added a bunch of code from old svn archive

kr-colab · Sep 6, 2018 · 07a15b3 · 07a15b3
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diff --git a/AFSDistFromSite.py b/AFSDistFromSite.py
@@ -0,0 +1,78 @@
+#!/usr/bin/env python
+import sys
+
+msFile, targetPos, maxDistanceFromTarget = sys.argv[1:]
+targetPos = float(targetPos)
+maxDistanceFromTarget = float(maxDistanceFromTarget)
+
+def processSimulation(samples, positions, targetPos, maxDistanceFromTarget, afs):
+    freqH = {}
+    for i in range(len(samples[0])):
+        if abs(targetPos - positions[i]) < maxDistanceFromTarget:
+            freqH[i] = {}
+            for sample in samples:
+                if not freqH[i].has_key(sample[i]):
+                    freqH[i][sample[i]] = 0
+                freqH[i][sample[i]] += 1
+    for i in freqH.keys():
+        alleles = sorted(freqH[i].keys())
+        if alleles == ['0', '1']:
+            freq = freqH[i]['1']
+            afs[freq] += 1
+
+if msFile == "stdin":
+    isFile = False
+    msStream = sys.stdin
+else:
+    isFile = True
+    msStream = open(msFile)
+
+header = msStream.readline()
+program,numSamples,numSims = header.strip().split()[:3]
+numSamples, numSims = int(numSamples), int(numSims)
+
+processedSims = 0
+#advance to first simulation
+line = msStream.readline()
+while line.strip() != "//":
+    line = msStream.readline()
+afs = -1
+while line:
+    if line.strip() != "//":
+        sys.exit("Malformed ms-style output file: read '%s' instead of '//'. AAAARRRRGGHHH!!!!!\n" %(line.strip()))
+    segsitesBlah,segsites = msStream.readline().strip().split()
+    segsites = int(segsites)
+    if segsitesBlah != "segsites:":
+        sys.exit("Malformed ms-style output file. AAAARRRRGGHHH!!!!!\n")
+
+    if segsites != 0:
+        positionsLine = msStream.readline().strip().split()
+        if not positionsLine[0] == "positions:":
+            sys.exit("Malformed ms-style output file. AAAARRRRGGHHH!!!!!\n")
+        positions = [float(x) for x in positionsLine[1:]]
+
+        samples = []
+        for i in range(numSamples):
+            sampleLine = msStream.readline().strip()
+            if len(sampleLine) != segsites:
+                sys.exit("Malformed ms-style output file %s segsites but %s columns in line: %s; line %s of %s samples AAAARRRRGGHHH!!!!!\n" %(segsites, len(sampleLine), sampleLine, i, numSamples))
+            samples.append(sampleLine)
+        if len(samples) != numSamples:
+            raise Exception
+        if afs == -1:
+            afs = [0]*len(samples)
+        processSimulation(samples, positions, targetPos, maxDistanceFromTarget, afs)
+    processedSims += 1
+    line = msStream.readline()
+    #advance to the next non-empty line or EOF
+    while line and line.strip() == "":
+        line = msStream.readline()
+#print afs[1:]
+denom = float(sum(afs[1:]))
+for i in range(1,len(afs)):
+    print "%i %le" %(i, afs[i]/denom)
+if processedSims != numSims:
+    sys.exit("Malformed ms-style output file: %s of %s sims processed. AAAARRRRGGHHH!!!!!\n" %(processedSims, numSims))
+
+if isFile:
+    msStream.close()
diff --git a/Makefile b/Makefile
@@ -0,0 +1,98 @@
+CC = gcc
+CFLAGS = -O3 -Wall -lm 
+
+msMask:	msMask.c 
+	$(CC) msMask.c  -o msMask $(CFLAGS)
+
+msMaskAllRows:	msMaskAllRows.c 
+	$(CC) msMaskAllRows.c  -o msMaskAllRows $(CFLAGS)
+
+maskedStats:	maskedStats.c msGeneralStats.c
+	$(CC) maskedStats.c msGeneralStats.c -o maskedStats $(CFLAGS)
+
+niceStatsDan:	niceStatsDan.c msGeneralStats.c
+		$(CC) niceStatsDan.c msGeneralStats.c -g -o niceStatsDan $(CFLAGS)
+
+niceStatsSFSRegular:	niceStatsSFSRegular.c msGeneralStats.c
+		$(CC) niceStatsSFSRegular.c msGeneralStats.c -g -o niceStatsSFSRegular $(CFLAGS)
+
+niceStats:	niceStats.c msGeneralStats.c
+		$(CC) niceStats.c msGeneralStats.c -o niceStats $(CFLAGS)
+
+maskedStatsSubpop:	maskedStatsSubpop.c msGeneralStats.c
+	$(CC) maskedStatsSubpop.c msGeneralStats.c -o maskedStatsSubpop $(CFLAGS)
+
+twoPopnNiceStats:	twoPopnNiceStats.c msGeneralStats.c
+	$(CC) twoPopnNiceStats.c msGeneralStats.c -o twoPopnNiceStats $(CFLAGS)
+
+twoPopnStats_forML:	twoPopnStats_forML.c msGeneralStats.c
+	$(CC) twoPopnStats_forML.c msGeneralStats.c -o twoPopnStats_forML $(CFLAGS) 	
+
+onePopnStats_forGhostIntroML:	onePopnStats_forGhostIntroML.c msGeneralStats.c
+	$(CC) onePopnStats_forGhostIntroML.c msGeneralStats.c -o onePopnStats_forGhostIntroML $(CFLAGS) 	
+
+threePopnStats:	threePopnStats.c msGeneralStats.c
+		$(CC) threePopnStats.c msGeneralStats.c -o threePopnStats $(CFLAGS)
+msParams: msParams.c
+	$(CC) msParams.c ../coalLib/ranlibComplete.c ../pgLib/bedFile.c -o msParams $(CFLAGS)
+
+msParamsSubpop: msParamsSubpop.c
+	$(CC) msParamsSubpop.c ../coalLib/ranlibComplete.c ../pgLib/bedFile.c -o msParamsSubpop $(CFLAGS)
+
+msParamsSubpopNoAd: msParamsSubpopNoAd.c
+	$(CC) msParamsSubpopNoAd.c ../coalLib/ranlibComplete.c ../pgLib/bedFile.c -o msParamsSubpopNoAd $(CFLAGS)
+
+msParamsSubpopTrans: msParamsSubpopTrans.c
+	$(CC) msParamsSubpopTrans.c ../coalLib/ranlibComplete.c ../pgLib/bedFile.c -o msParamsSubpopTrans $(CFLAGS)
+
+msParamsTest: msParamsTest.c
+	$(CC) msParamsTest.c ../coalLib/ranlibComplete.c ../pgLib/bedFile.c -o msParamsTest $(CFLAGS)
+
+pairDist:	pairDist.c msGeneralStats.c
+	$(CC) pairDist.c msGeneralStats.c -o pairDist $(CFLAGS)
+pairwiseDists:	pairwiseDists.c msGeneralStats.c
+	$(CC) pairwiseDists.c msGeneralStats.c -o pairwiseDists $(CFLAGS)
+
+pairwiseIBSTracts:	pairwiseIBSTracts.c msGeneralStats.c
+	$(CC) pairwiseIBSTracts.c msGeneralStats.c -o pairwiseIBSTracts $(CFLAGS)
+
+msHKA: msHKA.c msGeneralStats.c
+	$(CC) msHKA.c msGeneralStats.c -o msHKA $(CFLAGS)
+
+ms2TwoSite: ms2TwoSite.c msGeneralStats.c
+	$(CC) ms2TwoSite.c msGeneralStats.c -o ms2TwoSite $(CFLAGS)
+
+ms2TwoSite2Popn: ms2TwoSite2Popn.c msGeneralStats.c
+	$(CC) ms2TwoSite2Popn.c msGeneralStats.c -o ms2TwoSite2Popn $(CFLAGS)
+
+ms2SFS2D: ms2SFS2D.c msGeneralStats.c
+	$(CC) ms2SFS2D.c msGeneralStats.c -o ms2SFS2D $(CFLAGS)
+ms2SFS2D_discoal: ms2SFS2D_discoal.c msGeneralStats.c
+	$(CC) ms2SFS2D_discoal.c msGeneralStats.c -o ms2SFS2D_discoal $(CFLAGS)
+
+ms2SFSVector: ms2SFSVector.c msGeneralStats.c
+	$(CC) ms2SFSVector.c msGeneralStats.c -o ms2SFSVector $(CFLAGS)
+
+ms2SFSVectorWindow: ms2SFSVectorWindow.c msGeneralStats.c
+	$(CC) ms2SFSVectorWindow.c msGeneralStats.c -o ms2SFSVectorWindow $(CFLAGS)
+
+discoal_mig2hmm: discoal_mig2hmm.c msGeneralStats.c
+	$(CC) discoal_mig2hmm.c msGeneralStats.c -o discoal_mig2hmm $(CFLAGS)
+
+slideFST: slideFST.c msGeneralStats.c
+	$(CC) slideFST.c msGeneralStats.c -o slideFST $(CFLAGS)
+
+niceStatsNoOmega:	niceStatsNoOmega.c msGeneralStats.c
+		$(CC) niceStatsNoOmega.c msGeneralStats.c -g -o niceStatsNoOmega $(CFLAGS)	
+
+niceStatsShanku:	niceStatsShanku.c msGeneralStats.c
+		$(CC) niceStatsShanku.c msGeneralStats.c -o niceStatsShanku $(CFLAGS)
+
+niceStatsAchazSystem:	niceStatsAchazSystem.c msGeneralStats.c
+		$(CC) niceStatsAchazSystem.c msGeneralStats.c -O3 -o niceStatsAchazSystem $(CFLAGS)
+
+niceStatsDiploid:	niceStatsDiploid.c msGeneralStats.c msDiploidStats.c
+		$(CC) niceStatsDiploid.c msGeneralStats.c msDiploidStats.c -o niceStatsDiploid $(CFLAGS)
+niceStats4Gamete:	niceStats4Gamete.c msGeneralStats.c 
+			$(CC) niceStats4Gamete.c msGeneralStats.c -o niceStats4Gamete $(CFLAGS)	
+
diff --git a/bitStuff.c b/bitStuff.c
@@ -0,0 +1,35 @@
+//bitStuff.c
+// basic bit manipulations
+
+#include "bitStuff.h"
+
+int setBit(int x, unsigned char position)
+{
+  int mask = 1 << position;
+  return x | mask;
+}
+
+int clearBit(int x, unsigned char position)
+{
+  int mask = 1 << position;
+  return x & ~mask;
+}
+
+int modifyBit(int x, unsigned char position, bool newState)
+{
+  int mask = 1 << position;
+  int state = (int) newState; // relies on true = 1 and false = 0
+  return (x & ~mask) | (-state & mask);
+}
+
+int flipBit(int x, unsigned char position)
+{
+  int mask = 1 << position;
+  return x ^ mask;
+}
+
+bool isBitSet(int x, unsigned char position)
+ {
+   x >>= position;
+   return (x & 1) != 0;
+ }
diff --git a/bitStuff.h b/bitStuff.h
@@ -0,0 +1,9 @@
+#include <stdlib.h>
+#include <stdio.h>
+#include <stdbool.h>
+
+int setBit(int x, unsigned char position);
+int clearBit(int x, unsigned char position);
+int modifyBit(int x, unsigned char position, bool newState);
+int flipBit(int x, unsigned char position);
+bool isBitSet(int x, unsigned char position);
diff --git a/combineMSFileDir.py b/combineMSFileDir.py
@@ -0,0 +1,62 @@
+#!/usr/bin/env python
+import os, sys, gzip, random
+
+msFileDir, shuffle = sys.argv[1:]
+if not shuffle in ["shuffle", "no_shuffle"]:
+    sys.exit("shuffle must be set to either 'shuffle' or 'no_shuffle'. AAAARRRRGGGGHHHHHHHHHH!!!!\n")
+
+def readAllMSRepsFromFile(msFileName):
+    if msFileName.endswith(".gz"):
+        fopen = gzip.open
+    else:
+        fopen = open
+    msStream = fopen(msFileName)
+
+    header = msStream.readline().strip().split()
+    program,numSamples,numSims = header[:3]
+    if len(header) > 3:
+        otherParams = " " + " ".join(header[3:])
+    else:
+        otherParams = ""
+    numSamples, numSims = int(numSamples),int(numSims)
+
+    #advance to first simulation
+    line = msStream.readline()
+    while not line.strip().startswith("//"):
+        line = msStream.readline()
+    repLs = []
+    while line:
+        if not line.strip().startswith("//"):
+            sys.exit("Malformed ms-style output file: read '%s' instead of '//'. AAAARRRRGGHHH!!!!!\n" %(line.strip()))
+        repStr = ["\n//"]
+        repStr.append(msStream.readline().strip()) #segsites line
+        positionsLine = msStream.readline().strip()
+        if not positionsLine.startswith("positions:"):
+            sys.exit("Malformed ms-style output file. AAAARRRRGGHHH!!!!!\n")
+        repStr.append(positionsLine) #positions line
+
+        for i in range(numSamples):
+            currLine = msStream.readline()
+            repStr.append(currLine.strip())
+        line = msStream.readline()
+        #advance to the next non-empty line or EOF
+        while line and line.strip() == "":
+            line = msStream.readline()
+        repStr = "\n".join(repStr)
+        repLs.append(repStr)
+    msStream.close()
+
+    return numSamples, repLs
+
+repLs = []
+allNumSamples = {}
+for msFileName in os.listdir(msFileDir):
+    sys.stderr.write("%s\n" %(msFileName))
+    currNumSamples, currRepLs = readAllMSRepsFromFile(msFileDir + "/" + msFileName)
+    allNumSamples[currNumSamples] = 1
+    repLs += currRepLs
+assert len(allNumSamples) == 1
+print "./msStyle %s %s\nblah\n" %(currNumSamples, len(repLs))
+if shuffle == "shuffle":
+    random.shuffle(repLs)
+print "\n".join(repLs)
diff --git a/combineMSFileSubsets.py b/combineMSFileSubsets.py
@@ -0,0 +1,57 @@
+#!/usr/bin/env python
+import sys, gzip, random
+
+msFileName1, numReps1, msFileName2, numReps2, shuffle = sys.argv[1:]
+numReps1, numReps2 = int(numReps1), int(numReps2)
+if not shuffle in ["shuffle", "no_shuffle"]:
+    sys.exit("shuffle must be set to either 'shuffle' or 'no_shuffle'. AAAARRRRGGGGHHHHHHHHHH!!!!\n")
+
+def readAllMSRepsFromFile(msFileName):
+    msStream = open(msFileName)
+
+    header = msStream.readline().strip().split()
+    program,numSamples,numSims = header[:3]
+    if len(header) > 3:
+        otherParams = " " + " ".join(header[3:])
+    else:
+        otherParams = ""
+    numSamples, numSims = int(numSamples),int(numSims)
+
+    #advance to first simulation
+    line = msStream.readline()
+    while line.strip() != "//":
+        line = msStream.readline()
+    repLs = []
+    while line:
+        if line.strip() != "//":
+            sys.exit("Malformed ms-style output file: read '%s' instead of '//'. AAAARRRRGGHHH!!!!!\n" %(line.strip()))
+        repStr = ["\n//"]
+        repStr.append(msStream.readline().strip()) #segsites line
+        positionsLine = msStream.readline().strip()
+        if not positionsLine.startswith("positions:"):
+            sys.exit("Malformed ms-style output file. AAAARRRRGGHHH!!!!!\n")
+        repStr.append(positionsLine) #positions line
+
+        for i in range(numSamples):
+            currLine = msStream.readline()
+            repStr.append(currLine.strip())
+        line = msStream.readline()
+        #advance to the next non-empty line or EOF
+        while line and line.strip() == "":
+            line = msStream.readline()
+        repStr = "\n".join(repStr)
+        repLs.append(repStr)
+    msStream.close()
+
+    return numSamples, repLs
+
+numSamples1, repLs1 = readAllMSRepsFromFile(msFileName1)
+numSamples2, repLs2 = readAllMSRepsFromFile(msFileName2)
+if numSamples1 != numSamples2:
+    sys.exit("sample size differs between %s (%s) and %s (%s). AAAARRRRGGGGHHHHHHHH!\n" %(msFileName1, numSamples1, msFileName2, numSamples2))
+print "./msStyle %s %s\nblah\n" %(numSamples1, numReps1+numReps2)
+if shuffle == "shuffle":
+    random.shuffle(repLs1)
+    random.shuffle(repLs2)
+print "\n".join(repLs1[:numReps1])
+print "\n".join(repLs2[:numReps2])