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Bio::Phylo::IO 0.17 RC6

  Date Added: June 19, 2010  |  Visits: 451

Bio::Phylo::IO 0.17

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Bio::Phylo::IO Perl module contains input and output of phylogenetic data. SYNOPSIS use Bio::Phylo::IO; # parsing a tree from a newick string my $tree_string = (((A,B),C),D);; my $tree = Bio::Phylo::IO->parse( -string => $tree_string, # old parser, always adds node labels -format => newick, )->first; # note: newick parsers return # Bio::Phylo::Forest! Call # ->first to retrieve the first # tree of the forest. # prints Bio::Phylo::Forest::Tree print ref $tree, "n"; # parsing a table my $table_string = qq(A,1,2|B,1,2|C,2,2|D,2,1); my $matrix = Bio::Phylo::IO->parse( -string => $table_string, -format => table, # Data type, see Bio::Phylo::Parsers::Table -type => STANDARD, # field separator -fieldsep => ,, # line separator -linesep => | ); # prints Bio::Phylo::Matrices::Matrix print ref $matrix, "n"; # parsing a list of taxa my $taxa_string = A:B:C:D; my $taxa = Bio::Phylo::IO->parse( -string => $taxa_string, -format => taxlist, -fieldsep => : ); # prints Bio::Phylo::Taxa print ref $taxa, "n"; # matches taxon names in tree to $taxa object $tree->cross_reference($taxa); # likewise for matrix $matrix->cross_reference($taxa); print Bio::Phylo::IO->unparse( # pass the tree object, # crossreferenced to taxa, which # are crossreferenced to the matrix -phylo => $tree, -format => pagel ); # prints a pagel data file: #4 2 #A,n1,0.000000,1,2 #B,n1,0.000000,1,2 #n1,n2,0.000000 #C,n2,0.000000,2,2 #n2,n3,0.000000 #D,n3,0.000000,2,1.

Requirements: No special requirements
Platforms: Linux
Keyword: Biophyloio Input And Output Io Io Perl Libraries Perl Module Phylogenetic Print Programming String Taxa Tree
Users rating: 0/10

License: Freeware Size: 143.36 KB
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