From d035d8eb7bd13bc9f2dec0bdf9e38c9aa10f4f23 Mon Sep 17 00:00:00 2001
From: chartl <chartl@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Wed, 8 Jun 2011 14:42:31 +0000
Subject: [PATCH] Updating the bam list is a bit trickier than most of us
 originally thought. Need to ensure that *3* files exist: the .bam, the .bai,
 and the finished.txt (or else bad things can happen)

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5960 348d0f76-0448-11de-a6fe-93d51630548a
---
 python/getRecentBamList.py | 30 ++++++++++++++++++++++++++++++
 1 file changed, 30 insertions(+)
 create mode 100644 python/getRecentBamList.py

diff --git a/python/getRecentBamList.py b/python/getRecentBamList.py
new file mode 100644
index 000000000..97f382797
--- /dev/null
+++ b/python/getRecentBamList.py
@@ -0,0 +1,30 @@
+import sys
+import os
+
+in_list = sys.argv[1]
+out_list = sys.argv[2]
+
+inp = open(in_list)
+out = open(out_list,'w')
+
+for line in inp.readlines():
+    path = line.strip()
+    #print(path)
+    tries = 0
+    index = path.strip(".bam")+".bai"
+    finished = path.rsplit("/",1)[0]+"/finished.txt"
+    while ( not (os.path.exists(path) and os.path.exists(finished) and os.path.exists(index) ) and tries < 15 ):
+        base = path.rsplit("/",1)[0]
+        vers = base.rsplit("/",1)[1]
+        base = base.rsplit("/",1)[0]
+        bam = path.rsplit("/",1)[1]
+        vers = "v%d" % (int(vers.lstrip("v"))+1)
+        path = "%s/%s/%s" % (base,vers,bam)
+        finished = "%s/%s/%s" % (base,vers,"finished.txt")
+        index = path.strip(".bam")+".bai"
+        #print(path)
+        tries += 1
+    if ( os.path.exists(path) and os.path.exists(finished) and os.path.exists(index) ):
+        out.write(path+"\n")
+    else:
+        print("No filepath on the file system contains bam, index, and finished.txt for entry "+path)