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Fixing bug on small alignment https://github.com/lbbe-software/seqinr/issues/10 #11

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merged 2 commits into from
Jul 16, 2024
Merged

Fixing bug on small alignment https://github.com/lbbe-software/seqinr/issues/10 #11

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1f9246b
Fixing bug on small alignment https://github.com/lbbe-software/seqinr…
simonpenel Jul 15, 2024
1aaf4bc
Improve fix https://github.com/lbbe-software/seqinr/issues/10 . Just …
simonpenel Jul 16, 2024
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2 changes: 1 addition & 1 deletion DESCRIPTION
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
Package: seqinr
Title: Biological Sequences Retrieval and Analysis
Version: 4.2-39
Version: 4.2-41
Depends: R (>= 2.10.0)
Imports: ade4,segmented
Authors@R: c(person("Delphine", "Charif", role = "aut"),
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8 changes: 6 additions & 2 deletions R/read.alignment.R
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Expand Up @@ -54,7 +54,6 @@ read.alignment <- function(file, format, forceToLower = TRUE,
white <- characters[-length(characters)] == " "
black <- characters[-1] != " "
istart <- which(white & black)[1]

# Get sequence names
nam <- character()
nseq <- 1
Expand All @@ -74,6 +73,12 @@ read.alignment <- function(file, format, forceToLower = TRUE,
nseq <- nseq - 1
break # alredy seen
}
# this happens with short alignments because seqname is never found
# in mam
if (seqname == 'NA') {
nseq <- nseq - 1
break
}
nam[nseq] <- seqname
nseq <- nseq + 1
}
Expand Down Expand Up @@ -101,7 +106,6 @@ read.alignment <- function(file, format, forceToLower = TRUE,
seq[[iseq]] <- paste0(filecontent[ii], collapse = "")
if(forceToLower) seq[[iseq]] <- tolower(seq[[iseq]])
}
#
return(as.alignment(nb = nseq, nam = nam, seq = seq, com = NA))
}

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