From: martinahansen Date: Tue, 2 Jun 2009 14:42:44 +0000 (+0000) Subject: 3 more X-Git-Url: https://git.donarmstrong.com/?a=commitdiff_plain;h=7831048f78fe7aadd60c660733959634ebc38591;p=biopieces.git 3 more git-svn-id: http://biopieces.googlecode.com/svn/trunk@464 74ccb610-7750-0410-82ae-013aeee3265d --- diff --git a/bp_bin/read_fixedstep b/bp_bin/read_fixedstep index fdf5bd2..93b4629 100755 --- a/bp_bin/read_fixedstep +++ b/bp_bin/read_fixedstep @@ -1,6 +1,99 @@ -#!/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__ diff --git a/bp_bin/read_gff b/bp_bin/read_gff index fdf5bd2..411c2a6 100755 --- a/bp_bin/read_gff +++ b/bp_bin/read_gff @@ -1,6 +1,97 @@ -#!/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__ diff --git a/bp_bin/read_ucsc_config b/bp_bin/read_ucsc_config index fdf5bd2..35e6d2d 100755 --- a/bp_bin/read_ucsc_config +++ b/bp_bin/read_ucsc_config @@ -1,6 +1,99 @@ -#!/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__ diff --git a/code_perl/Maasha/BioRun.pm b/code_perl/Maasha/BioRun.pm index 5383aa3..7dbd694 100644 --- a/code_perl/Maasha/BioRun.pm +++ b/code_perl/Maasha/BioRun.pm @@ -112,15 +112,12 @@ sub run_script 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 ) } @@ -165,13 +162,6 @@ sub get_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( @@ -198,13 +188,6 @@ sub get_options num|n=s ); } - elsif ( $script eq "read_gff" ) - { - @options = qw( - data_in|i=s - num|n=s - ); - } elsif ( $script eq "read_solexa" ) { @options = qw( @@ -231,13 +214,6 @@ sub get_options 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( @@ -505,51 +481,6 @@ sub script_read_psl } -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. @@ -742,50 +673,6 @@ sub script_read_soft } -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. @@ -948,51 +835,6 @@ sub script_read_mysql } -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.