Write PIR Formated Sequences
Write aligned or un-aligned sequences to a PIR format file.
write.pir(alignment=NULL, ids=NULL, seqs=alignment$ali, pdb.file = NULL, chain.first = NULL, resno.first = NULL, chain.last = NULL, resno.last = NULL, file, append = FALSE)
alignment |
an alignment list object with |
ids |
a vector of sequence names to serve as sequence identifers |
seqs |
an sequence or alignment character matrix or vector with a row per sequence |
pdb.file |
a vector of pdb filenames; For sequence, provide "". |
chain.first |
a vector of chain id for the first residue. |
resno.first |
a vector of residue number for the first residue. |
chain.last |
a vector of chain id for the last residue. |
resno.last |
a vector of residue number for the last residue. |
file |
name of output file. |
append |
logical, if TRUE output will be appended to
|
Called for its effect.
PIR is required format for input alignment file to use Modeller. For a description of PIR format see: https://salilab.org/modeller/manual/node488.html.
Xin-Qiu Yao
Grant, B.J. et al. (2006) Bioinformatics 22, 2695–2696.
# Needs MUSCLE installed - testing excluded
if(check.utility("muscle")) {
## Generate an input file for structural modeling of
## transducin G-alpha subunit using the template 3SN6_A
## Read transducin alpha subunit sequence
seq <- get.seq("P04695", outfile = tempfile())
## Read structure template
path = tempdir()
pdb.file <- get.pdb("3sn6_A", path = path, split = TRUE)
pdb <- read.pdb(pdb.file)
## Build an alignment between template and target
aln <- seqaln(seqbind(pdbseq(pdb), seq), id = c("3sn6_A", seq$id), outfile = tempfile())
## Write PIR format alignment file
outfile = file.path(tempdir(), "eg.pir")
write.pir(aln, pdb.file = c(pdb.file, ""), file = outfile)
invisible( cat("\nSee the output file:", outfile, sep = "\n") )
}Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.