From 61ede0a4aa00bb7770243d573872562bdc878524 Mon Sep 17 00:00:00 2001
From: martinahansen <martinahansen@74ccb610-7750-0410-82ae-013aeee3265d>
Date: Tue, 2 Jun 2009 11:12:26 +0000
Subject: [PATCH] migration of all write tools done
git-svn-id: http://biopieces.googlecode.com/svn/trunk@458 74ccb610-7750-0410-82ae-013aeee3265d
---
bp_bin/write_psl | 93 +++++++++++++++++++++++++++-
bp_bin/write_solid | 93 +++++++++++++++++++++++++++-
bp_bin/write_ucsc_config | 86 ++++++++++++++++++++++++-
code_perl/Maasha/BioRun.pm | 124 -------------------------------------
4 files changed, 263 insertions(+), 133 deletions(-)
diff --git a/bp_bin/write_psl b/bp_bin/write_psl
index fdf5bd2..975b369 100755
--- a/bp_bin/write_psl
+++ b/bp_bin/write_psl
@@ -1,6 +1,93 @@
-#!/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 PSL entries from stream.
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
-use warnings;
use strict;
+use Maasha::Biopieces;
+use Maasha::UCSC::PSL;
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+my ( $run_time_beg, $run_time_end, $options, $in, $out, $fh, $record, @output, $first );
+
+$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( $options->{ "stream_out" } );
+
+$first = 1;
+
+$fh = Maasha::Biopieces::write_stream( $options->{ "data_out" }, $options->{ "compress" } );
+
+while ( $record = Maasha::Biopieces::get_record( $in ) )
+{
+ Maasha::Biopieces::put_record( $record, $out ) if not $options->{ "no_stream" };
+
+ if ( $record->{ "REC_TYPE" } and $record->{ "REC_TYPE" } eq "PSL" )
+ {
+ Maasha::UCSC::psl_put_header( $fh ) if $first;
+ Maasha::UCSC::psl_put_entry( $record, $fh );
+ $first = 0;
+ }
+}
+
+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__
diff --git a/bp_bin/write_solid b/bp_bin/write_solid
index fdf5bd2..7a71e51 100755
--- a/bp_bin/write_solid
+++ b/bp_bin/write_solid
@@ -1,6 +1,93 @@
-#!/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 sequences from the stream in SOLID format.
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
-use warnings;
use strict;
+use Maasha::Biopieces;
+use Maasha::Fasta;
+use Maasha::Solid;
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+my ( $run_time_beg, $run_time_end, $options, $in, $out, $record, $fh, $entry );
+
+$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 => 'wrap', short => 'w', type => 'uint', mandatory => 'no', default => undef, allowed => undef, disallowed => '0' },
+ { 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::Fasta::biopiece2fasta( $record ) )
+ {
+ $record->{ 'SEQ' } = Maasha::Solid::seq2color_space( uc $record->{ 'SEQ' } );
+
+ Maasha::Fasta::put_entry( $entry, $fh, $options->{ "wrap" } );
+ }
+
+ 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__
diff --git a/bp_bin/write_ucsc_config b/bp_bin/write_ucsc_config
index fdf5bd2..b566281 100755
--- a/bp_bin/write_ucsc_config
+++ b/bp_bin/write_ucsc_config
@@ -1,6 +1,86 @@
-#!/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 UCSC Genome Browser track configuration format (`.ra` files).
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
-use warnings;
use strict;
+use Maasha::Biopieces;
+use Maasha::UCSC;
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+my ( $run_time_beg, $run_time_end, $options, $in, $out, $record, $fh );
+
+$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 },
+ ]
+);
+
+$in = Maasha::Biopieces::read_stream( $options->{ "stream_in" } );
+$out = Maasha::Biopieces::write_stream( $options->{ "stream_out" } );
+
+
+$fh = Maasha::Biopieces::write_stream( $options->{ "data_out" } );
+
+while ( $record = Maasha::Biopieces::get_record( $in ) )
+{
+ Maasha::UCSC::ucsc_config_entry_put( $record, $fh ) if $record->{ "REC_TYPE" } eq "UCSC Config";
+
+ 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__
diff --git a/code_perl/Maasha/BioRun.pm b/code_perl/Maasha/BioRun.pm
index cdf1f46..aebeb94 100644
--- a/code_perl/Maasha/BioRun.pm
+++ b/code_perl/Maasha/BioRun.pm
@@ -135,9 +135,6 @@ sub run_script
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_psl" ) { script_write_psl( $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 ) }
elsif ( $script eq "remove_ucsc_tracks" ) { script_remove_ucsc_tracks( $in, $out, $options ) }
elsif ( $script eq "upload_to_ucsc" ) { script_upload_to_ucsc( $in, $out, $options ) }
@@ -317,30 +314,6 @@ sub get_options
cpus|c=s
);
}
- elsif ( $script eq "write_psl" )
- {
- @options = qw(
- no_stream|x
- data_out|o=s
- compress|Z
- );
- }
- elsif ( $script eq "write_solid" )
- {
- @options = qw(
- wrap|w=s
- no_stream|x
- data_out|o=s
- compress|Z
- );
- }
- elsif ( $script eq "write_ucsc_config" )
- {
- @options = qw(
- no_stream|x
- data_out|o=s
- );
- }
elsif ( $script eq "remove_mysql_tables" )
{
@options = qw(
@@ -1579,103 +1552,6 @@ sub script_soap_seq
}
-sub script_write_psl
-{
- # Martin A. Hansen, August 2007.
-
- # Write PSL output from stream.
-
- my ( $in, # handle to in stream
- $out, # handle to out stream
- $options, # options hash
- ) = @_;
-
- # Returns nothing.
-
- my ( $fh, $record, @output, $first );
-
- $first = 1;
-
- $fh = Maasha::Biopieces::write_stream( $options->{ "data_out" }, $options->{ "compress" } );
-
- while ( $record = Maasha::Biopieces::get_record( $in ) )
- {
- Maasha::Biopieces::put_record( $record, $out ) if not $options->{ "no_stream" };
-
- if ( $record->{ "REC_TYPE" } and $record->{ "REC_TYPE" } eq "PSL" )
- {
- Maasha::UCSC::psl_put_header( $fh ) if $first;
- Maasha::UCSC::psl_put_entry( $record, $fh );
- $first = 0;
- }
- }
-
- close $fh;
-}
-
-
-sub script_write_solid
-{
- # Martin A. Hansen, April 2008.
-
- # Write di-base encoded Solid sequence from entries in stream.
-
- my ( $in, # handle to in stream
- $out, # handle to out stream
- $options, # options hash
- ) = @_;
-
- # Returns nothing.
-
- my ( $record, $fh, $entry );
-
- $fh = Maasha::Biopieces::write_stream( $options->{ "data_out" }, $options->{ "compress" } );
-
- while ( $record = Maasha::Biopieces::get_record( $in ) )
- {
- if ( $entry = Maasha::Fasta::biopiece2fasta( $record ) )
- {
- $entry->[ SEQ ] = Maasha::Solid::seq2color_space( uc $entry->[ SEQ ] );
-
- Maasha::Fasta::put_entry( $entry, $fh, $options->{ "wrap" } );
- }
-
- Maasha::Biopieces::put_record( $record, $out ) if not $options->{ "no_stream" };
- }
-
- close $fh;
-}
-
-
-sub script_write_ucsc_config
-{
- # Martin A. Hansen, November 2008.
-
- # Write UCSC Genome Broser configuration (.ra file type) from
- # records in the stream.
-
- my ( $in, # handle to in stream
- $out, # handle to out stream
- $options, # options hash
- ) = @_;
-
- # Returns nothing.
-
- my ( $record, $fh );
-
- $fh = Maasha::Biopieces::write_stream( $options->{ "data_out" } );
-
- while ( $record = Maasha::Biopieces::get_record( $in ) )
- {
- Maasha::UCSC::ucsc_config_entry_put( $record, $fh ) if $record->{ "REC_TYPE" } eq "UCSC Config";
-
- Maasha::Biopieces::put_record( $record, $out ) if not $options->{ "no_stream" };
- }
-
- close $fh;
-}
-
-
sub script_remove_mysql_tables
{
# Martin A. Hansen, November 2008.
--
2.39.5