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)
