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run 2to3 (only changes one import and adds '()' to a lot of print statements #55

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b6ef9c9
run 2to3 (only changes one import and adds '()' to a lot of print sta…
moritzschaefer Mar 8, 2021
640ff37
Fix percent and make proper integer division
moritzschaefer Mar 9, 2021
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103 changes: 52 additions & 51 deletions src/CombineNearbyInteraction.py
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Original file line number Diff line number Diff line change
Expand Up @@ -26,12 +26,14 @@
Vijay-Ay lab, LJI
"""

import heapq
import math
import os
import sys
import math
from optparse import OptionParser

import networkx as nx
from Queue import heapq


#==========================================================
# this function returns the element below which top K % of
Expand Down Expand Up @@ -145,21 +147,21 @@ def main():

# print the parameters
if 1:
print '****** Merge filtering of adjacent loops is enabled *****'
print '***** within function of merged filtering - printing the parameters ***'
print '*** bin_size: ', bin_size
print '*** headerInp: ', headerInp
print '*** connectivity_rule: ', connectivity_rule
print '*** TopPctElem: ', TopPctElem
print '*** NeighborHoodBinThr: ', NeighborHoodBinThr
print '*** QValCol: ', QValCol
print '*** PValCol: ', PValCol
print '*** SortOrder: ', SortOrder
print('****** Merge filtering of adjacent loops is enabled *****')
print('***** within function of merged filtering - printing the parameters ***')
print('*** bin_size: ', bin_size)
print('*** headerInp: ', headerInp)
print('*** connectivity_rule: ', connectivity_rule)
print('*** TopPctElem: ', TopPctElem)
print('*** NeighborHoodBinThr: ', NeighborHoodBinThr)
print('*** QValCol: ', QValCol)
print('*** PValCol: ', PValCol)
print('*** SortOrder: ', SortOrder)

# output directory
OutDir = os.path.dirname(os.path.realpath(OutFile))
if 1:
print 'OutDir: ', str(OutDir)
print('OutDir: ', str(OutDir))

# open the output file
# if input interaction file has header information,
Expand Down Expand Up @@ -196,7 +198,7 @@ def main():
for l in fp_in.readlines():
currchrname = (l.rstrip()).split()[0]
TargetChrList.append(currchrname)
print 'list of chromosomes: ', str(TargetChrList)
print('list of chromosomes: ', str(TargetChrList))
# remove temporary files
sys_cmd = "rm " + temp_chr_log_file
os.system(sys_cmd)
Expand All @@ -207,7 +209,7 @@ def main():
for chridx in range(len(TargetChrList)):
curr_chr = TargetChrList[chridx]
if 1:
print 'Processing the chromosome: ', str(curr_chr)
print('Processing the chromosome: ', str(curr_chr))

# extract the interactions of current chromosome from the complete set of interactions
tempchrdumpfile = OutDir + '/Temp_chr_Dump.bed'
Expand All @@ -222,11 +224,11 @@ def main():

if (num_Int == 0):
if 0:
print 'Number of interactions for this chromosome = 0 --- continue'
print('Number of interactions for this chromosome = 0 --- continue')
continue

if 0:
print 'Extracted interactions for the current chromosome'
print('Extracted interactions for the current chromosome')

# # extract also the max span of interactions (6th column maximum element)
# # so as to estimate the matrix size
Expand Down Expand Up @@ -259,8 +261,8 @@ def main():
for line in fp:
linecontents = (line.rstrip()).split()
# we set the bin number according to the end coordinate
bin1 = int(linecontents[2]) / bin_size
bin2 = int(linecontents[5]) / bin_size
bin1 = int(linecontents[2]) // bin_size
bin2 = int(linecontents[5]) // bin_size
if (bin1 < bin2):
curr_key = (bin1, bin2)
else:
Expand All @@ -271,7 +273,7 @@ def main():
# add the node to the given graph as well
G.add_node(curr_key)
if 0:
print 'Current interaction: ', str(line), ' ------ curr_key: ', curr_key
print('Current interaction: ', str(line), ' ------ curr_key: ', curr_key)

# now check the nodes of G
# assign edges of G according to the 8 / 4 connectivity rule (according to the input parameter)
Expand All @@ -282,35 +284,35 @@ def main():
for j in range(i+1, len(nodelist)):
node2 = nodelist[j]
if 0:
print 'Checking the edge between node 1: ', node1, ' and node 2: ', node2
print('Checking the edge between node 1: ', node1, ' and node 2: ', node2)
# check if there should be an edge between node1 and node2
# according to the desired connectivity rule
if (connectivity_rule == 8):
if (abs(node1[0] - node2[0]) <= 1) and (abs(node1[1] - node2[1]) <= 1):
G.add_edge(node1, node2)
if 0:
print '8 connectivity Edge between node 1: ', node1, ' and node 2: ', node2
print('8 connectivity Edge between node 1: ', node1, ' and node 2: ', node2)
if (connectivity_rule == 4):
if ((abs(node1[0] - node2[0]) + abs(node1[1] - node2[1])) <= 1):
G.add_edge(node1, node2)
if 0:
print '4 connectivity Edge between node 1: ', node1, ' and node 2: ', node2
print('4 connectivity Edge between node 1: ', node1, ' and node 2: ', node2)

# check the edges of G
edgelist = list(G.edges())

if 1:
print 'No of nodes of G: ', G.number_of_nodes()
print 'No of edges of G: ', G.number_of_edges()
print 'Number of connected components of G: ', nx.number_connected_components(G)
print('No of nodes of G: ', G.number_of_nodes())
print('No of edges of G: ', G.number_of_edges())
print('Number of connected components of G: ', nx.number_connected_components(G))

# scan through individual connected components
# for each such connected component (list of interactions)
# we find a representative interaction and print it in the final output file
list_conn_comp = sorted(nx.connected_components(G), key = len, reverse=True)

if 0:
print '\n\n**** Number of connected components: ', len(list_conn_comp), ' ****\n\n'
print('\n\n**** Number of connected components: ', len(list_conn_comp), ' ****\n\n')

#====================
# process individual connected components
Expand All @@ -319,31 +321,31 @@ def main():
# a connected component - a particular list of connected nodes
curr_comp_list = list(list_conn_comp[i])
if 0:
print '\n\n\n ===>>>>> Processing the connected component no: ', i, ' list: ', str(curr_comp_list), ' number of elements: ', len(curr_comp_list)
print('\n\n\n ===>>>>> Processing the connected component no: ', i, ' list: ', str(curr_comp_list), ' number of elements: ', len(curr_comp_list))

# from the first interacting bin set, get the lower and higher bin index
min_idx_bin1 = min([x[0] for x in curr_comp_list])
max_idx_bin1 = max([x[0] for x in curr_comp_list])
if 0:
print 'min_idx_bin1: ', min_idx_bin1, ' max_idx_bin1: ', max_idx_bin1
print('min_idx_bin1: ', min_idx_bin1, ' max_idx_bin1: ', max_idx_bin1)

# get the span of coordinates for the first interacting bin (set)
span_low_bin1 = (min_idx_bin1 - 1) * bin_size
span_high_bin1 = max_idx_bin1 * bin_size
if 0:
print 'span_low_bin1: ', span_low_bin1, ' span_high_bin1: ', span_high_bin1
print('span_low_bin1: ', span_low_bin1, ' span_high_bin1: ', span_high_bin1)

# from the second interacting bin set, get the lower and higher bin index
min_idx_bin2 = min([x[1] for x in curr_comp_list])
max_idx_bin2 = max([x[1] for x in curr_comp_list])
if 0:
print 'min_idx_bin2: ', min_idx_bin2, ' max_idx_bin2: ', max_idx_bin2
print('min_idx_bin2: ', min_idx_bin2, ' max_idx_bin2: ', max_idx_bin2)

# get the span of coordinates for the first interacting bin (set)
span_low_bin2 = (min_idx_bin2 - 1) * bin_size
span_high_bin2 = max_idx_bin2 * bin_size
if 0:
print 'span_low_bin2: ', span_low_bin2, ' span_high_bin2: ', span_high_bin2
print('span_low_bin2: ', span_low_bin2, ' span_high_bin2: ', span_high_bin2)

# sum of contact counts for all the interacting bins
# within this set of connected nodes
Expand All @@ -362,10 +364,10 @@ def main():
# % of bin pairs within the region spanned by this connected component
# having significant interaction
# the higher the %, the better this component is strongly connected
Percent_Significant_BinPair = (possible_bin_pairs * 1.0) / total_possible_bin_pairs
Percent_Significant_BinPair = (possible_bin_pairs * 100) // total_possible_bin_pairs

if 0:
print ' ==>>> total_possible_bin_pairs: ', total_possible_bin_pairs, ' possible_bin_pairs: ', possible_bin_pairs, ' % clique: ', Percent_Significant_BinPair
print(' ==>>> total_possible_bin_pairs: ', total_possible_bin_pairs, ' possible_bin_pairs: ', possible_bin_pairs, ' % clique: ', Percent_Significant_BinPair)


#==================================================
Expand All @@ -387,7 +389,7 @@ def main():
curr_key_bin1_mid = (((curr_key[0] - 1) * bin_size) + (curr_key[0] * bin_size)) / 2
curr_key_bin2_mid = (((curr_key[1] - 1) * bin_size) + (curr_key[1] * bin_size)) / 2
if 0:
print ' Connected component index: ', j, ' curr_key: ', curr_key, ' bin 1 mid: ', curr_key_bin1_mid, ' bin 2 mid: ', curr_key_bin2_mid, ' CC: ', curr_cc, ' Pval: ', curr_pval, ' Qval: ', curr_qval
print(' Connected component index: ', j, ' curr_key: ', curr_key, ' bin 1 mid: ', curr_key_bin1_mid, ' bin 2 mid: ', curr_key_bin2_mid, ' CC: ', curr_cc, ' Pval: ', curr_pval, ' Qval: ', curr_qval)
if (j == 0):
# first index
rep_bin_key = curr_key
Expand All @@ -412,7 +414,7 @@ def main():
qval = CurrChrDict[rep_bin_key]._GetQVal()

if 0:
print '**** Selected bin key: ', rep_bin_key, ' start bin mid: ', (rep_bin1_low + rep_bin1_high)/2, ' end bin mid: ', (rep_bin2_low + rep_bin2_high) / 2, ' cc: ', cc, ' pval: ', pval, ' qval: ', qval
print('**** Selected bin key: ', rep_bin_key, ' start bin mid: ', (rep_bin1_low + rep_bin1_high)/2, ' end bin mid: ', (rep_bin2_low + rep_bin2_high) / 2, ' cc: ', cc, ' pval: ', pval, ' qval: ', qval)

# write the interaction in the specified output file
fp_outInt.write('\n' + str(curr_chr) + '\t' + str(rep_bin1_low) + '\t' + str(rep_bin1_high) + '\t' + str(curr_chr) + '\t' + str(rep_bin2_low) + '\t' + str(rep_bin2_high) + '\t' + str(cc) + '\t' + str(pval) + '\t' + str(qval) + '\t' + str(span_low_bin1) + '\t' + str(span_high_bin1) + '\t' + str(span_low_bin2) + '\t' + str(span_high_bin2) + '\t' + str(sum_cc) + '\t' + str(Percent_Significant_BinPair))
Expand Down Expand Up @@ -468,7 +470,7 @@ def main():
custom_qval = custom_percent(curr_conn_comp_QValList, TopPctElem, (SortOrder+1))

if 0:
print ' --> current connected component: max CC: ', max_cc, ' min Q val: ', min_qval, ' top K (TopPctElem): ', TopPctElem, ' custom_cc threshold: ', custom_cc, ' custom_qval threshold: ', custom_qval
print(' --> current connected component: max CC: ', max_cc, ' min Q val: ', min_qval, ' top K (TopPctElem): ', TopPctElem, ' custom_cc threshold: ', custom_cc, ' custom_qval threshold: ', custom_qval)

# this list stores the candidate interactions
# from this particular connected component
Expand All @@ -479,7 +481,7 @@ def main():
while (len(Curr_Comp_Tuple_List) > 0):
curr_elem = heapq.heappop(Curr_Comp_Tuple_List)
if 0:
print 'extracted element from heap: ', curr_elem
print('extracted element from heap: ', curr_elem)

#===================================
# earlier condition - 1 - sourya
Expand Down Expand Up @@ -509,7 +511,7 @@ def main():
subl = [curr_elem[2], curr_elem[3]]
Final_Rep_Key_List.append(subl)
if 0:
print '\t\t *** inserted element in the final list: ', str(subl), ' generated Final_Rep_Key_List: ', str(Final_Rep_Key_List)
print('\t\t *** inserted element in the final list: ', str(subl), ' generated Final_Rep_Key_List: ', str(Final_Rep_Key_List))
continue

# otherwise, check with the existing interactions
Expand All @@ -523,7 +525,7 @@ def main():
if (((abs(Final_Rep_Key_List[i][0] - curr_elem[2])) * bin_size) <= NeighborHoodBinThr) and (((abs(Final_Rep_Key_List[i][1] - curr_elem[3])) * bin_size) <= NeighborHoodBinThr):
flag = True
if 0:
print ' --- current element is within neighborhood of the bins indexed by ', i, ' of Final_Rep_Key_List'
print(' --- current element is within neighborhood of the bins indexed by ', i, ' of Final_Rep_Key_List')
break

if (flag == False):
Expand All @@ -532,7 +534,7 @@ def main():
subl = [curr_elem[2], curr_elem[3]]
Final_Rep_Key_List.append(subl)
if 0:
print '\t\t *** inserted element in the final list: ', str(subl), ' generated Final_Rep_Key_List: ', str(Final_Rep_Key_List)
print('\t\t *** inserted element in the final list: ', str(subl), ' generated Final_Rep_Key_List: ', str(Final_Rep_Key_List))

# now print the candidate interactions
# of the current component
Expand All @@ -549,7 +551,7 @@ def main():
qval = CurrChrDict[rep_bin_key]._GetQVal()

if 0:
print '**** Selected bin key: ', rep_bin_key, ' start bin mid: ', (rep_bin1_low + rep_bin1_high)/2, ' end bin mid: ', (rep_bin2_low + rep_bin2_high) / 2, ' cc: ', cc, ' pval: ', pval, ' qval: ', qval
print('**** Selected bin key: ', rep_bin_key, ' start bin mid: ', (rep_bin1_low + rep_bin1_high)/2, ' end bin mid: ', (rep_bin2_low + rep_bin2_high) / 2, ' cc: ', cc, ' pval: ', pval, ' qval: ', qval)

# write the interaction in the specified output file
fp_outInt.write('\n' + str(curr_chr) + '\t' + str(rep_bin1_low) + '\t' + str(rep_bin1_high) + '\t' + str(curr_chr) + '\t' + str(rep_bin2_low) + '\t' + str(rep_bin2_high) + '\t' + str(cc) + '\t' + str(pval) + '\t' + str(qval) + '\t' + str(span_low_bin1) + '\t' + str(span_high_bin1) + '\t' + str(span_low_bin2) + '\t' + str(span_high_bin2) + '\t' + str(sum_cc) + '\t' + str(Percent_Significant_BinPair))
Expand Down Expand Up @@ -599,23 +601,23 @@ def main():
Final_Rep_Key_List = []

if 0:
print ' **** Processing the connected component ===== number of elements: ', len(Curr_Comp_Tuple_List)
print(' **** Processing the connected component ===== number of elements: ', len(Curr_Comp_Tuple_List))

# now extract elements from the constructed queue
while (len(Curr_Comp_Tuple_List) > 0):
# extract the first element from the min-heap
# element with the lowest value
curr_elem = heapq.heappop(Curr_Comp_Tuple_List)
if 0:
print 'extracted element from heap: ', curr_elem
print('extracted element from heap: ', curr_elem)

# if this is the first element
# then insert they key in the candidate set of interactions
if (len(Final_Rep_Key_List) == 0):
subl = [curr_elem[2], curr_elem[3]]
Final_Rep_Key_List.append(subl)
if 0:
print '*** inserted element in the final list: ', str(subl)
print('*** inserted element in the final list: ', str(subl))
continue

# otherwise, check with the existing interactions
Expand All @@ -629,7 +631,7 @@ def main():
if (((abs(Final_Rep_Key_List[i][0] - curr_elem[2])) * bin_size) <= NeighborHoodBinThr) and (((abs(Final_Rep_Key_List[i][1] - curr_elem[3])) * bin_size) <= NeighborHoodBinThr):
flag = True
if 0:
print ' --- current element is within neighborhood of the existing (included) bin ', Final_Rep_Key_List[i]
print(' --- current element is within neighborhood of the existing (included) bin ', Final_Rep_Key_List[i])
break

if (flag == False):
Expand All @@ -638,12 +640,12 @@ def main():
subl = [curr_elem[2], curr_elem[3]]
Final_Rep_Key_List.append(subl)
if 0:
print '*** inserted element in the final list: ', str(subl)
print('*** inserted element in the final list: ', str(subl))

# now print the candidate interactions
# of the current component
if 0:
print '\n\n**** Printing selected loops of the connected component ***\n\n'
print('\n\n**** Printing selected loops of the connected component ***\n\n')

for i in range(len(Final_Rep_Key_List)):
rep_bin_key = (Final_Rep_Key_List[i][0], Final_Rep_Key_List[i][1])
Expand All @@ -657,7 +659,7 @@ def main():
pval = CurrChrDict[rep_bin_key]._GetPVal()
qval = CurrChrDict[rep_bin_key]._GetQVal()
if 0:
print 'Selected bin key: ', rep_bin_key, ' start bin mid: ', (rep_bin1_low + rep_bin1_high)/2, ' end bin mid: ', (rep_bin2_low + rep_bin2_high) / 2, ' cc: ', cc, ' pval: ', pval, ' qval: ', qval
print('Selected bin key: ', rep_bin_key, ' start bin mid: ', (rep_bin1_low + rep_bin1_high)/2, ' end bin mid: ', (rep_bin2_low + rep_bin2_high) / 2, ' cc: ', cc, ' pval: ', pval, ' qval: ', qval)

# write the interaction in the specified output file
fp_outInt.write('\n' + str(curr_chr) + '\t' + str(rep_bin1_low) + '\t' + str(rep_bin1_high) + '\t' + str(curr_chr) + '\t' + str(rep_bin2_low) + '\t' + str(rep_bin2_high) + '\t' + str(cc) + '\t' + str(pval) + '\t' + str(qval) + '\t' + str(span_low_bin1) + '\t' + str(span_high_bin1) + '\t' + str(span_low_bin2) + '\t' + str(span_high_bin2) + '\t' + str(sum_cc) + '\t' + str(Percent_Significant_BinPair))
Expand All @@ -677,9 +679,8 @@ def main():
os.system(sys_cmd)

if 1:
print '==================== End of merge filtering adjacent interactions !!! ======================'
print('==================== End of merge filtering adjacent interactions !!! ======================')

#===============================================
if __name__ == "__main__":
main()