From: martinahansen Date: Tue, 2 Jun 2009 10:57:14 +0000 (+0000) Subject: migrated 3 write tools X-Git-Url: https://git.donarmstrong.com/?a=commitdiff_plain;h=bd49cececb55175641d9b9af6bfb9a9ce56cdab8;p=biopieces.git migrated 3 write tools git-svn-id: http://biopieces.googlecode.com/svn/trunk@457 74ccb610-7750-0410-82ae-013aeee3265d --- diff --git a/bp_bin/write_2bit b/bp_bin/write_2bit index fdf5bd2..1a1f756 100755 --- a/bp_bin/write_2bit +++ b/bp_bin/write_2bit @@ -1,6 +1,112 @@ -#!/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__ diff --git a/bp_bin/write_bed b/bp_bin/write_bed index fdf5bd2..ceabb1b 100755 --- a/bp_bin/write_bed +++ b/bp_bin/write_bed @@ -1,6 +1,92 @@ -#!/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__ diff --git a/bp_bin/write_fixedstep b/bp_bin/write_fixedstep index fdf5bd2..3c30074 100755 --- a/bp_bin/write_fixedstep +++ b/bp_bin/write_fixedstep @@ -1,6 +1,88 @@ -#!/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__ diff --git a/code_perl/Maasha/BioRun.pm b/code_perl/Maasha/BioRun.pm index 9ff29a1..cdf1f46 100644 --- a/code_perl/Maasha/BioRun.pm +++ b/code_perl/Maasha/BioRun.pm @@ -135,10 +135,7 @@ 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_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 ) } @@ -320,16 +317,6 @@ sub get_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( @@ -338,22 +325,6 @@ sub get_options 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( @@ -1608,40 +1579,6 @@ sub script_soap_seq } -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. @@ -1677,80 +1614,6 @@ sub script_write_psl } -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.