From 06b84ea91736e1c28d15a9c9e25f0f3006c14a2e Mon Sep 17 00:00:00 2001 From: martinahansen Date: Mon, 10 Aug 2009 07:25:31 +0000 Subject: [PATCH] added --no_gaps switch in blast_seq git-svn-id: http://biopieces.googlecode.com/svn/trunk@625 74ccb610-7750-0410-82ae-013aeee3265d --- bp_bin/blast_seq | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/bp_bin/blast_seq b/bp_bin/blast_seq index 55d0530..e567e77 100755 --- a/bp_bin/blast_seq +++ b/bp_bin/blast_seq @@ -48,6 +48,7 @@ $options = Maasha::Biopieces::parse_options( { long => 'e_val', short => 'e', type => 'float', mandatory => 'no', default => 10, allowed => undef, disallowed => undef }, { long => 'filter', short => 'f', type => 'string', mandatory => 'no', default => 'no', allowed => 'yes,no', disallowed => undef }, { long => 'cpus', short => 'c', type => 'uint', mandatory => 'no', default => 1, allowed => undef, disallowed => 0 }, + { long => 'no_gaps', short => 'G', type => 'flag', mandatory => 'no', default => undef, allowed => undef, disallowed => undef }, ] ); @@ -89,6 +90,12 @@ if ( $options->{ 'filter' } eq 'yes' ) { $options->{ 'filter' } = 'F'; } +if ( $options->{ 'no_gaps' } ) { + $options->{ 'gapped' } = 'F'; +} else { + $options->{ 'gapped' } = 'T'; +} + if ( $options->{ 'verbose' } ) { Maasha::Common::run( @@ -97,6 +104,7 @@ if ( $options->{ 'verbose' } ) "-p $program", "-e $options->{ 'e_val' }", "-a $options->{ 'cpus' }", + "-g $options->{ 'gapped' }", "-m 8", "-i $tmp_in", "-d $options->{ 'database' }", -- 2.39.5