fixed seq qual length check

[biopieces.git] / bp_bin / read_mysql

diff --git a/bp_bin/read_mysql b/bp_bin/read_mysql
index 003320767033cb5c0b370c98989434f4341eba59..2d8f7b1674c3704cb2bb554554fb703a70505a8a 100755 (executable)
--- a/bp_bin/read_mysql
+++ b/bp_bin/read_mysql
@@ -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::SQL;
@@ -35,17 +36,17 @@ use Maasha::UCSC;
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
-my ( $run_time_beg, $run_time_end, $default_user, $default_password, $options, $in, $out, $record, $dbh, $results );
+my ( $user, $password, $options, $in, $out, $record, $dbh, $results );
 
-$default_user     = Maasha::UCSC::ucsc_get_user();
-$default_password = Maasha::UCSC::ucsc_get_password();
+$user     = Maasha::Biopieces::biopiecesrc( "MYSQL_USER" );
+$password = Maasha::Biopieces::biopiecesrc( "MYSQL_PASSWORD" );
 
 $options = Maasha::Biopieces::parse_options(
     [
-        { long => 'database', short => 'd', type => 'string', mandatory => 'yes', default => undef,             allowed => undef, disallowed => undef },
-        { long => 'query',    short => 'q', type => 'string', mandatory => 'yes', default => undef,             allowed => undef, disallowed => undef },
-        { long => 'user',     short => 'u', type => 'string', mandatory => 'no',  default => $default_user,     allowed => undef, disallowed => undef },
-        { long => 'password', short => 'p', type => 'string', mandatory => 'no',  default => $default_password, allowed => undef, disallowed => undef },
+        { long => 'database', short => 'd', type => 'string', mandatory => 'yes', default => undef,     allowed => undef, disallowed => undef },
+        { long => 'query',    short => 'q', type => 'string', mandatory => 'yes', default => undef,     allowed => undef, disallowed => undef },
+        { long => 'user',     short => 'u', type => 'string', mandatory => 'no',  default => $user,     allowed => undef, disallowed => undef },
+        { long => 'password', short => 'p', type => 'string', mandatory => 'no',  default => $password, allowed => undef, disallowed => undef },
     ]   
 );
 
@@ -64,25 +65,22 @@ Maasha::SQL::disconnect( $dbh );
 
 map { Maasha::Biopieces::put_record( $_ ) } @{ $results };
 
+Maasha::Biopieces::close_stream( $in );
+Maasha::Biopieces::close_stream( $out );
+
 
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
 BEGIN
 {
-    $run_time_beg = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::log_biopiece();
+    Maasha::Biopieces::status_set();
 }
 
+
 END
 {
-    Maasha::Biopieces::close_stream( $in );
-    Maasha::Biopieces::close_stream( $out );
-
-    $run_time_end = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::run_time_print( $run_time_beg, $run_time_end, $options );
+    Maasha::Biopieces::status_log();
 }