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)

Arguments

alignment	an alignment list object with id and ali components, similar to that generated by read.fasta.
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 file; otherwise, it will overwrite the contents of file.

Value

Called for its effect.

References

Grant, B.J. et al. (2006) Bioinformatics 22, 2695--2696.

Author

Xin-Qiu Yao

Note

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.

See also

read.fasta, read.fasta.pdb, write.fasta

Examples

# \donttest{
# 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") )

}
#> Fetching... Please wait. Done.
#> 
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  |======================================================================| 100%
#> 
#> See the output file:
#> /var/folders/xf/qznxnpf91vb1wm4xwgnbt0xr0000gn/T//Rtmp4WslmZ/eg.pir
# }