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lookupRegion.py
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#!/usr/bin/env python3
#
# Created by Bruno Costa @ITQB
# 19/10/2017
#
# Lookup functions to identify region in genome
#
class LookupRegion:
#Lookup function to identify regions in genome
def __init__(self,genome,region):
#Loads genome and region. Checks if seqname in region exists on genome
self.genome=genome.genome
self.region=region
self.debug=False
try:
self.seqname=self.genome[self.region[0]]
if self.debug:
print(" --------")
print(" | |")
print(str(self.region[1])+" "+str(self.region[2]))
except KeyError:
if self.debug:
print(region[0]+" not in genome annotation")
self.seqname=None
def get_surrounding_genes(self):
#Get the downstream and upstream genes of the region
if not self.is_across_gene_boundries() and not self.is_inside_gene():
return [self.get_downstream_gene(),self.get_upstream_gene()]
elif not self.is_across_gene_boundries() and self.is_inside_gene():
return [self.get_downstream_gene(),self.get_outermost_gene(),self.get_upstream_gene()]
#elif self.is_across_gene_boundries:
# if self.is_across_left_gene_boundry() and not self.is_across_right_gene_boundry():
# return [self.get_downstream_gene(),,self.get_upstream_gene()]
# return [None]
# elif: self.is_across_right_gene_boundry() and not self.is_across_left_gene_boundry():
# ##Need to change the def to get more than one up down steam gene by choice.
# ##return [self.get_downstream_gene(),,self.get_upstream_gene()]
# return [None]
#
else:
print("Not implemented - Is inside gene or is across both gene boundary")
return [None]
def is_inside_gene(self):
#self.region if a tuple with start and end for a seqname (seqname,start,end)
if self.seqname is not None:
downstream=[ gene for gene in self.seqname if self.region[1]>gene.start and self.region[2]<gene.end ]
return len(downstream)==1
else:
return False
def get_outermost_gene(self):
#This applies if strictly inside gene and if across one gene boundary
if self.seqname is not None:
if self.is_inside_gene():
outermost_gene=[ gene for gene in self.seqname if self.region[1]>gene.start and self.region[2]<gene.end ] #Change this variable
if len(outermost_gene)==1:
return outermost_gene[0]
else:
return None
elif self.is_across_gene_boundries():
if self.is_across_left_gene_boundry(multiple=False):
#get upstream gene get u the current gene
return self.get_upstream_gene()
if self.is_across_right_gene_boundry(multiple=False):
#get downstream gene get u the current gene
return self.get_downstream_gene()
else:
return False
def is_across_left_gene_boundry(self,multiple):
#Check if region crosses a left gene boundary
if self.seqname is None:
return False
else:
acrossBoundry=[ gene for gene in self.seqname if self.region[1]<gene.start and self.region[2]>gene.start and self.region[2]<gene.end ]
if multiple:
return len(acrossBoundry)>1
else:
return len(acrossBoundry)==1
def is_across_right_gene_boundry(self,multiple):
#Check if region crosses a right gene boundary
if self.seqname is None:
return False
else:
acrossBoundry=[ gene for gene in self.seqname if self.region[1]>gene.start and self.region[1]<gene.end and self.region[2]>gene.end ]
if multiple:
return len(acrossBoundry)>1
else:
return len(acrossBoundry)==1
def is_across_gene_boundries(self):
#Check if self.region is across gene 1 boundary
return self.is_across_left_gene_boundry(multiple=False) or self.is_across_right_gene_boundry(multiple=False)
def percentagem_of_region_outside_gene(self):
if self.is_across_gene_boundries():
regionSize=int(self.region[2])-int(self.region[1])
if self.is_across_left_gene_boundry(multiple=False):
#get upstream gene get u the current gene
return round(float(( self.get_upstream_gene().start - self.region[1] )/regionSize),2)
if self.is_across_right_gene_boundry(multiple=False):
#get downstream gene get u the current gene
return round(float(( self.region[2] - self.get_downstream_gene().end ) / regionSize),2)
else:
return -1
def contains_serveral_genes(self):
#Test if self.region crossed multiple gene boundaries
#Not implemented or maybe it is. | Didn't test the logic
return self.is_across_left_gene_boundry(multiple=True) or self.is_across_right_gene_boundry(multiple=True)
def get_downstream_gene(self):
if self.seqname is not None:
downstream=[ gene for gene in self.seqname if self.region[1]>gene.start and self.region[2]>gene.end ]
##print((downstream[-1].start,downstream[-1].end))
if len(downstream)>0:
if self.debug:
print(" --------")
print(" | |")
print(str(downstream[0].start)+" "+str(downstream[0].end))
return downstream[-1]
else:
return None
else:
return None
def get_upstream_gene(self):
if self.seqname is not None:
upstream=[ gene for gene in self.seqname if self.region[1]<gene.start and self.region[2]<gene.end ]
#print((upstream[0].start,upstream[0].end))
if len(upstream)>0:
if self.debug:
print(" --------")
print(" | |")
print(str(upstream[0].start)+" "+str(upstream[0].end))
return upstream[0]
else:
return None
else:
return None