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--- scripts/ldmap.py.orig 2021-01-23 17:32:15 UTC
+++ scripts/ldmap.py
@@ -29,10 +29,10 @@ class MapMaker:
coordinates of the haplotype marker genomic positions.
'''
def __init__(self, markerFilename, haplotypesFilename):
- print "reading haplotype base coordinates ...."
+ print("reading haplotype base coordinates ....")
self.coords, self.coordIndexes, self.refs, self.alts = self.readMarkers(markerFilename)
# self.haplotypes = self.readHaplotypes(haplotypesFilename)
- print "reading haplotype panel ...."
+ print("reading haplotype panel ....")
self.markerCalls = self.readHaplotypes(haplotypesFilename, transpose = True)
# reads from a vcf file of defined positions representing the haplotype data
@@ -118,7 +118,7 @@ class MapMaker:
# 1) COLLECT MARGINALS AND IDENTIFY SITES THAT ARE POLYMORPHIC
# If a site has only one allele in the haplotype panel it is not informative, so it won't be used
# in LD calculations. We may want to consider setting some minimum threshold for a minor allele frequency.
- print "collecting marginal allele counts and identifying polymorphic sites from haplotype panel ...."
+ print("collecting marginal allele counts and identifying polymorphic sites from haplotype panel ....")
for index in range(0,len(self.markerCalls)):
ref = self.refs[index]
alt = self.alts[index]
@@ -152,7 +152,7 @@ class MapMaker:
log.write("Num non-polymorphic sites: " + str(numNonpolymorphicSites) + "\n")
# 2) CALCULATE D FOR POLYMORPHIC SITES COMPARED WITH N SITES TO THE RIGHT THAT ARE POLYMORPHIC
- print "calculating D between polymorphic sites and their neighbors ...."
+ print("calculating D between polymorphic sites and their neighbors ....")
dVals = []
for i in range(0, len(polymorphicIndexes)): # the last coordinate won't have any partners
index_i = polymorphicIndexes[i]
@@ -244,7 +244,7 @@ class LDMap:
return ldMap
def save(self, filename):
- print "saving ldmap to " + filename
+ print("saving ldmap to " + filename)
ldMapFile = open(filename, 'w')
ldMapFile.write("\t".join(["COORD","REF","ALT","PAIRED_ALLELES"]) + "\n")
for i in range(0,len(self.coords)):
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