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currocam / HMMERutils

A bunch of convenient functions to search for homologous sequences using the HMMER API, annotate them taxonomically, calculate physicochemical properties and facilitate exploratory analysis of homologous sequence data.
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Bug: filter_hmmer creates empty rows #21

Closed currocam closed 1 year ago

currocam commented 1 year ago

La función filter_hmmer en lugar de filtrar crea filas con todos los valores inicializados a NA.

Replicar:

uniprot.url <- "https://rest.uniprot.org/uniprotkb/stream?compressed=true&format=fasta&query=%28%28proteome%3AUP000464024%29%29"
sars.cov.fasta <- readAAStringSet(uniprot.url)
names(sars.cov.fasta) <- names(sars.cov.fasta) %>%
  parse_fasta_headers()
VEMP_SARS <- sars.cov.fasta$VEMP_SARS #Envelope small membrane protein
hmmer.VEMP_SARS <- search_phmmer(
  seq = VEMP_SARS, seqdb = "swissprot", verbose = FALSE
  )
(
 hmmer.VEMP_SARS <- filter_hmmer(hmmer.VEMP_SARS,threshold = 10^-5)
)
Juane99 commented 1 year ago

Buenas Curro,

Estoy teniendo problemas para replicar el bug. Parece ser que sars.cov.fasta$VEMP_SARS vale NULL.

Un saludo,

Juan