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);
}
&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);
}
}
$command = $dir."rsem-gen-transcript-plots $ARGV[0] $ARGV[1] $gene_list $show_unique $ARGV[2]";
&runCommand($command);
+
# command, {err_msg}
sub runCommand {
print $_[0]."\n";
if ($status != 0) {
my $errmsg;
if (scalar(@_) > 1) { $errmsg = $_[1]; }
- else { $errmsg = "\"$command\" failed! Plase check if you provide correct parameters/options for the pipeline!"; }
+ else { $errmsg = "\"$command\" failed! Please check if you provide correct parameters/options for the pipeline!"; }
print $errmsg."\n";
exit(-1);
}