-#!/usr/bin/env perl
+#!/usr/bin/env perl -w
+
+# Copyright (C) 2007-2009 Martin A. Hansen.
+
+# This program is free software; you can redistribute it and/or
+# modify it under the terms of the GNU General Public License
+# as published by the Free Software Foundation; either version 2
+# of the License, or (at your option) any later version.
+
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+
+# You should have received a copy of the GNU General Public License
+# along with this program; if not, write to the Free Software
+# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
+
+# http://www.gnu.org/copyleft/gpl.html
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> DESCRIPTION <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+# Remove MySQL database tables.
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
-use warnings;
use strict;
+use Maasha::Biopieces;
+use Maasha::Common;
+use Maasha::SQL;
+use Maasha::UCSC;
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+my ( $run_time_beg, $run_time_end, $options, $in, $out, $record, %table_hash, $dbh, $table );
+
+$options = Maasha::Biopieces::parse_options(
+ [
+ { long => 'database', short => 'd', type => 'string', mandatory => 'yes', default => undef, allowed => undef, disallowed => undef },
+ { long => 'tables', short => 't', type => 'list', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
+ { long => 'keys', short => 'k', type => 'list', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
+ { long => 'user', short => 'u', type => 'string', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
+ { long => 'password', short => 'p', type => 'string', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
+ ]
+);
+
+$in = Maasha::Biopieces::read_stream( $options->{ "stream_in" } );
+$out = Maasha::Biopieces::write_stream( $options->{ "stream_out" } );
+
+Maasha::Common::error( qq(both --tables and --keys specified) ) if $options->{ "tables" } and $options->{ "keys" };
+Maasha::Common::error( qq(no --tables or --keys specified) ) if not $options->{ "tables" } and not $options->{ "keys" };
+
+$options->{ "user" } ||= Maasha::UCSC::ucsc_get_user();
+$options->{ "password" } ||= Maasha::UCSC::ucsc_get_password();
+
+map { $table_hash{ $_ } = 1 } @{ $options->{ 'tables' } };
+
+while ( $record = Maasha::Biopieces::get_record( $in ) )
+{
+ map { $table_hash{ $record->{ $_ } } = 1 } @{ $options->{ 'keys' } };
+
+ Maasha::Biopieces::put_record( $record, $out ) if not $options->{ 'no_stream' };
+}
+
+$dbh = Maasha::SQL::connect( $options->{ "database" }, $options->{ "user" }, $options->{ "password" } );
+
+foreach $table ( sort keys %table_hash )
+{
+ if ( Maasha::SQL::table_exists( $dbh, $table ) )
+ {
+ print STDERR qq(Removing table "$table" from database "$options->{ 'database' }" ... ) if $options->{ 'verbose' };
+ Maasha::SQL::delete_table( $dbh, $table );
+ print STDERR "done.\n" if $options->{ 'verbose' };
+ }
+ else
+ {
+ print STDERR qq(WARNING: table "$table" not found in database "$options->{ 'database' }\n");
+ }
+}
+
+Maasha::SQL::disconnect( $dbh );
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+BEGIN
+{
+ $run_time_beg = Maasha::Biopieces::run_time();
+
+ Maasha::Biopieces::log_biopiece();
+}
+
+
+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 );
+}
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+__END__
-use Maasha::BioRun;
-#!/usr/bin/env perl
+#!/usr/bin/env perl -w
+
+# Copyright (C) 2007-2009 Martin A. Hansen.
+
+# This program is free software; you can redistribute it and/or
+# modify it under the terms of the GNU General Public License
+# as published by the Free Software Foundation; either version 2
+# of the License, or (at your option) any later version.
+
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+
+# You should have received a copy of the GNU General Public License
+# along with this program; if not, write to the Free Software
+# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
+
+# http://www.gnu.org/copyleft/gpl.html
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> DESCRIPTION <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+# Remove MySQL database tables.
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
-use warnings;
use strict;
+use Maasha::Biopieces;
+use Maasha::Common;
+use Maasha::SQL;
+use Maasha::UCSC;
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+my ( $run_time_beg, $run_time_end, $options, $in, $out, $record, $conf_file, %track_hash, $fh_in, $fh_out, $track, @tracks, $dbh, @new_tracks );
+
+$conf_file = $ENV{ 'HOME' } . "/ucsc/my_tracks.ra";
+
+$options = Maasha::Biopieces::parse_options(
+ [
+ { long => 'database', short => 'd', type => 'string', mandatory => 'yes', default => undef, allowed => undef, disallowed => undef },
+ { long => 'tables', short => 't', type => 'list', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
+ { long => 'keys', short => 'k', type => 'list', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
+ { long => 'config_file', short => 'c', type => 'file!', mandatory => 'no', default => $conf_file, allowed => undef, disallowed => undef },
+ { long => 'user', short => 'u', type => 'string', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
+ { long => 'password', short => 'p', type => 'string', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
+ ]
+);
+
+$in = Maasha::Biopieces::read_stream( $options->{ "stream_in" } );
+$out = Maasha::Biopieces::write_stream( $options->{ "stream_out" } );
+
+Maasha::Common::error( qq(both --tables and --keys specified) ) if $options->{ "tables" } and $options->{ "keys" };
+Maasha::Common::error( qq(no --tables or --keys specified) ) if not $options->{ "tables" } and not $options->{ "keys" };
+
+$options->{ "user" } ||= Maasha::UCSC::ucsc_get_user();
+$options->{ "password" } ||= Maasha::UCSC::ucsc_get_password();
+
+map { $track_hash{ $_ } = 1 } @{ $options->{ 'tracks' } };
+
+while ( $record = Maasha::Biopieces::get_record( $in ) )
+{
+ map { $track_hash{ $record->{ $_ } } = 1 } @{ $options->{ 'keys' } };
+
+ Maasha::Biopieces::put_record( $record, $out ) if not $options->{ 'no_stream' };
+}
+
+$fh_in = Maasha::Filesys::file_read_open( $options->{ 'config_file' } );
+
+while ( $track = Maasha::UCSC::ucsc_config_entry_get( $fh_in ) ) {
+ push @tracks, $track;
+}
+
+close $fh_in;
+
+foreach $track ( @tracks )
+{
+ if ( $track->{ 'database' } eq $options->{ 'database' } and exists $track_hash{ $track->{ 'track' } } ) {
+ print STDERR qq(Removing track "$track->{ 'track' }" from config file.\n) if $options->{ 'verbose' };
+ } else {
+ push @new_tracks, $track;
+ }
+}
+
+rename "$options->{ 'config_file' }", "$options->{ 'config_file' }~";
+
+$fh_out = Maasha::Filesys::file_write_open( $options->{ 'config_file' } );
+
+map { Maasha::UCSC::ucsc_config_entry_put( $_, $fh_out ) } @new_tracks;
+
+close $fh_out;
+
+# ---- locate track in database ----
+
+$dbh = Maasha::SQL::connect( $options->{ "database" }, $options->{ "user" }, $options->{ "password" } );
+
+foreach $track ( sort keys %track_hash )
+{
+ if ( Maasha::SQL::table_exists( $dbh, $track ) )
+ {
+ print STDERR qq(Removing table "$track" from database "$options->{ 'database' }" ... ) if $options->{ 'verbose' };
+ Maasha::SQL::delete_table( $dbh, $track );
+ print STDERR "done.\n" if $options->{ 'verbose' };
+ }
+ else
+ {
+ print STDERR qq(WARNING: table "$track" not found in database "$options->{ 'database' }\n");
+ }
+}
+
+Maasha::SQL::disconnect( $dbh );
+
+Maasha::Common::run( "ucscMakeTracks.pl", "-b > /dev/null 2>&1" );
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+BEGIN
+{
+ $run_time_beg = Maasha::Biopieces::run_time();
+
+ Maasha::Biopieces::log_biopiece();
+}
+
+
+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 );
+}
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+__END__
-use Maasha::BioRun;
elsif ( $script eq "complexity_seq" ) { script_complexity_seq( $in, $out, $options ) }
elsif ( $script eq "get_genome_align" ) { script_get_genome_align( $in, $out, $options ) }
elsif ( $script eq "get_genome_phastcons" ) { script_get_genome_phastcons( $in, $out, $options ) }
- elsif ( $script eq "remove_mysql_tables" ) { script_remove_mysql_tables( $in, $out, $options ) }
- elsif ( $script eq "remove_ucsc_tracks" ) { script_remove_ucsc_tracks( $in, $out, $options ) }
close $in if defined $in;
close $out;
flank|f=s
);
}
- elsif ( $script eq "remove_mysql_tables" )
- {
- @options = qw(
- database|d=s
- tables|t=s
- keys|k=s
- user|u=s
- password|p=s
- no_stream|x
- );
- }
- elsif ( $script eq "remove_ucsc_tracks" )
- {
- @options = qw(
- database|d=s
- tracks|t=s
- keys|k=s
- config_file|c=s
- user|u=s
- password|p=s
- no_stream|x
- );
- }
push @options, qw(
stream_in|I=s
}
}
- Maasha::Common::error( qq(no --database specified) ) if $script eq "remove_ucsc_tracks" and not $options{ "database" };
Maasha::Common::error( qq(no --genome specified) ) if $script =~ /get_genome_align|get_genome_phastcons/ and not $options{ "genome" };
return wantarray ? %options : \%options;
}
-sub script_remove_mysql_tables
-{
- # Martin A. Hansen, November 2008.
-
- # Remove MySQL tables from values in stream.
-
- my ( $in, # handle to in stream
- $out, # handle to out stream
- $options, # options hash
- ) = @_;
-
- # Returns nothing.
-
- my ( $record, %table_hash, $dbh, $table );
-
- $options->{ "user" } ||= Maasha::UCSC::ucsc_get_user();
- $options->{ "password" } ||= Maasha::UCSC::ucsc_get_password();
-
- map { $table_hash{ $_ } = 1 } @{ $options->{ 'tables' } };
-
- while ( $record = Maasha::Biopieces::get_record( $in ) )
- {
- map { $table_hash{ $record->{ $_ } } = 1 } @{ $options->{ 'keys' } };
-
- Maasha::Biopieces::put_record( $record, $out ) if not $options->{ 'no_stream' };
- }
-
- $dbh = Maasha::SQL::connect( $options->{ "database" }, $options->{ "user" }, $options->{ "password" } );
-
- foreach $table ( sort keys %table_hash )
- {
- if ( Maasha::SQL::table_exists( $dbh, $table ) )
- {
- print STDERR qq(Removing table "$table" from database "$options->{ 'database' }" ... ) if $options->{ 'verbose' };
- Maasha::SQL::delete_table( $dbh, $table );
- print STDERR "done.\n" if $options->{ 'verbose' };
- }
- else
- {
- print STDERR qq(WARNING: table "$table" not found in database "$options->{ 'database' }\n");
- }
- }
-
- Maasha::SQL::disconnect( $dbh );
-}
-
-
-sub script_remove_ucsc_tracks
-{
- # Martin A. Hansen, November 2008.
-
- # Remove track from MySQL tables and config file.
-
- my ( $in, # handle to in stream
- $out, # handle to out stream
- $options, # options hash
- ) = @_;
-
- # Returns nothing.
-
- my ( $record, %track_hash, $fh_in, $fh_out, $track, @tracks, @new_tracks, $dbh );
-
- $options->{ 'user' } ||= Maasha::UCSC::ucsc_get_user();
- $options->{ 'password' } ||= Maasha::UCSC::ucsc_get_password();
- $options->{ 'config_file' } ||= "$ENV{ 'HOME' }/ucsc/my_tracks.ra";
-
- map { $track_hash{ $_ } = 1 } @{ $options->{ 'tracks' } };
-
- while ( $record = Maasha::Biopieces::get_record( $in ) )
- {
- map { $track_hash{ $record->{ $_ } } = 1 } @{ $options->{ 'keys' } };
-
- Maasha::Biopieces::put_record( $record, $out ) if not $options->{ 'no_stream' };
- }
-
- $fh_in = Maasha::Filesys::file_read_open( $options->{ 'config_file' } );
-
- while ( $track = Maasha::UCSC::ucsc_config_entry_get( $fh_in ) ) {
- push @tracks, $track;
- }
-
- close $fh_in;
-
- foreach $track ( @tracks )
- {
- if ( $track->{ 'database' } eq $options->{ 'database' } and exists $track_hash{ $track->{ 'track' } } ) {
- print STDERR qq(Removing track "$track->{ 'track' }" from config file.\n) if $options->{ 'verbose' };
- } else {
- push @new_tracks, $track;
- }
- }
-
- rename "$options->{ 'config_file' }", "$options->{ 'config_file' }~";
-
- $fh_out = Maasha::Filesys::file_write_open( $options->{ 'config_file' } );
-
- map { Maasha::UCSC::ucsc_config_entry_put( $_, $fh_out ) } @new_tracks;
-
- close $fh_out;
-
- # ---- locate track in database ----
-
- $dbh = Maasha::SQL::connect( $options->{ "database" }, $options->{ "user" }, $options->{ "password" } );
-
- foreach $track ( sort keys %track_hash )
- {
- if ( Maasha::SQL::table_exists( $dbh, $track ) )
- {
- print STDERR qq(Removing table "$track" from database "$options->{ 'database' }" ... ) if $options->{ 'verbose' };
- Maasha::SQL::delete_table( $dbh, $track );
- print STDERR "done.\n" if $options->{ 'verbose' };
- }
- else
- {
- print STDERR qq(WARNING: table "$track" not found in database "$options->{ 'database' }\n");
- }
- }
-
- Maasha::SQL::disconnect( $dbh );
-
- Maasha::Common::run( "ucscMakeTracks.pl", "-b > /dev/null 2>&1" );
-}
-
-
# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
1;
projects / biopieces.git / commitdiff