ecolog ecolog - 2 months ago 6
R Question

r - Last match of regular expression

I am looking for an

R
pattern matching expression that extracts the last fully populated taxonomy in each element in the list. The taxonomies have always the same format (one letter two underscores and a word (some times inside square brackets). Taxonomies that are not fully populated they don't have the word after the two underscores.

I was able to build a expression that worked in one regular expression builder website
(.\_\_[A-Za-z\[\]]+)(?!.*__[A-Za-z\[\])

but had not luck using it or transforming it to use an
R
pattern matching methods in
grep {base}
or anything similar. Here is one of the things I tried

clean=gsub("(.\_\_[A-Za-z[]]+)(?!.*__[A-Za-z[]])","\\1",taxonomies,perl = TRUE)


Any suggestions?
Thanks!

taxonomies=
list('k__Bacteria; p__Bacteroidetes; c__[Saprospirae]; o__[Saprospirales]; f__Chitinophagaceae; g__; s__'
,'k__Bacteria; p__Actinobacteria; c__MB-A2-108; o__0319-7L14; f__; g__; s__'
,'k__Bacteria; p__Actinobacteria; c__Actinobacteria; o__Actinomycetales;f__Corynebacteriaceae; g__Corynebacterium; s__'
,'k__Bacteria; p__Proteobacteria; c__Betaproteobacteria; o__Rhodocyclales; f__Rhodocyclaceae; g__Methyloversatilis; s__'
,'k__Bacteria; p__Proteobacteria; c__Deltaproteobacteria; o__Myxococcales; f__; g__; s__'
,'k__Bacteria; p__Proteobacteria; c__[Deltaproteobacteria]; o__[W123]; f__[W123]; g__[W123]; s__[W123.012.123]'
,'k__Bacteria; p__Bacteroidetes; c__[Saprospirae]; o__[Saprospirales]; f__Chitinophagaceae')


Desired output

[1] "f__Chitinophagaceae" "o__0319-7L14" "g__Corynebacterium"
[4] "g__Methyloversatilis" "o__Myxococcales" "s__[W123.012.123]"
[7] "f__Chitinophagaceae"


Edit
Included desired output, example code gsub that is not working.

Answer

We can use stri_extract_last from stringi

library(stringi)
stri_extract_last(unlist(taxonomies), regex = '[A-Za-z]__\\[*[[:alnum:].-]+\\]*')
#[1] "f__Chitinophagaceae"  "o__0319-7L14" "g__Corynebacterium"   
#[4] "g__Methyloversatilis" "o__Myxococcales"  "s__[W123.012.123]"   
#[7] "f__Chitinophagaceae" 

Here, I assumed that the OP meant to extract the characters within **...**. It must be some formatting issue as it was not shown in BOLD.

data

taxonomies=list(
  'k__Bacteria; p__Bacteroidetes; c__[Saprospirae]; o__[Saprospirales]; f__Chitinophagaceae; g__; s__'
  ,'k__Bacteria; p__Actinobacteria; c__MB-A2-108; o__0319-7L14; f__; g__; s__'
  ,'k__Bacteria; p__Actinobacteria; c__Actinobacteria; o__Actinomycetales;f__Corynebacteriaceae; g__Corynebacterium; s__'
 ,'k__Bacteria; p__Proteobacteria; c__Betaproteobacteria; o__Rhodocyclales; f__Rhodocyclaceae; g__Methyloversatilis; s__'
 ,'k__Bacteria; p__Proteobacteria; c__Deltaproteobacteria; o__Myxococcales; f__; g__; s__'
  ,'k__Bacteria; p__Proteobacteria; c__[Deltaproteobacteria]; o__[W123]; f__[W123]; g__[W123]; s__[W123.012.123]'
  ,'k__Bacteria; p__Bacteroidetes; c__[Saprospirae]; o__[Saprospirales]; f__Chitinophagaceae'
  )