erange version 4.0a dev release

[erange.git] / distalPairs.py

diff --git a/distalPairs.py b/distalPairs.py
index d24781a0db7c0ee3702e71cf97f6c2d62ea21c41..5bc25321b25b8a30e9b09511cabbee4355010b71 100755 (executable)
--- a/distalPairs.py
+++ b/distalPairs.py
@@ -12,15 +12,18 @@ try:
 except:
     pass
 
-from commoncode import readDataset
-import sys, time, optparse
+import sys
+import time
+import optparse
+import ReadDataset
+from commoncode import getConfigParser, getConfigOption, getConfigIntOption, getConfigBoolOption
 
 
 def main(argv=None):
     if not argv:
         argv = sys.argv
 
-    print "%prog: version 3.3"
+    print "distalPairs: version 3.4"
     print "looks at all chromosomes simultaneously: is both slow and takes up large amount of RAM"
     usage = "usage: python %prog minDist rdsfile outfile [--sameChrom] [--splices] [--maxDist bp] [--verbose] [--cache cachepages]"
 
@@ -44,6 +47,27 @@ def main(argv=None):
     distalPairs(minDist, rdsfile, outfilename, options.sameChromOnly, options.doSplices, options.doVerbose, options.maxDist, options.cachePages)
 
 
+def makeParser(usage=""):
+    parser = optparse.OptionParser(usage=usage)
+    parser.add_option("--sameChrom", action="store_true", dest="sameChromOnly")
+    parser.add_option("--splices", action="store_true", dest="doSplices")
+    parser.add_option("--verbose", action="store_true", dest="doVerbose")
+    parser.add_option("--maxDist", type="int", dest="maxDist")
+    parser.add_option("--cache", type="int", dest="cachePages")
+
+    configParser = getConfigParser()
+    section = "distalPairs"
+    sameChromOnly = getConfigBoolOption(configParser, section, "sameChromOnly", False)
+    doSplices = getConfigBoolOption(configParser, section, "doSplices", False)
+    doVerbose = getConfigBoolOption(configParser, section, "doVerbose", False)
+    maxDist = getConfigIntOption(configParser, section, "maxDist", 1000000000)
+    cachePages = getConfigOption(configParser, section, "cachePages", None)
+
+    parser.set_defaults(sameChromOnly=sameChromOnly, doSplices=doSplices, doVerbose=doVerbose, maxDist=maxDist, cachePages=cachePages)
+
+    return parser
+
+
 def distalPairs(minDist, rdsfile, outfilename, sameChromOnly=False, doSplices=False, doVerbose=False, maxDist=1000000000, cachePages=None):
     if cachePages is not None:
         doCache = True
@@ -51,7 +75,7 @@ def distalPairs(minDist, rdsfile, outfilename, sameChromOnly=False, doSplices=Fa
         doCache = False
         cachePages = -1
 
-    RDS = readDataset(rdsfile, verbose = True, cache=doCache)
+    RDS = ReadDataset.ReadDataset(rdsfile, verbose = True, cache=doCache)
     if not RDS.hasIndex():
         print "Will not attempt to run on unIndexed dataset - please index with rdsmetadata.py and rerun"
         sys.exit(1)
@@ -95,8 +119,12 @@ def distalPairs(minDist, rdsfile, outfilename, sameChromOnly=False, doSplices=Fa
         readList = uniqDict[readID]
         if len(readList) == 2:
             total += 1
-            (start1, sense1, chrom1, pair1) = readList[0]
-            (start2, sense2, chrom2, pair2) = readList[1]
+            start1 = readList[0]["start"]
+            sense1 = readList[0]["sense"]
+            chrom1 = readList[0]["chrom"]
+            start2 = readList[1]["start"]
+            sense2 = readList[1]["sense"]
+            chrom2 = readList[1]["chrom"]
 
             if chrom1 != chrom2:
                 diffChrom += 1