Top Level Namespace
Defined Under Namespace
Modules: Bio
Instance Method Summary collapse
- #getTreeObjFromMcmctree(tree_file) ⇒ Object
- #getTreeObjFromNwkString(nwk_str) ⇒ Object
- #getTreeObjs(tree_file, num = 1000000) ⇒ Object
Instance Method Details
#getTreeObjFromMcmctree(tree_file) ⇒ Object
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# File 'lib/bio/nwk.rb', line 248 def getTreeObjFromMcmctree(tree_file) first_line = `head -1 #{tree_file}`.chomp tree_txt = `tail -1 #{tree_file}`.chomp treeio = Bio::Newick.new(tree_txt).tree return([first_line, treeio]) end |
#getTreeObjFromNwkString(nwk_str) ⇒ Object
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# File 'lib/bio/nwk.rb', line 241 def getTreeObjFromNwkString(nwk_str) nwk = Bio::Newick.new(nwk_str) tree = nwk.tree return(tree) end |
#getTreeObjs(tree_file, num = 1000000) ⇒ Object
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# File 'lib/bio/nwk.rb', line 227 def getTreeObjs(tree_file, num=1000000) trees = Array.new treeio = Bio::FlatFile.open(Bio::Newick, tree_file=='-' ? $stdin : tree_file) while newick = treeio.next_entry tree = newick.tree tree.[:bootstrap_style] = :traditional next if tree.nodes.empty? trees << tree break if trees.size >= num end return(trees) end |