From 06b84ea91736e1c28d15a9c9e25f0f3006c14a2e Mon Sep 17 00:00:00 2001
From: martinahansen <martinahansen@74ccb610-7750-0410-82ae-013aeee3265d>
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