Update wrapper a bit

mourisl · Aug 3, 2016 · 41dfcc9 · 41dfcc9
1 parent 353d425
commit 41dfcc9
Showing 1 changed file with 19 additions and 12 deletions.
diff --git a/rascaf-wrapper.pl b/rascaf-wrapper.pl
@@ -16,12 +16,14 @@
 my $WD = dirname( abs_path( $0 ) ) ;
 
 my $usage = "perl rascaf-wrapper.pl [OPTIONS]:\n".
-	    "\t-b STRING: bam file. Can use multiple -b to specify multiple alignment files[required]\n".
+	    "\t-b STRING: bam file. Can use comma-separator to specify multiple alignment files[required]\n".
 	    "\t-f STRING: path to the raw assembly fasta file\n".
-	    "\t-o STRING : prefix of the output file (default: rascaf_scaffold)".
-	    "\t-ms INT: minimum support for connecting two contigs(default: 2)".
-	    "\t-ml INT: minimum exonic length if no intron (default: 200)".
-	    "\t-k INT: the size of a kmer(<=32. default: 21)" ;
+	    "\t-o STRING : prefix of the output file (default: rascaf_scaffold)\n".
+	    "\t-ms INT: minimum support for connecting two contigs(default: 2)\n".
+	    "\t-ml INT: minimum exonic length if no intron (default: 200)\n".
+	    "\t-k INT: the size of a kmer(<=32. default: 21)\n" ;
+
+die $usage if ( scalar( @ARGV ) == 0 ) ;
 
 my %oneParaOptions ;
 $oneParaOptions{ "-f" } = 1 ;
@@ -33,12 +35,17 @@
 {
 	if ( $ARGV[ $i ] eq "-b" )
 	{
-		my $tmp = $ARGV[$i + 1] ;
-		push @bamFiles, $tmp ;
-
-		$tmp = basename( $tmp ) ;
-		$tmp =~ s/\.bam$// ;
-		push @bamFilePrefix, $tmp ;
+		my @files = split /,/, $ARGV[$i + 1] ;
+
+		for ( my $j = 0 ; $j < scalar( @files ) ; ++$j )
+		{
+			my $tmp = $files[$j] ;
+			push @bamFiles, $tmp ;
+
+			$tmp = basename( $tmp ) ;
+			$tmp =~ s/\.bam$// ;
+			push @bamFilePrefix, $tmp ;
+		}
 
 		++$i ;
 
@@ -75,7 +82,7 @@
 	my $cmd = "$WD/rascaf -b ".$bamFiles[$i]." -o ".$bamFilePrefix[$i]."_$i @rascafARGV" ;
 	print STDERR $cmd, "\n" ;
 	die "rascaf failed.\n" if ( system( $cmd ) != 0 ) ;
-	$joinList .= "-r ".$bamFilePrefix[$i]."_$i".".out" ;
+	$joinList .= " -r ".$bamFilePrefix[$i]."_$i".".out" ;
 }
 
 my $cmd = "$WD/rascaf-join $joinList @rascafJoinARGV" ;