Invalid Strata object

[champ52018]

tid<-'47426'
strata=uniprot_strata(tid, from = 2) %>% strata_apply(f= diverse_subtree,n=5,weights=uniprot_weight_by_ref()) %>% use_recommended_prokaryotes() %>% add_taxa(c('4932', '9606')) %>% uniprot_fill_strata()

#it shows the following error
Error in is_valid_strata(strata) :
Invalid Strata object, the focal species '47426' is not found in the tree

May I know what might be the issue? I checked the organism 'A.cepistipes'; it exist in NCBI taxonomy but, the program could not identify it. Please help me solve the issue.

Any help would be appreciated! Thanks

[arendsee]

@champ52018 Thanks for the reproducible report! The problem here is that Armillaria cepistipes is not in the UniProt database. This is a real bug though, since phylostratr should give you a chance to add your own sequence before blowing up. Pull the latest version of phylostratr from github and the problem should be fixed. You will still have to provide your own proteome for the focal species. See the code below:

require('phylostratr')
tid<-'47426'
strata=uniprot_strata(tid, from = 5) %>% 
  strata_apply(f=diverse_subtree,n=2,weights=uniprot_weight_by_ref()) %>% 
  use_recommended_prokaryotes() %>%
  add_taxa(c('4932', '9606')) %>%
  uniprot_fill_strata()
strata@data$faa[[tid]] <- '/path/to/your/file.faa'

Let me know if this works for you.

[champ52018]

@arendsee Thank you so much for your reply! I tried again using the latest version of pylostratr (BMC Release (https://github.com/arendsee/phylostratr/releases/tag/0.2.0) but I got the same error. It blows up again.

I am copying the steps I followed so that I can explain better:

1. I removed the previous version that I installed from github.
2. I downloaded the source code: https://github.com/arendsee/phylostratr/archive/0.2.0.tar.gz and installed it using

install.packages("phylostratr_v_0.2.0_bmc_release.tar.gz", repos=NULL)

3. I tried to rerun the previous analysis but it showed the same error

tid<-'47426'
strata=uniprot_strata(tid, from = 5) %>%
strata_apply(f=diverse_subtree,n=2,weights=uniprot_weight_by_ref()) %>%
use_recommended_prokaryotes() %>%
add_taxa(c('4932', '9606')) %>%
uniprot_fill_strata()

Error in is_valid_strata(strata) :
Invalid Strata object, the focal species '47426' is not found in the tree

Any help would be highly appreciated!

Thanks again!

[arendsee]

Ah, you are downloading the last tagged release, not the most recent one. Try installing like so:

devtools::install_github("arendsee/phylostratr")

That will retrieve the very latest version.

[champ52018]

Hi, at first I downloaded and installed using:

devtools::install_github("arendsee/phylostratr")

The second time, after seeing your message I did using

install.packages("phylostratr_v_0.2.0_bmc_release.tar.gz", repos=NULL)

[arendsee]

The command

install.packages("phylostratr_v_0.2.0_bmc_release.tar.gz", repos=NULL)

installs the old version, you should use the version I just committed to github. You can get that through devtools::install_github.

[champ52018]

Hi I did that as well. It gives the same problem.

[arendsee]

Can you show me the output of devtools::session_info()?

[arendsee]

@champ52018 Did you find a solution to the problem?