update

Author: Bill Majoros

ProgramName.py

@@ -0,0 +1,6 @@
+import sys
+import os
+
+def programName():
+  return os.path.basename(sys.argv[0])
+

extract-gaa.py

@@ -4,7 +4,7 @@
 import gzip
 
 if(len(sys.argv)!=4):
-   print sys.argv[0]+" <in.vcf.gz> <begin> <end>"
+   print(sys.argv[0]+" <in.vcf.gz> <begin> <end>")
    sys.exit(0)
 [infile,begin,end]=sys.argv[1:]
 begin=int(begin)
@@ -17,10 +17,10 @@
    if len(fields)<7: continue
    if fields[0]=="#CHROM":
       header=fields
-      print line
+      print(line)
    elif fields[6]=="PASS":
       [chr,pos,id,ref,alt]=fields[:5]
       pos=int(pos)
-      if pos>=begin and pos<=end: print line
+      if pos>=begin and pos<=end: print(line)
 
 

get-SNP-IDs.py

@@ -6,7 +6,7 @@
 
 name=sys.argv[0];
 if(len(sys.argv)!=2):
-   print name+" <*.vcf>"
+   print(name+" <*.vcf>")
    sys.exit(0)
 [name,vcfFile]=sys.argv;
 
@@ -23,6 +23,6 @@
   if(len(ref)!=1 or len(alt)!=1): continue
   if(not re.search("rs",id)):
      id=chr+"at"+pos;
-  print id+"\t"+chr+"\t"+pos+"\t"+ref+"\t"+alt
+  print(id+"\t"+chr+"\t"+pos+"\t"+ref+"\t"+alt)
 IN.close();
 

hello-world.py

@@ -0,0 +1,17 @@
+#!/bin/env python
+from __future__ import (absolute_import, division, print_function, 
+   unicode_literals, generators, nested_scopes, with_statement)
+from builtins import (bytes, dict, int, list, object, range, str, ascii, chr, 
+   hex, input, next, oct, open, pow, round, super, filter, map, zip)
+from ProgramName import *
+
+name=programName();
+print(name)
+
+print ("Hello, world\n")
+
+for i in range(1,10):
+  print (i,end="")
+print("\n")
+
+

make-bam-slurms.py

@@ -0,0 +1,46 @@
+#!/usr/bin/env python
+import sys
+import os
+import basic
+import glob
+import re
+
+# Global variables
+jobName="bam"
+slurmDir="/data/chilab/bill/slurm-bam"
+samDir="/data/chilab/bill/sam"
+memory=10000
+samtools="/usr/local/bin/samtools"
+
+# Make output directories
+if(not os.path.exists(slurmDir)):
+    os.makedirs(slurmDir)
+
+# Get list of sam files
+samFiles=glob.glob(samDir+"/*.sam")
+
+# Process each sam file
+jobID=1
+for samfile in samFiles:
+  match=re.search("([^/]+)\.sam",samfile); 
+  bamfile=samDir+"/"+match.group(1)+".bam"
+  bamStem=samDir+"/"+match.group(1)
+  slurmFile=slurmDir+"/"+str(jobID)+".slurm"
+  OUT=open(slurmFile,"w")
+  header="\n".join(["#!/bin/bash",
+  "#",
+  "#SBATCH -J %(jobName)s%(jobID)i" % locals(),
+  "#SBATCH -o %(jobName)s%(jobID)i.output" % locals(),
+  "#SBATCH -e %(jobName)s%(jobID)i.output" % locals(),
+  "#SBATCH -A %(jobName)s%(jobID)i" % locals(),
+  "#SBATCH --mem %(memory)i" %locals(),
+  "#"])
+  print >>OUT, header
+  print >>OUT, "cd "+samDir
+  command="%(samtools)s view -bS %(samfile)s | samtools sort - %(bamStem)s" % locals()
+  print >>OUT, command
+  command="%(samtools)s index %(bamfile)s" % locals()
+  print >>OUT, command
+  OUT.close()
+  jobID=jobID+1
+