From 61ede0a4aa00bb7770243d573872562bdc878524 Mon Sep 17 00:00:00 2001 From: martinahansen 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