first commit

utils/create_job.pl

@@ -0,0 +1,67 @@
+#!/usr/bin/perl
+
+use strict;
+use warnings;
+
+use 5.010;
+use utf8;
+
+use Getopt::Long;
+use File::Spec;
+
+sub _main {
+    GetOptions( \ my %opts,
+        'i=s',
+        'o=s',
+		'j=s',
+        's=s',
+        't=s',
+		'trans',
+    );
+	
+	_create_job_file(
+		File::Spec->rel2abs($opts{i}),
+		File::Spec->rel2abs($opts{o}),
+		File::Spec->rel2abs($opts{j}),
+		$opts{s},
+		$opts{t},
+		$opts{trans}
+	);
+}
+
+sub _create_job_file {
+	my ($data_dir, $auto_dir, $job_fn, $src, $tgt, $trans) = @_;
+	my ($src_fns, $tgt_fns) = _get_src_tgt_fns($data_dir, $src, $tgt);
+    my @align_fns = map { my ($id) = $_ =~ /(\d+)\./; $id . '.align'; } @{$src_fns};
+    my @table     = map { join "\t", File::Spec->catfile($data_dir, $src_fns->[$_]),
+                                     File::Spec->catfile($data_dir, $tgt_fns->[$_]),
+                                     File::Spec->catfile($auto_dir, $align_fns[$_]) } ( 0 .. scalar @{$src_fns} - 1 );
+	if ( $trans ) {
+		my @trans_fns = map { my ($id) = $_ =~ /(\d+)\./; $id . '.trans'; } @{$src_fns};
+		@table = map { join "\t", (File::Spec->catfile($data_dir, $trans_fns[$_]), $table[$_]) } ( 0 .. scalar @table - 1 );
+	}
+
+	#my $job_fn = File::Spec->catfile($job_dir, $aligner . '.job');
+	open my $OUT, '>:utf8', $job_fn;
+    binmode $OUT; # output unix-like LF(\n) instead of CRLF(\r\n)
+    print $OUT join "\n", @table;
+}
+
+sub _get_src_tgt_fns {
+	my ($dir, $src, $tgt) = @_;
+	my ($src_fns, $tgt_fns);
+	opendir(my $DH, $dir);
+    foreach my $fn ( sort readdir $DH ) {
+		next if $fn =~ /^\./;
+		push @{$src_fns}, $fn if $fn =~ /\.$src\z/;
+        push @{$tgt_fns}, $fn if $fn =~ /\.$tgt\z/;
+	}
+	return ($src_fns, $tgt_fns);
+}
+
+
+unless ( caller ) {
+	_main();
+}
+
+__END__