Error getting all children of M tuberculosis complex

[pgcudahy]

Session info

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 setting  value                       
 version  R version 3.6.3 (2020-02-29)
 os       Ubuntu 18.04.5 LTS          
 system   x86_64, linux-gnu           
 ui       X11                         
 language (EN)                        
 collate  en_US.UTF-8                 
 ctype    en_US.UTF-8                 
 tz       America/New_York            
 date     2020-10-06                  

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[1] /usr/local/lib/R/site-library
[2] /usr/lib/R/site-library
[3] /usr/lib/R/library

I'm trying to get all of the children taxon ids of Mycobacterium tuberculosis complex (uid = 77643) but the downstream command fails with

downstream(as.uid(77643), db = 'ncbi', downto = 'no rank', intermediate = TRUE)

Number of ids long; we're splitting up into chunks for multiple HTTP requests
Error in intermed[[iter]]: subscript out of bounds
Traceback:

1. downstream(as.uid(77643), db = "ncbi", downto = "no rank", intermediate = TRUE)
2. downstream.uid(as.uid(77643), db = "ncbi", downto = "no rank", 
 .     intermediate = TRUE)
3. lapply(sci_id, fun, downto = downto, intermediate = intermediate, 
 .     ...)
4. FUN(X[[i]], ...)
5. ncbi_downstream(id = y, downto = downto, intermediate = intermediate, 
 .     ...)

Any idea where I'm going wrong?

[sckott]

thanks for the issue and for including your session info. i'll have a look

[sckott]

there was a bug in there that I fixed, but the main issue is that "no rank" is not a rank that can be used. It can be anywhere in the rank hierarchy, so can not be used in the context of downstream().

for your case perhaps "strain" would work?

z <- downstream(as.uid(77643), db = 'ncbi', downto = 'strain')
head(z[[1]])

  childtaxa_id                        childtaxa_name   rank
1      1305739        Mycobacterium orygis 112400015 strain
2      1246634 Mycobacterium canettii CIPT 140070007 strain
3      1246121 Mycobacterium canettii CIPT 140070013 strain
4      1246120 Mycobacterium canettii CIPT 140070005 strain
5      1246119 Mycobacterium canettii CIPT 140070002 strain
6      1205677 Mycobacterium canettii CIPT 140070017 strain