From 9556004dbb64c54ef280574f51dea52b9006dbaa Mon Sep 17 00:00:00 2001
From: depristo <depristo@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Sun, 29 Aug 2010 16:00:00 +0000
Subject: [PATCH] now supports -o option as well as verbose output mode

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4162 348d0f76-0448-11de-a6fe-93d51630548a
---
 python/mergeVCFs.py | 37 ++++++++++++++++++++++++++++---------
 1 file changed, 28 insertions(+), 9 deletions(-)

diff --git a/python/mergeVCFs.py b/python/mergeVCFs.py
index bca5db31c..7fb35f8a3 100755
--- a/python/mergeVCFs.py
+++ b/python/mergeVCFs.py
@@ -12,22 +12,36 @@ def main():
     parser.add_option("-f", "--f", dest="fai",
                         type='string', default=None,
                         help="FAI file defining the sort order of the VCF")
+    parser.add_option("-o", "--o", dest="output",
+                        type='string', default=None,
+                        help="if provided, output will go here instead of stdout")
     parser.add_option("-a", "--assumeSorted", dest="assumeSorted",
                         action='store_true', default=False,
                         help="If provided, this assumes the input VCF files are themselves sorted, enabling a simple efficent merge")         
+    parser.add_option("-v", "--verbose", dest="verbose",
+                        action='store_true', default=False,
+                        help="If provided, verbose progress will be enabled")         
          
     (OPTIONS, args) = parser.parse_args()
     if len(args) == 0:
         parser.error("Requires at least 1 VCF to merge")
 
     order = None
-    if OPTIONS.fai <> None: order = faiReader.readFAIContigOrdering(OPTIONS.fai)
+    if OPTIONS.fai <> None:
+        if OPTIONS.verbose: print 'reading FAI', OPTIONS.fai 
+
+        order = faiReader.readFAIContigOrdering(OPTIONS.fai)
     #print 'Order', order
 
-    if OPTIONS.assumeSorted:
-        mergeSort(args, order)
+    if OPTIONS.output != None:
+        out = open(OPTIONS.output,'w')
     else:
-        memSort(args, order)
+        out = sys.stdout
+
+    if OPTIONS.assumeSorted:
+        mergeSort(out, args, order)
+    else:
+        memSort(out, args, order)
 
 def cmpVCFRecords(order, r1, r2):
     if order <> None:
@@ -38,7 +52,7 @@ def cmpVCFRecords(order, r1, r2):
             return orderCmp
     return cmp(r1.getPos(), r2.getPos())
 
-def mergeSort(args, order):
+def mergeSort(out, args, order):
     #print 'MergeSort', args, order
     header = None
     
@@ -55,11 +69,16 @@ def mergeSort(args, order):
     sortedOrderMap = sorted(orderMap, key=lambda x: x[0], cmp = lambda r1, r2: cmpVCFRecords(order, r1, r2))
     #print sortedOrderMap
 
-    for headerLine in header: print headerLine
+    for headerLine in header: print >> out, headerLine
+    i = 0
+    n = len(sortedOrderMap)
     for file in map( lambda x: x[1], sortedOrderMap):
-        #print file
+        if OPTIONS.verbose: 
+            i += 1
+            print 'Processing', file, ':', i, 'of', n
+        
         for record in lines2VCF(open(file), extendedOutput = False, decodeAll = False):
-            print record.format()
+            print >> out, record.format()
         
 def memSort(args, order):
     header = None
@@ -72,7 +91,7 @@ def memSort(args, order):
     records.sort(lambda r1, r2: cmpVCFRecords(order, r1, r2)) 
     for line in formatVCF(header, records):
         #pass
-        print line
+        print >> out, line
 
 PROFILE = False
 if __name__ == "__main__":