X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=rsem-plot-transcript-wiggles;h=35dfd75544c7d50d6afa61a41d39ecd8c3241608;hb=52f1bd6f44f9b2630b839f192fb9ece18581983b;hp=5054f5bc0d4fa3256bc4ac4899162c4b4e570847;hpb=fc69cf6af24c0550e55447fc82f01cb6f90c1c42;p=rsem.git

diff --git a/rsem-plot-transcript-wiggles b/rsem-plot-transcript-wiggles
index 5054f5b..35dfd75 100755
--- a/rsem-plot-transcript-wiggles
+++ b/rsem-plot-transcript-wiggles
@@ -5,6 +5,8 @@ use Pod::Usage;
 use File::Basename;
 use strict;
 
+use rsem_perl_utils;
+
 my $gene_list = 0; # default is 0, means input is a transcript list; 1 means input is a gene list
 my $show_unique = 0; # 0, default value, means do not show unique transcript wiggles; 1 means show unique transcript wiggles
 my $help = 0;
@@ -19,8 +21,12 @@ pod2usage(-msg => "Invalid number of arguments!", -exitval => 2, -verbose => 2)
 my ($fn, $dir, $suf) = fileparse($0);
 my $command = "";
 
+unless (-e "$ARGV[0].transcript.sorted.bam") {
+    $command = $dir."sam/samtools sort $ARGV[0].transcript.bam $ARGV[0].transcript.sorted";
+    &runCommand($command);
+}
 unless (-e "$ARGV[0].transcript.readdepth") {
-    $command = $dir."rsem-bam2readdepth $ARGV[0].transcript.sorted.bam > $ARGV[0].transcript.readdepth";
+    $command = $dir."rsem-bam2readdepth $ARGV[0].transcript.sorted.bam $ARGV[0].transcript.readdepth";
     &runCommand($command);
 }
 
@@ -34,7 +40,7 @@ if ($show_unique) {
 	&runCommand($command);
     }
     unless (-e "$ARGV[0].uniq.transcript.readdepth") {
-	$command = $dir."rsem-bam2readdepth $ARGV[0].uniq.transcript.sorted.bam > $ARGV[0].uniq.transcript.readdepth";
+	$command = $dir."rsem-bam2readdepth $ARGV[0].uniq.transcript.sorted.bam $ARGV[0].uniq.transcript.readdepth";
 	&runCommand($command);
     }
 }
@@ -42,20 +48,6 @@ if ($show_unique) {
 $command = $dir."rsem-gen-transcript-plots $ARGV[0] $ARGV[1] $gene_list $show_unique $ARGV[2]";
 &runCommand($command);
 
-# command, {err_msg}
-sub runCommand {
-    print $_[0]."\n";
-    my $status = system($_[0]);
-    if ($status != 0) { 
-	my $errmsg;
-	if (scalar(@_) > 1) { $errmsg = $_[1]; }
-	else { $errmsg = "\"$command\" failed! Plase check if you provide correct parameters/options for the pipeline!"; }
-	print $errmsg."\n";
-	exit(-1);
-    }
-    print "\n";
-}
-
 __END__
 
 =head1 NAME