Minor bug fixes

	modified:   bedExt.pl
	modified:   extractPeak.pl
	modified:   joinWrapper.py
	modified:   tag2peak.pl

bedExt.pl

@@ -80,6 +80,10 @@
 	{
 		open ($fin, "gunzip -c $in |") || Carp::croak "cannot open file $in to read\n";
 	}
+	elsif ($in =~/\.bz2$/)
+    {
+        open ($fin, "bunzip2 -c $in |") || Carp::croak "cannot open file $in to read\n";
+    }
 	else
 	{
 		open ($fin, "<$in") || Carp::croak "cannot open file $in to read\n";

extractPeak.pl

@@ -93,6 +93,10 @@
     {
         open ($fin, "gunzip -c $inWiggleFile | ") || Carp::croak "cannot open file $inWiggleFile to read\n";
     }
+    elsif ($inWiggleFile =~/\.bz2$/)
+    {
+        open ($fin, "bunzip2 -c $inWiggleFile | ") || Carp::croak "cannot open file $inWiggleFile to read\n";
+    }
     else
     {
         open ($fin, "<$inWiggleFile") || Carp::croak "cannot open file $inWiggleFile to read\n";

joinWrapper.py

@@ -30,72 +30,74 @@
 
 #!/usr/bin/env python
 #Guruprasad Ananda
+#modifications to support python3 by sebastien weyn
 """
 This tool provides the UNIX "join" functionality.
 """
 import sys, os, tempfile, subprocess
 
 def stop_err(msg):
-    sys.stderr.write(msg)
-    sys.exit()
+	sys.stderr.write(msg)
+	sys.exit()
 
 def main():
-    infile1 = sys.argv[1]
-    infile2 = sys.argv[2]
-    field1 = int(sys.argv[3])
-    field2 = int(sys.argv[4])
-    mode =sys.argv[5]
-    outfile = sys.argv[6]
-
-    tmpfile1 = tempfile.NamedTemporaryFile()
-    tmpfile2 = tempfile.NamedTemporaryFile()
-
-    try:
-        #Sort the two files based on specified fields
-        os.system("sort -t '	' -k %d,%d -o %s %s" %(field1, field1, tmpfile1.name, infile1))
-        os.system("sort -t '	' -k %d,%d -o %s %s" %(field2, field2, tmpfile2.name, infile2))
-    except Exception, exc:
-        stop_err( 'Initialization error -> %s' %str(exc) )
-
-    option = ""
-    for line in file(tmpfile1.name):
-        line = line.strip()
-        if line:
-            elems = line.split('\t')
-            for j in range(1,len(elems)+1):
-                if j == 1:
-                    option = "1.1"
-                else:
-                    option = option + ",1." + str(j) 
-            break
-
-    #check if join has --version option. BSD join doens't have this option, while GNU join does. 
-    #The return value in the latter case will be 0, and non-zero in the latter case.
-    ret = subprocess.call('join --version 2>/dev/null', shell=True) 
-    # check if we are a version later than 7 of join. If so, we want to skip
-    # checking the order since join will raise an error with duplicated items in
-    # the two files being joined.
-    if ret == 0: 
-        cl = subprocess.Popen(["join", "--version"], stdout=subprocess.PIPE)
-        (stdout, _) = cl.communicate()
-        version_line = stdout.split("\n")[0]
-        (version, _) = version_line.split()[-1].split(".")
-        if int(version) >= 7:
-            flags = "--nocheck-order"
-        else:
-            flags = ""
-    else:
-        flags = ""
+	infile1 = sys.argv[1]
+	infile2 = sys.argv[2]
+	field1 = int(sys.argv[3])
+	field2 = int(sys.argv[4])
+	mode =sys.argv[5]
+	outfile = sys.argv[6]
+
+	tmpfile1 = tempfile.NamedTemporaryFile()
+	tmpfile2 = tempfile.NamedTemporaryFile()
+
+	try:
+		#Sort the two files based on specified fields
+		os.system("sort -t '	' -k %d,%d -o %s %s" %(field1, field1, tmpfile1.name, infile1))
+		os.system("sort -t '	' -k %d,%d -o %s %s" %(field2, field2, tmpfile2.name, infile2))
+	except:
+		stop_err( 'Initialization error -> %s' %str(exc) )
+
+	option = ""
+	with open(tmpfile1.name, 'r') as infile:
+		for line in infile:
+			line = line.strip()
+			if line:
+				elems = line.split('\t')
+				for j in range(1,len(elems)+1):
+					if j == 1:
+						option = "1.1"
+					else:
+						option = option + ",1." + str(j) 
+			break
+
+	#check if join has --version option. BSD join doens't have this option, while GNU join does. 
+	#The return value in the latter case will be 0, and non-zero in the latter case.
+	ret = subprocess.run('join --version 2>/dev/null', shell=True) 
+	# check if we are a version later than 7 of join. If so, we want to skip
+	# checking the order since join will raise an error with duplicated items in
+	# the two files being joined.
+	if ret.returncode == 0: 
+		cl = subprocess.Popen(["join", "--version"], stdout=subprocess.PIPE)
+		(stdout, _) = cl.communicate()
+		version_line = str(stdout).split("\\n")[0]
+		(version, _) = version_line.split()[-1].split(".")
+		if int(version) >= 7:
+			flags = "--nocheck-order"
+		else:
+			flags = ""
+	else:
+		flags = ""
 
-    if mode == "V":
-        cmdline = "join %s -t '	' -v 1 -o %s -1 %d -2 %d %s %s > %s" %(flags, option, field1, field2, tmpfile1.name, tmpfile2.name, outfile)
-    else:
-        cmdline = "join %s -t '	' -o %s -1 %d -2 %d %s %s > %s" %(flags, option, field1, field2, tmpfile1.name, tmpfile2.name, outfile)
-    
-    try:
-        os.system(cmdline) 
-    except Exception, exj:
-        stop_err('Error joining the two datasets -> %s' %str(exj))
-       
+	if mode == "V":
+		cmdline = "join %s -t '	' -v 1 -o %s -1 %d -2 %d %s %s > %s" %(flags, option, field1, field2, tmpfile1.name, tmpfile2.name, outfile)
+	else:
+		cmdline = "join %s -t '	' -o %s -1 %d -2 %d %s %s > %s" %(flags, option, field1, field2, tmpfile1.name, tmpfile2.name, outfile)
+	
+	try:
+		os.system(cmdline) 
+	except:
+		stop_err('Error joining the two datasets -> %s' %str(exj))
+	   
 if __name__ == "__main__":
-    main()
+	main()

tag2peak.pl

@@ -52,6 +52,7 @@
 
 GetOptions (
 	'big'=>\$big,
+	'minBlockSize:i'=>\$minBlockSize,
 	'p:f'=>\$pvalueThreshold,
 	'ss'=>\$separateStrand,
 	'valley-seeking'=>\$valleySeeking,
@@ -82,6 +83,7 @@
 	print "Options:\n";
 	#print " -e          : expression values indicated in the gene bed file\n";
     print " -big                   : big input file\n";
+	print " -minBlockSize  [int]   : minimim number of lines to read in each block for a big file ($minBlockSize)\n";
 	print " -ss                    : separate the two strands\n";
 	print " --valley-seeking       : find candidate peaks by valley seeking\n";
 	print " --valley-depth [float] : depth of valley if valley seeking ($valleyDepth)\n";
@@ -340,7 +342,7 @@
 	my $geneTagCountTotal = 0;
 	map {$geneTagCountTotal += $geneTagCountHash{$_}->{'count'}} keys %geneTagCountHash;
 
-	Carp::croak "no tags??" if $geneTagCountTotal <= 0;
+	Carp::croak "No match between tags and gene references? check your chromosome names in your tag file\n" if $geneTagCountTotal <= 0;
 
 	print "total number of tags overlapping with specified reions: $geneTagCountTotal\n" if $verbose;