chambm / ahocorasicktrie Goto Github PK
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License: Apache License 2.0
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loss of keyword labels
Dear Matt,
the AhoCorasickTrie search does a super fast job. Really cool. I tried to do the same with the normal pattern matching functions from bioc Biostrings, but that took forever. Martin Morgan finally advised me to try your package. But I have a little problem regarding how it deals with names/labels of keywords. Here is an example from my code:
ref.proteome <- readAAStringSet(filepath = "uniprot-proteome_UP000000589.fasta")
n <- 10
peptides <- strip.mods(strip.ends(GluC.endpoint.peptide$ComparisonResult$Protein[1:n])) #first 10 peptides
names(peptides) <- GluC.endpoint.peptide$ComparisonResult$Protein[1:n] #put mod peptide as labels
proteins <- BiocGenerics::sapply(ref.proteome, toString) # full reference proteome
l <- AhoCorasickSearch(keywords = peptides, text = proteins, alphabet = "aminoacid", groupByKeyword = TRUE)
So far everything works perfectly, but the returned data structure looks like:
> head(l)
$ADLAEEYSKDR
$ADLAEEYSKDR[[1]]
$ADLAEEYSKDR[[1]]$Text
[1] "sp|P68037|UB2L3_MOUSE Ubiquitin-conjugating enzyme E2 L3 OS=Mus musculus GN=Ube2l3 PE=1 SV=1"
$ADLAEEYSKDR[[1]]$Offset
[1] 123
$ADLIAYLKKATNE
$ADLIAYLKKATNE[[1]]
$ADLIAYLKKATNE[[1]]$Text
[1] "sp|P62897|CYC_MOUSE Cytochrome c, somatic OS=Mus musculus GN=Cycs PE=1 SV=2"
$ADLIAYLKKATNE[[1]]$Offset
[1] 93
...
The labels of the keywords are lost! Instead the keywords as such are used as labels. Remember I took care to have a named vector of keywords (peptides) to not lose the associated modification pattern:
> names(peptides)
[1] "AAC[+57.0]YTK[+28.0]LLE" "AAK[+28.0]LAPEFAK[+28.0]R"
[3] "AAMQQDPVASSHK[+28.0]IDAK[+28.0]TYR" "AASQPGELK[+28.0]DWFVGR"
[5] "AC[+57.0]IPQSFTVDSSK[+28.0]AGLAPLEVR" "ADGYVLEGK[+28.0]EL"
[7] "ADLAEEYSK[+28.0]DR" "ADLEC[+57.0]TK[+28.0]PAA"
[9] "ADLIAYLK[+28.0]K[+28.0]ATNE" "ADLPTLGFTHFQPAQLTTVGK[+28.0]R"
Would it be possible to tweek the package in a way that the keyword AND text labels are preserved in the data structure returned by the matching function?
Greetings,
Tobias Kockmann
Crash rather than error when alphabet = 'aminoacid'
package version 0.1.2
library(AhoCorasickTrie)
# this works fine
keywords = c("Abra", "cadabra", "is", "the", "Magic", "Word")
str( AhoCorasickSearchList(keywords, list(c("What in", "the world"), c("is"), "secret about", "the Magic Word?")) )
# this crashes my R session in RStudio
str( AhoCorasickSearchList(keywords, list(c("What in", "the world"), c("is"), "secret about", "the Magic Word?"), alphabet = 'aminoacid') )data.frame-like return value?
I quite like your package and it's focus, so have a suggestion that is meant to be constructive. List-of-list data structures are difficult and inefficient to deal with in R, and a good chunk of the community is into 'tidy' data which emphasizes 'long-form' data.frame-like structures. Thus the suggestion that the return value from, e.g.,
> keywords = c("AAA", "CC")
> text = c("CAAACCAAA", "CAAAC")
> res = AhoCorasickSearch(keywords, text)
might be
> res
Keyword Text_index Offset
1 AAA 1 2
2 CC 1 5
3 AAA 1 7
4 AAA 2 2
or perhaps Keyword_index. I recognize that the list-of-lists representation will be a more memory-efficient representation when a keyword matches many locations in text.
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