1 files changed, 0 insertions, 42 deletions
diff --git a/biology/haplohseq/files/patch-scripts_ldmap.py b/biology/haplohseq/files/patch-scripts_ldmap.py
deleted file mode 100644
index f9fb588048b1..000000000000
--- a/biology/haplohseq/files/patch-scripts_ldmap.py
+++ /dev/null
@@ -1,42 +0,0 @@
---- 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)):