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--- scripts/simple_phaser.py.orig 2021-01-23 17:25:56 UTC
+++ scripts/simple_phaser.py
@@ -108,7 +108,7 @@ class SimplePhaser:
return informativeHets, informativeCoords, informativeIndexes
def getRefPairedAllele(self, anchorIndex, pairedIndex):
-# print "\t".join([str(anchorIndex), str(pairedIndex - anchorIndex - 1), str(len(self.ldMap.dVals)),str(len(self.ldMap.dVals[anchorIndex]))]) # prints intermarker counts
+# print("\t".join([str(anchorIndex), str(pairedIndex - anchorIndex - 1), str(len(self.ldMap.dVals)),str(len(self.ldMap.dVals[anchorIndex]))]) # prints intermarker counts)
if (pairedIndex - anchorIndex - 1) >= len(self.ldMap.dVals[anchorIndex]):
pRef = random.uniform(0,1)
if pRef > 0.5:
@@ -166,8 +166,8 @@ class SimplePhaser:
altHap = temp
if pairedAllele not in [ref,alt]:
- print "pairedAllele not ref or alt " + ref + " " + alt
- print pairedAllele
+ print("pairedAllele not ref or alt " + ref + " " + alt)
+ print(pairedAllele)
return phasedAlleles, informativeCoords
@@ -182,7 +182,7 @@ class SimplePhaser:
elif candidateHap[i].upper() == phasedHaps[1][i].upper():
currentMatch = 1
else:
- print "ERROR: " + candidateHap[i] + " does not match " + phasedHaps[0][i] + " or " + phasedHaps[1][i] + "\t" + self.ldMap.coords[i] + "\t" + self.ldMap.refs[i] + "\t" + self.ldMap.alts[i]
+ print("ERROR: " + candidateHap[i] + " does not match " + phasedHaps[0][i] + " or " + phasedHaps[1][i] + "\t" + self.ldMap.coords[i] + "\t" + self.ldMap.refs[i] + "\t" + self.ldMap.alts[i])
# # randomly assign match
# p0 = random.uniform(0,1)
# if p0 > 0.5:
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