class TaxaClassifier(object): """Can assign taxonomy to a FASTA file of random shotgun sequences.""" all_paths = """ /tree.txt /annot.txt /graph.xml /graph.png """ def __repr__(self): return '<%s object of %s>' % (self.__class__.__name__, self.parent) def __init__(self): # Files # self.taxa_file = FilePath(self.base_dir + self.sample.name + '.txt') self.class_out_file = FilePath(self.base_dir + self.sample.type + '.txt') self.class_out_file.link_from(self.taxa_file, safe=True) # NMDS # self.coord = (0,0) def make_graph(self): # Convert # graphconv = sh.Command(home + "share/metaphlan/plotting_scripts/metaphlan2graphlan.py") graphconv(self.taxa_file, '--tree_file', self.p.tree, '--annot_file', self.p.annot) # Annotate # annotate = sh.Command(home + "share/graphlan/graphlan_annotate.py") annotate('--annot', self.p.annot, self.p.tree, self.p.xml) # Graph # graphlan = sh.Command(home + "share/graphlan/graphlan.py") graphlan('--dpi', 200, self.p.xml, self.p.png)