From 419be2f2a21320a51e973a046e942a8f3514a32b Mon Sep 17 00:00:00 2001 From: martinahansen Date: Fri, 10 Jul 2009 15:07:59 +0000 Subject: [PATCH] fixed bug in create_vmatch_index git-svn-id: http://biopieces.googlecode.com/svn/trunk@562 74ccb610-7750-0410-82ae-013aeee3265d --- bp_bin/create_vmatch_index | 13 +++++++------ 1 file changed, 7 insertions(+), 6 deletions(-) diff --git a/bp_bin/create_vmatch_index b/bp_bin/create_vmatch_index index f27e255..bf467b2 100755 --- a/bp_bin/create_vmatch_index +++ b/bp_bin/create_vmatch_index @@ -38,20 +38,20 @@ use Maasha::Fasta; # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< -my ( $default, $formats, $options, $in, $out, $record, $file_tmp, $fh_tmp, $type, $entry ); +my ( $default, $formats, $options, $in, $out, $record, $tmp_dir, $file_tmp, $fh_tmp, $type, $entry ); $options = Maasha::Biopieces::parse_options( [ { long => 'no_stream', short => 'x', type => 'flag', mandatory => 'no', default => undef, allowed => undef, disallowed => undef }, { long => 'index_name', short => 'i', type => 'string', mandatory => 'yes', default => undef, allowed => undef, disallowed => undef }, - { long => 'prefix_length', short => 'p', type => 'uint', mandatory => 'no', default => undef, allowed => undef, disallowed => 0 }, ] ); $in = Maasha::Biopieces::read_stream( $options->{ "stream_in" } ); $out = Maasha::Biopieces::write_stream( $options->{ "stream_out" } ); -$file_tmp = $options->{ 'index_name' }; +$tmp_dir = Maasha::Biopieces::get_tmpdir(); +$file_tmp = "$tmp_dir/create_vmatch_index.seq"; $fh_tmp = Maasha::Filesys::file_write_open( $file_tmp ); while ( $record = Maasha::Biopieces::get_record( $in ) ) @@ -68,13 +68,14 @@ while ( $record = Maasha::Biopieces::get_record( $in ) ) close $fh_tmp; -if ( $type eq "protein" ) { - Maasha::Common::run( "mkvtree", "-db $file_tmp -protein -pl $options->{ 'prefix_length' } -allout -indexname $file_tmp > /dev/null 2>&1" ); +if ( $options->{ 'verbose' } ) { + Maasha::Common::run( "mkvtree", "-db $file_tmp -$type -pl -allout -indexname $options->{ 'index_name' }" ); } else { - Maasha::Common::run( "mkvtree", "-db $file_tmp -dna -pl $options->{ 'prefix_length' } -allout -indexname $file_tmp > /dev/null 2>&1" ); + Maasha::Common::run( "mkvtree", "-db $file_tmp -$type -pl -allout -indexname $options->{ 'index_name' } > /dev/null 2>&1" ); } unlink $file_tmp; +Maasha::Filesys::dir_remove( $tmp_dir ); Maasha::Biopieces::close_stream( $in ); Maasha::Biopieces::close_stream( $out ); -- 2.39.2