Changeset 5769

Timestamp:

Dec 3, 2019, 9:38:37 AM (3 years ago)

Author:

Nicklas Nordborg

Message:

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

Added progress reporting to the python script that collect variant statistics.

File:

• other/pipeline/trunk/mut_stats.py (modified) (4 diffs)

other/pipeline/trunk/mut_stats.py

@@ -4 +4 @@
 
 Script that calculates statistics for variants in a list of VCF files.
-The script requries a tab-separated text file as input. Each line
-should have two columns:
+The script need two parameters:
+
+1: Path to text file with list of VCF files to process (se below)
+2: Path to progress reporting file
+
+The text file given as the first parameter should be a tab-separated 
+text file. Each line should have three columns:
 
 1: Patient identifier
 2: Path to VCF file
+3: Name of alignment (used for progress reporting)
 
 Counts and frequencies for all variants will calculated for the total and
@@ -24 +30 @@
 import gzip
 import datetime
+import time
 
 # Store all variants that we have seen in the VCF files we load
@@ -78 +85 @@
         vcf.close()
 
+# Report progress to the progressFile (1-90%)
+def progressReport(progressFile, alignment, current, total):
+    percent = 1+current * 89 /  total
+    with open(progressFile, 'w') as p:
+        p.write("{0} Reading VCF file for '{1}' ({2} of {3})".format(percent, alignment, current, total))
+
 # Read the patient/VCF list
 # Each line should be tab-separated <PAT>\t<PATH-TO-VCF>
@@ -88 +101 @@
 lines.sort()
 
+progressFile = sys.argv[2]
+
 # Load the VCF files and count the variants in them
+vcfCount = 0
+totalVcf = len(lines)
+nextProgressReport = time.time()+15
+
 for line in lines:
-    cols = line.split('\t')
+    cols = line.split('\t')    
+    vcfCount += 1
+    # Report progress every 15 seconds
+    if time.time() > nextProgressReport:
+        progressReport(progressFile, cols[2], vcfCount, totalVcf)
+        nextProgressReport = time.time()+15
     loadVcf(cols[1], cols[0])