-#!/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 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+# Write nucleotide sequences in 2bit format.
+
+# WARNING WARNING There is a bug that prevents 2bit output to be read by Jim Kents tools. WARNING WARNING
+# Possibly the padding is wrong.
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
-use warnings;
use strict;
+use Maasha::Fasta;
+use Maasha::Biopieces;
+use Maasha::Filesys;
+use Maasha::TwoBit;
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+my ( $run_time_beg, $run_time_end, $options, $in, $out, $record, $mask, $tmp_dir, $tmp_file, $fh_tmp, $fh_in, $fh_out, $entry );
+
+$options = Maasha::Biopieces::parse_options(
+ [
+ { long => 'no_stream', short => 'x', type => 'flag', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
+ { long => 'data_out', short => 'o', type => 'file', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
+ { long => 'no_mask', short => 'N', type => 'flag', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
+ ]
+);
+
+$in = Maasha::Biopieces::read_stream( $options->{ "stream_in" } );
+$out = Maasha::Biopieces::write_stream( $options->{ "stream_out" } );
+
+$mask = 1 if not $options->{ "no_mask" };
+
+$tmp_dir = Maasha::Biopieces::get_tmpdir();
+
+$tmp_file = "$tmp_dir/write_2bit.fna";
+
+$fh_tmp = Maasha::Filesys::file_write_open( $tmp_file );
+
+$fh_out = Maasha::Biopieces::write_stream( $options->{ "data_out" } );
+
+while ( $record = Maasha::Biopieces::get_record( $in ) )
+{
+ if ( $entry = Maasha::Fasta::biopiece2fasta( $record ) ) {
+ Maasha::Fasta::put_entry( $entry, $fh_tmp );
+ }
+
+ Maasha::Biopieces::put_record( $record, $out ) if not $options->{ "no_stream" };
+}
+
+close $fh_tmp;
+
+$fh_in = Maasha::Filesys::file_read_open( $tmp_file );
+
+Maasha::TwoBit::fasta2twobit( $fh_in, $fh_out, $mask );
+
+close $fh_in;
+close $fh_out;
+
+unlink $tmp_file;
+
+Maasha::Filesys::dir_remove( $tmp_dir );
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+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 );
+}
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
-use Maasha::BioRun;
+__END__
-#!/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 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+# Write BED entries from stream.
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
-use warnings;
use strict;
+use Maasha::Biopieces;
+use Maasha::UCSC::BED;
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+my ( $run_time_beg, $run_time_end, $options, $in, $out, $fh, $record, $bed_entry, $new_record );
+
+$options = Maasha::Biopieces::parse_options(
+ [
+ { long => 'cols', short => 'c', type => 'uint', mandatory => 'no', default => undef, allowed => undef, disallowed => '0' },
+ { long => 'check', short => 'C', type => 'flag', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
+ { long => 'no_stream', short => 'x', type => 'flag', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
+ { long => 'data_out', short => 'o', type => 'file', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
+ { long => 'compress', short => 'Z', type => 'flag', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
+ ]
+);
+
+$in = Maasha::Biopieces::read_stream( $options->{ "stream_in" } );
+$out = Maasha::Biopieces::write_stream( $options->{ "stream_out" } );
+
+$fh = Maasha::Biopieces::write_stream( $options->{ 'data_out' }, $options->{ 'compress' } );
+
+while ( $record = Maasha::Biopieces::get_record( $in ) )
+{
+ $record = Maasha::UCSC::psl2record( $record ) if $record->{ 'tBaseInsert' }; # Dirty addition to allow Affy data from MySQL to be dumped
+
+ if ( $bed_entry = Maasha::UCSC::BED::biopiece2bed( $record, $options->{ 'cols' } ) ) {
+ Maasha::UCSC::BED::bed_entry_put( $bed_entry, $fh, $options->{ 'cols' }, $options->{ 'check' } );
+ }
+
+ Maasha::Biopieces::put_record( $record, $out ) if not $options->{ 'no_stream' };
+}
+
+close $fh;
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+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 );
+}
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
-use Maasha::BioRun;
+__END__
-#!/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 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+# Write fixedStep from records in the stream.
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
-use warnings;
use strict;
+use Maasha::Biopieces;
+use Maasha::UCSC::Wiggle;
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+my ( $run_time_beg, $run_time_end, $options, $in, $out, $fh, $record, $entry );
+
+$options = Maasha::Biopieces::parse_options(
+ [
+ { long => 'no_stream', short => 'x', type => 'flag', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
+ { long => 'data_out', short => 'o', type => 'file', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
+ { long => 'compress', short => 'Z', type => 'flag', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
+ ]
+);
+
+$in = Maasha::Biopieces::read_stream( $options->{ "stream_in" } );
+$out = Maasha::Biopieces::write_stream( $options->{ "stream_out" } );
+
+$fh = Maasha::Biopieces::write_stream( $options->{ "data_out" }, $options->{ "compress" } );
+
+while ( $record = Maasha::Biopieces::get_record( $in ) )
+{
+ if ( $entry = Maasha::UCSC::Wiggle::biopiece2fixedstep( $record ) ) {
+ Maasha::UCSC::Wiggle::fixedstep_entry_put( $entry, $fh );
+ }
+
+ Maasha::Biopieces::put_record( $record, $out ) if not $options->{ "no_stream" };
+}
+
+close $fh;
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+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 );
+}
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
-use Maasha::BioRun;
+__END__
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 "soap_seq" ) { script_soap_seq( $in, $out, $options ) }
- elsif ( $script eq "write_bed" ) { script_write_bed( $in, $out, $options ) }
elsif ( $script eq "write_psl" ) { script_write_psl( $in, $out, $options ) }
- elsif ( $script eq "write_fixedstep" ) { script_write_fixedstep( $in, $out, $options ) }
- elsif ( $script eq "write_2bit" ) { script_write_2bit( $in, $out, $options ) }
elsif ( $script eq "write_solid" ) { script_write_solid( $in, $out, $options ) }
elsif ( $script eq "write_ucsc_config" ) { script_write_ucsc_config( $in, $out, $options ) }
elsif ( $script eq "remove_mysql_tables" ) { script_remove_mysql_tables( $in, $out, $options ) }
cpus|c=s
);
}
- elsif ( $script eq "write_bed" )
- {
- @options = qw(
- cols|c=s
- check|C
- no_stream|x
- data_out|o=s
- compress|Z
- );
- }
elsif ( $script eq "write_psl" )
{
@options = qw(
compress|Z
);
}
- elsif ( $script eq "write_fixedstep" )
- {
- @options = qw(
- no_stream|x
- data_out|o=s
- compress|Z
- );
- }
- elsif ( $script eq "write_2bit" )
- {
- @options = qw(
- no_stream|x
- data_out|o=s
- no_mask|N
- );
- }
elsif ( $script eq "write_solid" )
{
@options = qw(
}
-sub script_write_bed
-{
- # Martin A. Hansen, August 2007.
-
- # Write BED format for the UCSC genome browser using records in stream.
-
- my ( $in, # handle to in stream
- $out, # handle to out stream
- $options, # options hash
- ) = @_;
-
- # Returns nothing.
-
- my ( $cols, $fh, $record, $bed_entry, $new_record );
-
- $cols = $options->{ 'cols' }->[ 0 ];
-
- $fh = Maasha::Biopieces::write_stream( $options->{ 'data_out' }, $options->{ 'compress' } );
-
- while ( $record = Maasha::Biopieces::get_record( $in ) )
- {
- $record = Maasha::UCSC::psl2record( $record ) if $record->{ 'tBaseInsert' }; # Dirty addition to allow Affy data from MySQL to be dumped
-
- if ( $bed_entry = Maasha::UCSC::BED::biopiece2bed( $record, $cols ) ) {
- Maasha::UCSC::BED::bed_entry_put( $bed_entry, $fh, $cols, $options->{ 'check' } );
- }
-
- Maasha::Biopieces::put_record( $record, $out ) if not $options->{ 'no_stream' };
- }
-
- close $fh;
-}
-
-
sub script_write_psl
{
# Martin A. Hansen, August 2007.
}
-sub script_write_fixedstep
-{
- # Martin A. Hansen, Juli 2008.
-
- # Write fixedStep entries from recrods in the stream.
-
- my ( $in, # handle to in stream
- $out, # handle to out stream
- $options, # options hash
- ) = @_;
-
- # Returns nothing.
-
- my ( $fh, $record, $entry );
-
- $fh = Maasha::Biopieces::write_stream( $options->{ "data_out" }, $options->{ "compress" } );
-
- while ( $record = Maasha::Biopieces::get_record( $in ) )
- {
- if ( $entry = Maasha::UCSC::Wiggle::biopiece2fixedstep( $record ) ) {
- Maasha::UCSC::Wiggle::fixedstep_entry_put( $entry, $fh );
- }
-
- Maasha::Biopieces::put_record( $record, $out ) if not $options->{ "no_stream" };
- }
-
- close $fh;
-}
-
-
-sub script_write_2bit
-{
- # Martin A. Hansen, March 2008.
-
- # Write sequence entries from stream in 2bit format.
-
- my ( $in, # handle to in stream
- $out, # handle to out stream
- $options, # options hash
- ) = @_;
-
- # Returns nothing.
-
- my ( $record, $mask, $tmp_file, $fh_tmp, $fh_in, $fh_out, $entry );
-
- $mask = 1 if not $options->{ "no_mask" };
-
- $tmp_file = "$BP_TMP/write_2bit.fna";
- $fh_tmp = Maasha::Common::write_open( $tmp_file );
-
- $fh_out = Maasha::Biopieces::write_stream( $options->{ "data_out" } );
-
- while ( $record = Maasha::Biopieces::get_record( $in ) )
- {
- if ( $entry = Maasha::Fasta::biopiece2fasta( $record ) ) {
- Maasha::Fasta::put_entry( $entry, $fh_tmp );
- }
-
- Maasha::Biopieces::put_record( $record, $out ) if not $options->{ "no_stream" };
- }
-
- close $fh_tmp;
-
- $fh_in = Maasha::Common::read_open( $tmp_file );
-
- Maasha::TwoBit::fasta2twobit( $fh_in, $fh_out, $mask );
-
- close $fh_in;
- close $fh_out;
-
- unlink $tmp_file;
-}
-
-
sub script_write_solid
{
# Martin A. Hansen, April 2008.
projects / biopieces.git / commitdiff