Write pli files used by SIFTER

Write pli files used by SIFTER

write_pli(
  family_id,
  protein_name,
  protein_number,
  go_number,
  moc = "EXP",
  file = ""
)

Arguments

family_id

Character scalar. Name of the family

protein_name, protein_number, go_number, moc

Vectors of the same length

file

Character scalar passed to cat.

Value

A string with the XML file.

Examples

set.seed(882)
atree <- raphylo(5)
write_pli(
  family_id      = "a family",
  protein_name   = atree$tree$tip.label,
  protein_number = 1:Ntip(atree),
  go_number      = "GO:123123123123"
)
#> <?xml version="1.0"?>
#> <Family>
#>   <FamilyID>a family</FamilyID>
#>   <Protein>
#>     <ProteinName>1</ProteinName>
#>     <ProteinNumber>1</ProteinNumber>
#>     <GONumber>[GO:123123123123]</GONumber>
#>     <MOC>[EXP]</MOC>
#>   </Protein>
#>   <Protein>
#>     <ProteinName>2</ProteinName>
#>     <ProteinNumber>2</ProteinNumber>
#>     <GONumber>[GO:123123123123]</GONumber>
#>     <MOC>[EXP]</MOC>
#>   </Protein>
#>   <Protein>
#>     <ProteinName>3</ProteinName>
#>     <ProteinNumber>3</ProteinNumber>
#>     <GONumber>[GO:123123123123]</GONumber>
#>     <MOC>[EXP]</MOC>
#>   </Protein>
#>   <Protein>
#>     <ProteinName>4</ProteinName>
#>     <ProteinNumber>4</ProteinNumber>
#>     <GONumber>[GO:123123123123]</GONumber>
#>     <MOC>[EXP]</MOC>
#>   </Protein>
#>   <Protein>
#>     <ProteinName>5</ProteinName>
#>     <ProteinNumber>5</ProteinNumber>
#>     <GONumber>[GO:123123123123]</GONumber>
#>     <MOC>[EXP]</MOC>
#>   </Protein>
#> </Family>
# Possible outcome:
#<?xml version="1.0"?>
#<Family>
#  <FamilyID>a family</FamilyID>
#  <Protein>
#    <ProteinName>1</ProteinName>
#    <ProteinNumber>1</ProteinNumber>
#    <GONumber>[GO:123123123123]</GONumber>
#    <MOC>[EXP]</MOC>
#  </Protein>
#  <Protein>
#    <ProteinName>2</ProteinName>
#    <ProteinNumber>2</ProteinNumber>
#    <GONumber>[GO:123123123123]</GONumber>
#    <MOC>[EXP]</MOC>
#  </Protein>
#  <Protein>
#    <ProteinName>3</ProteinName>
#    <ProteinNumber>3</ProteinNumber>
#    <GONumber>[GO:123123123123]</GONumber>
#    <MOC>[EXP]</MOC>
#  </Protein>
#  <Protein>
#    <ProteinName>4</ProteinName>
#    <ProteinNumber>4</ProteinNumber>
#    <GONumber>[GO:123123123123]</GONumber>
#    <MOC>[EXP]</MOC>
#  </Protein>
#  <Protein>
#    <ProteinName>5</ProteinName>
#    <ProteinNumber>5</ProteinNumber>
#    <GONumber>[GO:123123123123]</GONumber>
#    <MOC>[EXP]</MOC>
#  </Protein>
#</Family>