From 12091d5be89c118ee80344528099925922da3933 Mon Sep 17 00:00:00 2001 From: martinahansen Date: Thu, 29 Nov 2012 13:12:46 +0000 Subject: [PATCH] added 3 parameters to blast_seq git-svn-id: http://biopieces.googlecode.com/svn/trunk@2009 74ccb610-7750-0410-82ae-013aeee3265d --- bp_bin/blast_seq | 31 +++++++++++++++++++++++-------- 1 file changed, 23 insertions(+), 8 deletions(-) diff --git a/bp_bin/blast_seq b/bp_bin/blast_seq index ccca6d4..e371b5c 100755 --- a/bp_bin/blast_seq +++ b/bp_bin/blast_seq @@ -44,14 +44,17 @@ $progs_ok = 'blastn,blastp,tblastn,blastx,tblastx'; $options = Maasha::Biopieces::parse_options( [ - { long => 'database', short => 'd', type => 'file', mandatory => 'no', default => undef, allowed => undef, disallowed => undef }, - { long => 'genome', short => 'g', type => 'genome', mandatory => 'no', default => undef, allowed => undef, disallowed => undef }, - { long => 'program', short => 'p', type => 'string', mandatory => 'no', default => undef, allowed => $progs_ok, disallowed => undef }, - { 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 }, - { long => 'megablast', short => 'm', type => 'flag', mandatory => 'no', default => undef, allowed => undef, disallowed => undef }, + { long => 'database', short => 'd', type => 'file', mandatory => 'no', default => undef, allowed => undef, disallowed => undef }, + { long => 'genome', short => 'g', type => 'genome', mandatory => 'no', default => undef, allowed => undef, disallowed => undef }, + { long => 'program', short => 'p', type => 'string', mandatory => 'no', default => undef, allowed => $progs_ok, disallowed => undef }, + { 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 }, + { long => 'megablast', short => 'm', type => 'flag', mandatory => 'no', default => undef, allowed => undef, disallowed => undef }, + { long => 'extend_threshold', short => 'E', type => 'uint', mandatory => 'no', default => 0, allowed => undef, disallowed => undef }, + { long => 'word_size', short => 'W', type => 'uint', mandatory => 'no', default => 0, allowed => undef, disallowed => undef }, + { long => 'single_hit', short => 's', type => 'flag', mandatory => 'no', default => undef, allowed => undef, disallowed => undef }, ] ); @@ -105,6 +108,12 @@ if ( $options->{ 'megablast' } ) { $options->{ 'megablast' } = 'F'; } +if ( $options->{ 'single_hit' } ) { + $options->{ 'single_hit' } = 1 +} else { + $options->{ 'single_hit' } = 0 +} + if ( $options->{ 'verbose' } ) { Maasha::Common::run( @@ -119,6 +128,9 @@ if ( $options->{ 'verbose' } ) "-i $tmp_in", "-d $options->{ 'database' }", "-F $options->{ 'filter' }", + "-P $options->{ 'single_hit' }", + "-W $options->{ 'word_size' }", + "-f $options->{ 'extend_threshold' }", "-o $tmp_out", ), 1 @@ -136,6 +148,9 @@ else "-i $tmp_in", "-d $options->{ 'database' }", "-F $options->{ 'filter' }", + "-P $options->{ 'single_hit' }", + "-W $options->{ 'word_size' }", + "-f $options->{ 'extend_threshold' }", "-o $tmp_out", "> /dev/null 2>&1" ), -- 2.39.2