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. #> | | | 0% | |======================================================================| 100% #> #> See the output file: #> /var/folders/xf/qznxnpf91vb1wm4xwgnbt0xr0000gn/T//Rtmp4WslmZ/eg.pir
# }