write.pir: Write PIR Formated Sequences

In bio3d: Biological Structure Analysis

Write PIR Formated Sequences

Description

Write aligned or un-aligned sequences to a PIR format file.

Usage

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.

Note

PIR is required format for input alignment file to use Modeller. For a description of PIR format see: https://salilab.org/modeller/manual/node501.html.

Author(s)

Xin-Qiu Yao

References

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

See Also

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

Examples

# Needs MUSCLE installed - testing excluded

if(check.utility("muscle")) {

try({

## 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") )

}, silent=TRUE)
if(inherits(.Last.value, "try-error")) {
   message("Need internet to run the example")
}
}

bio3d documentation built on Oct. 30, 2024, 1:08 a.m.