From: martinahansen Date: Fri, 5 Jun 2009 08:03:41 +0000 (+0000) Subject: migrated removers X-Git-Url: https://git.donarmstrong.com/?a=commitdiff_plain;h=8615d63d95a3da435ad0fc61d98bfc6c15d454f8;p=biopieces.git migrated removers git-svn-id: http://biopieces.googlecode.com/svn/trunk@480 74ccb610-7750-0410-82ae-013aeee3265d --- diff --git a/bp_bin/remove_mysql_tables b/bp_bin/remove_mysql_tables index fdf5bd2..b2e9e34 100755 --- a/bp_bin/remove_mysql_tables +++ b/bp_bin/remove_mysql_tables @@ -1,6 +1,114 @@ -#!/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; diff --git a/bp_bin/remove_ucsc_tracks b/bp_bin/remove_ucsc_tracks index fdf5bd2..82db5d5 100755 --- a/bp_bin/remove_ucsc_tracks +++ b/bp_bin/remove_ucsc_tracks @@ -1,6 +1,146 @@ -#!/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; diff --git a/code_perl/Maasha/BioRun.pm b/code_perl/Maasha/BioRun.pm index 0171465..5cd943a 100644 --- a/code_perl/Maasha/BioRun.pm +++ b/code_perl/Maasha/BioRun.pm @@ -113,8 +113,6 @@ sub run_script 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; @@ -166,29 +164,6 @@ sub get_options 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 @@ -285,7 +260,6 @@ sub get_options } } - 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; @@ -508,130 +482,6 @@ sub script_get_genome_phastcons } -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;