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