-#!/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 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+# Read fixedStep format from one or more files.
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
-use warnings;
use strict;
+use Maasha::Biopieces;
+use Maasha::Filesys;
+use Maasha::UCSC::Wiggle;
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+my ( $run_time_beg, $run_time_end, $options, $in, $out, $record, $data_in, $num, $entry );
+
+$options = Maasha::Biopieces::parse_options(
+ [
+ { long => 'data_in', short => 'i', type => 'files!', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
+ { long => 'num', short => 'n', type => 'uint', mandatory => 'no', default => undef, allowed => undef, disallowed => '0' },
+ ]
+);
+
+$in = Maasha::Biopieces::read_stream( $options->{ "stream_in" } );
+$out = Maasha::Biopieces::write_stream( $options->{ "stream_out" } );
+
+while ( $record = Maasha::Biopieces::get_record( $in ) ) {
+ Maasha::Biopieces::put_record( $record, $out );
+}
+
+if ( $options->{ 'data_in' } )
+{
+ $data_in = Maasha::Filesys::files_read_open( $options->{ 'data_in' } );
+
+ $num = 1;
+
+ while ( $entry = Maasha::UCSC::Wiggle::fixedstep_entry_get( $data_in ) )
+ {
+ $record = Maasha::UCSC::Wiggle::fixedstep2biopiece( $entry );
+
+ Maasha::Biopieces::put_record( $record, $out );
+
+ last if $options->{ "num" } and $num == $options->{ "num" };
+
+ $num++;
+ }
+
+ close $data_in;
+}
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+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 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+# Read GFF data from one or more files.
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
-use warnings;
use strict;
+use Maasha::Biopieces;
+use Maasha::Filesys;
+use Maasha::GFF;
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+my ( $run_time_beg, $run_time_end, $options, $in, $out, $record, $data_in, $num, $entry );
+
+$options = Maasha::Biopieces::parse_options(
+ [
+ { long => 'data_in', short => 'i', type => 'files!', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
+ { long => 'num', short => 'n', type => 'uint', mandatory => 'no', default => undef, allowed => undef, disallowed => '0' },
+ ]
+);
+
+$in = Maasha::Biopieces::read_stream( $options->{ "stream_in" } );
+$out = Maasha::Biopieces::write_stream( $options->{ "stream_out" } );
+
+while ( $record = Maasha::Biopieces::get_record( $in ) ) {
+ Maasha::Biopieces::put_record( $record, $out );
+}
+
+if ( $options->{ 'data_in' } )
+{
+ $data_in = Maasha::Filesys::files_read_open( $options->{ 'data_in' } );
+
+ $num = 1;
+
+ while ( $entry = Maasha::GFF::get_entry( $data_in ) )
+ {
+ Maasha::Biopieces::put_record( $entry, $out );
+
+ last if $options->{ "num" } and $num == $options->{ "num" };
+
+ $num++;
+ }
+
+ close $data_in;
+}
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+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 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+# Read FASTA entries from one or more files.
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
-use warnings;
use strict;
+use Maasha::Biopieces;
+use Maasha::Filesys;
+use Maasha::UCSC;
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+my ( $run_time_beg, $run_time_end, $options, $in, $out, $record, $data_in, $num, $entry );
+
+$options = Maasha::Biopieces::parse_options(
+ [
+ { long => 'data_in', short => 'i', type => 'files!', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
+ { long => 'num', short => 'n', type => 'uint', mandatory => 'no', default => undef, allowed => undef, disallowed => '0' },
+ ]
+);
+
+$in = Maasha::Biopieces::read_stream( $options->{ "stream_in" } );
+$out = Maasha::Biopieces::write_stream( $options->{ "stream_out" } );
+
+while ( $record = Maasha::Biopieces::get_record( $in ) ) {
+ Maasha::Biopieces::put_record( $record, $out );
+}
+
+if ( $options->{ 'data_in' } )
+{
+ $data_in = Maasha::Filesys::files_read_open( $options->{ 'data_in' } );
+
+ $num = 1;
+
+ while ( $record = Maasha::UCSC::ucsc_config_entry_get( $data_in ) )
+ {
+ $record->{ 'REC_TYPE' } = "UCSC Config";
+
+ Maasha::Biopieces::put_record( $record, $out );
+
+ last if $options->{ "num" } and $num == $options->{ "num" };
+
+ $num++;
+ }
+
+ close $data_in;
+}
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+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__
if ( $script eq "print_usage" ) { script_print_usage( $in, $out, $options ) }
elsif ( $script eq "read_psl" ) { script_read_psl( $in, $out, $options ) }
- elsif ( $script eq "read_fixedstep" ) { script_read_fixedstep( $in, $out, $options ) }
elsif ( $script eq "read_stockholm" ) { script_read_stockholm( $in, $out, $options ) }
elsif ( $script eq "read_phastcons" ) { script_read_phastcons( $in, $out, $options ) }
elsif ( $script eq "read_soft" ) { script_read_soft( $in, $out, $options ) }
- elsif ( $script eq "read_gff" ) { script_read_gff( $in, $out, $options ) }
elsif ( $script eq "read_solexa" ) { script_read_solexa( $in, $out, $options ) }
elsif ( $script eq "read_solid" ) { script_read_solid( $in, $out, $options ) }
elsif ( $script eq "read_mysql" ) { script_read_mysql( $in, $out, $options ) }
- elsif ( $script eq "read_ucsc_config" ) { script_read_ucsc_config( $in, $out, $options ) }
elsif ( $script eq "uppercase_seq" ) { script_uppercase_seq( $in, $out, $options ) }
elsif ( $script eq "complexity_seq" ) { script_complexity_seq( $in, $out, $options ) }
elsif ( $script eq "get_genome_align" ) { script_get_genome_align( $in, $out, $options ) }
num|n=s
);
}
- elsif ( $script eq "read_fixedstep" )
- {
- @options = qw(
- data_in|i=s
- num|n=s
- );
- }
elsif ( $script eq "read_stockholm" )
{
@options = qw(
num|n=s
);
}
- elsif ( $script eq "read_gff" )
- {
- @options = qw(
- data_in|i=s
- num|n=s
- );
- }
elsif ( $script eq "read_solexa" )
{
@options = qw(
password|p=s
);
}
- elsif ( $script eq "read_ucsc_config" )
- {
- @options = qw(
- data_in|i=s
- num|n=s
- );
- }
elsif ( $script eq "get_genome_align" )
{
@options = qw(
}
-sub script_read_fixedstep
-{
- # Martin A. Hansen, Juli 2008.
-
- # Read fixedstep wiggle format from stream or file.
-
- my ( $in, # handle to in stream
- $out, # handle to out stream
- $options, # options hash
- ) = @_;
-
- # Returns nothing.
-
- my ( $file, $record, $entry, $data_in, $num );
-
- while ( $record = Maasha::Biopieces::get_record( $in ) ) {
- Maasha::Biopieces::put_record( $record, $out );
- }
-
- $num = 1;
-
- foreach $file ( @{ $options->{ "files" } } )
- {
- $data_in = Maasha::Common::read_open( $file );
-
- while ( $entry = Maasha::UCSC::Wiggle::fixedstep_entry_get( $data_in ) )
- {
- $record = Maasha::UCSC::Wiggle::fixedstep2biopiece( $entry );
-
- Maasha::Biopieces::put_record( $record, $out );
-
- goto NUM if $options->{ "num" } and $num == $options->{ "num" };
-
- $num++;
- }
-
- close $data_in;
- }
-
- NUM:
-
- close $data_in if $data_in;
-}
-
-
sub script_read_stockholm
{
# Martin A. Hansen, August 2007.
}
-sub script_read_gff
-{
- # Martin A. Hansen, February 2008.
-
- # Read soft format.
- # http://www.ncbi.nlm.nih.gov/geo/info/soft2.html
-
- my ( $in, # handle to in stream
- $out, # handle to out stream
- $options, # options hash
- ) = @_;
-
- # Returns nothing.
-
- my ( $data_in, $file, $fh, $num, $record, $entry );
-
- while ( $record = Maasha::Biopieces::get_record( $in ) ) {
- Maasha::Biopieces::put_record( $record, $out );
- }
-
- $num = 1;
-
- foreach $file ( @{ $options->{ "files" } } )
- {
- $fh = Maasha::Common::read_open( $file );
-
- while ( $entry = Maasha::GFF::get_entry( $fh ) )
- {
- Maasha::Biopieces::put_record( $entry, $out );
-
- goto NUM if $options->{ "num" } and $num == $options->{ "num" };
-
- $num++;
- }
-
- close $fh;
- }
-
- NUM:
-
- close $data_in if $data_in;
-}
-
-
sub script_read_solexa
{
# Martin A. Hansen, March 2008.
}
-sub script_read_ucsc_config
-{
- # Martin A. Hansen, November 2008.
-
- # Read track entries from UCSC Genome Browser '.ra' files.
-
- my ( $in, # handle to in stream
- $out, # handle to out stream
- $options, # options hash
- ) = @_;
-
- # Returns nothing.
-
- my ( $record, $file, $data_in, $entry, $num );
-
- while ( $record = Maasha::Biopieces::get_record( $in ) ) {
- Maasha::Biopieces::put_record( $record, $out );
- }
-
- $num = 1;
-
- foreach $file ( @{ $options->{ "files" } } )
- {
- $data_in = Maasha::Common::read_open( $file );
-
- while ( $record = Maasha::UCSC::ucsc_config_entry_get( $data_in ) )
- {
- $record->{ 'REC_TYPE' } = "UCSC Config";
-
- Maasha::Biopieces::put_record( $record, $out );
-
- goto NUM if $options->{ "num" } and $num == $options->{ "num" };
-
- $num++;
- }
-
- close $data_in;
- }
-
- NUM:
-
- close $data_in if $data_in;
-}
-
-
sub script_complexity_seq
{
# Martin A. Hansen, May 2008.
projects / biopieces.git / commitdiff