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Update ReadTaxonomyCanSNPer.py #69

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Update ReadTaxonomyCanSNPer.py #69

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14 changes: 8 additions & 6 deletions flextaxd/modules/ReadTaxonomyCanSNPer.py
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Original file line number Diff line number Diff line change
Expand Up @@ -26,7 +26,7 @@ def __str__(self):

class ReadTaxonomyCanSNPer(ReadTaxonomy):
"""docstring for ReadTaxonomyCanSNPer."""
def __init__(self, taxonomy_file=False, database=".canSNPdb", taxid_base=1,root_name=False,rank="family", verbose=False,**kwargs):
def __init__(self, taxonomy_file=False, database=".canSNPdb", taxid_base=1,root_name=False,rank="family", cnp=False, verbose=False,**kwargs):
super(ReadTaxonomyCanSNPer, self).__init__(taxonomy_file=taxonomy_file, database=database,verbose=verbose,**kwargs)
self.input = taxonomy_file
self.taxonomy = {}
Expand All @@ -37,18 +37,20 @@ def __init__(self, taxonomy_file=False, database=".canSNPdb", taxid_base=1,root
if not root_name:
logger.info("Fetching root name from file")
root_name = self.get_root_name(taxonomy_file)
logger.info("Adding, cellular organism node")
c_i = self.add_node("cellular organisms")
logger.info("Adding root node {node}!".format(node=root_name))
if not cnp:
logger.info("Adding, cellular organism node")
c_i = self.add_node("cellular organisms")
logger.info("Adding root node {node}!".format(node=root_name))
root_i = self.add_node(root_name)
self.taxid_num =taxid_base ## reset
logger.debug("Adding ranks!")
if rank != "no rank":
self.add_rank("no rank")
self.add_rank(rank)
if root_name != "cellular organisms":

if root_name != "cellular organisms" and not cnp:
self.add_link(c_i,1)
if root_name != "root":
if root_name != "root" and not cnp:
self.add_link(root_i,c_i,rank=rank) ## root is always added as top parent if not one force 1
self.taxonomy[root_i] = 1 ## Add local link to root
self.names = {}
Expand Down