From e6842cd1c6c7eeb8304896a50a9741ec7e49c28d Mon Sep 17 00:00:00 2001 From: martinahansen Date: Tue, 2 Jun 2009 12:34:05 +0000 Subject: [PATCH] more read_ tools migrated git-svn-id: http://biopieces.googlecode.com/svn/trunk@462 74ccb610-7750-0410-82ae-013aeee3265d --- bp_bin/read_blast_tab | 127 ++++++++++++++++++++++++++- bp_bin/read_embl | 134 ++++++++++++++++++++++++++++- code_perl/Maasha/BioRun.pm | 170 ------------------------------------- 3 files changed, 255 insertions(+), 176 deletions(-) diff --git a/bp_bin/read_blast_tab b/bp_bin/read_blast_tab index fdf5bd2..2ed0a55 100755 --- a/bp_bin/read_blast_tab +++ b/bp_bin/read_blast_tab @@ -1,6 +1,127 @@ -#!/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 BLAST records in tabular format from one or more files. + +# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + -use warnings; use strict; +use Maasha::Biopieces; +use Maasha::Filesys; + + +# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + +my ( $run_time_beg, $run_time_end, $options, $in, $out, $file, $record, $line, @fields, $data_in, $num ); + +$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' } ) +{ + $num = 1; + + $data_in = Maasha::Filesys::files_read_open( $options->{ 'data_in' } ); + + while ( $line = <$data_in> ) + { + chomp $line; + + next if $line =~ /^#/; + + @fields = split /\t/, $line; + + $record->{ "REC_TYPE" } = "BLAST"; + $record->{ "Q_ID" } = $fields[ 0 ]; + $record->{ "S_ID" } = $fields[ 1 ]; + $record->{ "IDENT" } = $fields[ 2 ]; + $record->{ "ALIGN_LEN" } = $fields[ 3 ]; + $record->{ "MISMATCHES" } = $fields[ 4 ]; + $record->{ "GAPS" } = $fields[ 5 ]; + $record->{ "Q_BEG" } = $fields[ 6 ] - 1; # BLAST is 1-based + $record->{ "Q_END" } = $fields[ 7 ] - 1; # BLAST is 1-based + $record->{ "S_BEG" } = $fields[ 8 ] - 1; # BLAST is 1-based + $record->{ "S_END" } = $fields[ 9 ] - 1; # BLAST is 1-based + $record->{ "E_VAL" } = $fields[ 10 ]; + $record->{ "BIT_SCORE" } = $fields[ 11 ]; + + if ( $record->{ "S_BEG" } > $record->{ "S_END" } ) + { + $record->{ "STRAND" } = '-'; + + ( $record->{ "S_BEG" }, $record->{ "S_END" } ) = ( $record->{ "S_END" }, $record->{ "S_BEG" } ); + } + else + { + $record->{ "STRAND" } = '+'; + } + + 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_embl b/bp_bin/read_embl index fdf5bd2..e0ba8b7 100755 --- a/bp_bin/read_embl +++ b/bp_bin/read_embl @@ -1,6 +1,134 @@ -#!/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 EMBL entries from one or more files. + +# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + -use warnings; use strict; +use Maasha::Biopieces; +use Maasha::Filesys; +use Maasha::EMBL; + + +# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + +my ( $run_time_beg, $run_time_end, $options, $in, $out, %options2, $file, $data_in, $num, $entry, $record ); + +$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' }, + { long => 'keys', short => 'k', type => 'list', mandatory => 'no', default => undef, allowed => undef, disallowed => undef }, + { long => 'feats', short => 'f', type => 'list', mandatory => 'no', default => undef, allowed => undef, disallowed => undef }, + { long => 'quals', short => 'q', type => 'list', mandatory => 'no', default => undef, allowed => undef, disallowed => undef }, + ] +); + +$in = Maasha::Biopieces::read_stream( $options->{ "stream_in" } ); +$out = Maasha::Biopieces::write_stream( $options->{ "stream_out" } ); + +map { $options2{ "keys" }{ $_ } = 1 } @{ $options->{ "keys" } }; +map { $options2{ "feats" }{ $_ } = 1 } @{ $options->{ "feats" } }; +map { $options2{ "quals" }{ $_ } = 1 } @{ $options->{ "quals" } }; + +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::EMBL::get_embl_entry( $data_in ) ) + { + $record = Maasha::EMBL::parse_embl_entry( $entry, \%options2 ); + + my ( $feat, $feat2, $qual, $qual_val, $record_copy ); + + $record_copy = dclone $record; + + delete $record_copy->{ "FT" }; + + Maasha::Biopieces::put_record( $record_copy, $out ); + + delete $record_copy->{ "SEQ" }; + + foreach $feat ( keys %{ $record->{ "FT" } } ) + { + $record_copy->{ "FEAT_TYPE" } = $feat; + + foreach $feat2 ( @{ $record->{ "FT" }->{ $feat } } ) + { + foreach $qual ( keys %{ $feat2 } ) + { + $qual_val = join "; ", @{ $feat2->{ $qual } }; + + $qual =~ s/^_//; + $qual = uc $qual; + + $record_copy->{ $qual } = $qual_val; + } + + Maasha::Biopieces::put_record( $record_copy, $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 7b5a9da..5383aa3 100644 --- a/code_perl/Maasha/BioRun.pm +++ b/code_perl/Maasha/BioRun.pm @@ -113,8 +113,6 @@ 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_blast_tab" ) { script_read_blast_tab( $in, $out, $options ) } - elsif ( $script eq "read_embl" ) { script_read_embl( $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 ) } @@ -174,23 +172,6 @@ sub get_options num|n=s ); } - elsif ( $script eq "read_blast_tab" ) - { - @options = qw( - data_in|i=s - num|n=s - ); - } - elsif ( $script eq "read_embl" ) - { - @options = qw( - data_in|i=s - num|n=s - keys|k=s - feats|f=s - quals|q=s - ); - } elsif ( $script eq "read_stockholm" ) { @options = qw( @@ -569,157 +550,6 @@ sub script_read_fixedstep } -sub script_read_blast_tab -{ - # Martin A. Hansen, September 2007. - - # Read tabular BLAST output from NCBI blast run with -m8 or -m9. - - my ( $in, # handle to in stream - $out, # handle to out stream - $options, # options hash - ) = @_; - - # Returns nothing. - - my ( $file, $line, @fields, $strand, $record, $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 ( $line = <$data_in> ) - { - chomp $line; - - next if $line =~ /^#/; - - @fields = split /\t/, $line; - - $record->{ "REC_TYPE" } = "BLAST"; - $record->{ "Q_ID" } = $fields[ 0 ]; - $record->{ "S_ID" } = $fields[ 1 ]; - $record->{ "IDENT" } = $fields[ 2 ]; - $record->{ "ALIGN_LEN" } = $fields[ 3 ]; - $record->{ "MISMATCHES" } = $fields[ 4 ]; - $record->{ "GAPS" } = $fields[ 5 ]; - $record->{ "Q_BEG" } = $fields[ 6 ] - 1; # BLAST is 1-based - $record->{ "Q_END" } = $fields[ 7 ] - 1; # BLAST is 1-based - $record->{ "S_BEG" } = $fields[ 8 ] - 1; # BLAST is 1-based - $record->{ "S_END" } = $fields[ 9 ] - 1; # BLAST is 1-based - $record->{ "E_VAL" } = $fields[ 10 ]; - $record->{ "BIT_SCORE" } = $fields[ 11 ]; - - if ( $record->{ "S_BEG" } > $record->{ "S_END" } ) - { - $record->{ "STRAND" } = '-'; - - ( $record->{ "S_BEG" }, $record->{ "S_END" } ) = ( $record->{ "S_END" }, $record->{ "S_BEG" } ); - } - else - { - $record->{ "STRAND" } = '+'; - } - - 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_embl -{ - # Martin A. Hansen, August 2007. - - # Read EMBL format. - - my ( $in, # handle to in stream - $out, # handle to out stream - $options, # options hash - ) = @_; - - # Returns nothing. - - my ( %options2, $file, $data_in, $num, $entry, $record ); - - map { $options2{ "keys" }{ $_ } = 1 } @{ $options->{ "keys" } }; - map { $options2{ "feats" }{ $_ } = 1 } @{ $options->{ "feats" } }; - map { $options2{ "quals" }{ $_ } = 1 } @{ $options->{ "quals" } }; - - 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::EMBL::get_embl_entry( $data_in ) ) - { - $record = Maasha::EMBL::parse_embl_entry( $entry, \%options2 ); - - my ( $feat, $feat2, $qual, $qual_val, $record_copy ); - - $record_copy = dclone $record; - - delete $record_copy->{ "FT" }; - - Maasha::Biopieces::put_record( $record_copy, $out ); - - delete $record_copy->{ "SEQ" }; - - foreach $feat ( keys %{ $record->{ "FT" } } ) - { - $record_copy->{ "FEAT_TYPE" } = $feat; - - foreach $feat2 ( @{ $record->{ "FT" }->{ $feat } } ) - { - foreach $qual ( keys %{ $feat2 } ) - { - $qual_val = join "; ", @{ $feat2->{ $qual } }; - - $qual =~ s/^_//; - $qual = uc $qual; - - $record_copy->{ $qual } = $qual_val; - } - - Maasha::Biopieces::put_record( $record_copy, $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. -- 2.39.5