Changeset 5771

Timestamp:

Dec 3, 2019, 11:54:18 AM (4 years ago)

Author:

Nicklas Nordborg

Message:

References #1208: Implement wizard for building database of variant frequencies in SCAN-B samples

Added a logfile to get some summary statistics.

File:

• other/pipeline/trunk/mut_stats.py (modified) (3 diffs)

other/pipeline/trunk/mut_stats.py

@@ -4 +4 @@
 
 Script that calculates statistics for variants in a list of VCF files.
-The script need two parameters:
+The script need three parameters:
 
 1: Path to text file with list of VCF files to process (se below)
 2: Path to progress reporting file
+3: Path to a log file
 
 The text file given as the first parameter should be a tab-separated 
@@ -102 +103 @@
 
 progressFile = sys.argv[2]
+logFile = sys.argv[3]
 
 # Load the VCF files and count the variants in them
@@ -116 +118 @@
         nextProgressReport = time.time()+15
     loadVcf(cols[1], cols[0])
+
+# Write the log file
+with open(logFile, 'w') as log:
+    log.write("NumberOfVCF: {0}\n".format(tots[0]))
+    log.write("NumberOfPatients: {0}\n".format(tots[1]))
+    log.write("NumberOfVariants: {0}\n".format(len(allVariants)))
 
 # Generate header for the output VCF