rep_fasta_path <- system.file("extdata", "rep.fna", package="file2meco")
# contruct microtable object
d1 <- qiime1meco(otu_file_path, sample_table = sample_file_path, phylo_tree = phylo_file_path)
library(Biostrings)
seq_ds <- readDNAStringSet(rep_fasta_path)
d1$rep_fasta <- seq_ds

physeq1 <- meco2phyloseq(d1)
physeq1

meco1 <- phyloseq2meco(physeq1)
meco1

Chi

[koutnymarek]

Dear Chi,

Thanks for your support. I have v0.5.0 of file2meco.

There must some problem in my code. Please look:

> ps2 <- subset_samples(ps, Digestate=="N")
> add_refseq(ps2, tag = "ASV")
phyloseq-class experiment-level object
otu_table()   OTU Table:         [ 18135 taxa and 24 samples ]
sample_data() Sample Data:       [ 24 samples by 19 sample variables ]
tax_table()   Taxonomy Table:    [ 18135 taxa by 6 taxonomic ranks ]
phy_tree()    Phylogenetic Tree: [ 18135 tips and 18133 internal nodes ]
refseq()      DNAStringSet:      [ 18135 reference sequences ]

So you can see that the sequences are there.

Then:

otu_file_path <- system.file("extdata", "otu_table_raw.txt", package="file2meco")
sample_file_path <- system.file("extdata", "sample_info.csv", package="file2meco")
phylo_file_path <- system.file("extdata", "rep_phylo.tre", package="file2meco")
rep_fasta_path <- system.file("extdata", "rep.fna", package="file2meco")

> meco1 <- phyloseq2meco(ps2)
6441 taxa are removed from the otu_table, as the abundance is 0 ...
> meco1
microtable-class object:
sample_table have 24 rows and 19 columns
otu_table have 11694 rows and 24 columns
tax_table have 18135 rows and 6 columns
phylo_tree have 18135 tips


> meco1[["rep_fasta"]]
NULL

So the sequences are not there.

In your code provided above were also some qiime files related functions. I guess it was only as an alternative, I work with phyloseq.

Thanks a lot for any advice.

Marek

[koutnymarek]

Hi Chi,

May be I have found the problem. I did not add the sequencess to phyloseq:
add_refseq(ps2, tag = "ASV")

This is better:
ps2 <- add_refseq(ps2, tag = "ASV")

Marek

[koutnymarek]

So it worked!
Thanks