X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bp_bin%2Fblast_seq;h=be2b8163cd99bdc6e2f9f7f8da14d4f4bda37a0f;hb=49915827e5d35284f24e7149d039478abd1e2139;hp=de78c35d4a2c1419027617068e2257f1c8f8452d;hpb=68b0d2096e200e63bb06f1e20c04761ddb9bc68b;p=biopieces.git

diff --git a/bp_bin/blast_seq b/bp_bin/blast_seq
index de78c35..be2b816 100755
--- a/bp_bin/blast_seq
+++ b/bp_bin/blast_seq
@@ -1,4 +1,4 @@
-#!/usr/bin/env perl -w
+#!/usr/bin/env perl
 
 # Copyright (C) 2007-2009 Martin A. Hansen.
 
@@ -26,6 +26,7 @@
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
+use warnings;
 use strict;
 use Maasha::Biopieces;
 use Maasha::Common;
@@ -37,16 +38,20 @@ use Maasha::Fasta;
 
 
 my ( $options, $in, $out, $tmp_dir, $tmp_in, $tmp_out, $q_type, $s_type, $record, $entry,
-     $fh_in, $fh_out, $program );
+     $fh_in, $fh_out, $progs_ok, $program );
+
+$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 => 'blastn,blastp,tblastn,blastx,tblastx', 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 => '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 },
     ]   
 );
 
@@ -88,6 +93,18 @@ if ( $options->{ 'filter' } eq 'yes' ) {
      $options->{ 'filter' } = 'F';
 }
 
+if ( $options->{ 'no_gaps' } ) {
+    $options->{ 'gapped' } = 'F';
+} else {
+    $options->{ 'gapped' } = 'T';
+}
+
+if ( $options->{ 'megablast' } ) {
+    $options->{ 'megablast' } = 'T';
+} else {
+    $options->{ 'megablast' } = 'F';
+}
+
 if ( $options->{ 'verbose' } )
 {
     Maasha::Common::run(
@@ -96,6 +113,8 @@ if ( $options->{ 'verbose' } )
             "-p $program",
             "-e $options->{ 'e_val' }",
             "-a $options->{ 'cpus' }",
+            "-g $options->{ 'gapped' }",
+            "-n $options->{ 'megablast' }",
             "-m 8",
             "-i $tmp_in",
             "-d $options->{ 'database' }",