use strict;
use Maasha::Biopieces;
use Maasha::Filesys;
-use Maasha::KISS::IO;
+use Maasha::KISS;
# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
$num = 1;
- while ( $entry = Maasha::KISS::IO::kiss_entry_get( $data_in ) )
+ while ( $entry = Maasha::KISS::kiss_entry_get( $data_in ) )
{
- if ( $record = Maasha::KISS::IO::kiss2biopiece( $entry ) ) {
+ if ( $record = Maasha::KISS::kiss2biopiece( $entry ) ) {
Maasha::Biopieces::put_record( $record, $out );
}
use warnings;
use strict;
use Maasha::Common;
-use Maasha::KISS::IO;
+use Maasha::KISS;
use Maasha::Biopieces;
use Maasha::Fasta;
use Maasha::Filesys;
while ( $record = Maasha::Biopieces::get_record( $in ) )
{
- if ( $entry = Maasha::KISS::IO::biopiece2kiss( $record ) )
+ if ( $entry = Maasha::KISS::biopiece2kiss( $record ) )
{
if ( not exists $fh_hash{ $entry->{ 'S_ID' } } ) {
$fh_hash{ $entry->{ 'S_ID' } } = Maasha::Filesys::file_write_open( "$tmp_dir/$entry->{ 'S_ID' }" );
$fh_out = $fh_hash{ $entry->{ 'S_ID' } };
- Maasha::KISS::IO::kiss_entry_put( $entry, $fh_out );
+ Maasha::KISS::kiss_entry_put( $entry, $fh_out );
}
Maasha::Biopieces::put_record( $record, $out ) if not $options->{ "no_stream" };
Maasha::Filesys::file_copy( "$tmp_dir/$key", "$dst_dir/track_data.kiss" );
- Maasha::KISS::IO::kiss_sort( "$dst_dir/track_data.kiss" );
- Maasha::KISS::IO::kiss_index( "$dst_dir/track_data.kiss" );
+ Maasha::KISS::kiss_sort( "$dst_dir/track_data.kiss" );
+ Maasha::KISS::kiss_index( "$dst_dir/track_data.kiss" );
unlink "$tmp_dir/$key";
}
--- /dev/null
+#!/usr/bin/env perl
+
+# 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 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+# Upload data to local UCSC Genome Browser Database.
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+use warnings;
+use strict;
+use Maasha::Common;
+use Maasha::Biopieces;
+use Maasha::Filesys;
+use Maasha::UCSC;
+use Maasha::UCSC::Wiggle;
+use Maasha::UCSC::PSL;
+use Maasha::UCSC::BED;
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+my ( $options, $in, $out, $record, $tmp_dir, $file, $wib_file, $wig_file, $wib_dir, $fh_out, $i, $first, $format, $type, $columns, $append, $entry );
+
+$options = Maasha::Biopieces::parse_options(
+ [
+ { long => 'database', short => 'd', type => 'string', mandatory => 'yes', default => undef, allowed => undef, disallowed => undef },
+ { long => 'table', short => 't', type => 'string', mandatory => 'yes', default => undef, allowed => undef, disallowed => undef },
+ { long => 'no_stream', short => 'x', type => 'flag', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
+ { long => 'short_label', short => 's', type => 'string', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
+ { long => 'long_label', short => 'l', type => 'string', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
+ { long => 'group', short => 'g', type => 'string', mandatory => 'no', default => $ENV{ 'LOGNAME' }, allowed => undef, disallowed => undef },
+ { long => 'priority', short => 'p', type => 'float', mandatory => 'no', default => 1, allowed => undef, disallowed => undef },
+ { long => 'use_score', short => 'u', type => 'flag', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
+ { long => 'visibility', short => 'V', type => 'string', mandatory => 'no', default => 'pack', allowed => 'hide,dense,squish,pack,full', disallowed => undef },
+ { long => 'color', short => 'c', type => 'string', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
+ { long => 'check', short => 'C', type => 'flag', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
+ ]
+);
+
+$in = Maasha::Biopieces::read_stream( $options->{ "stream_in" } );
+$out = Maasha::Biopieces::write_stream( $options->{ "stream_out" } );
+
+$tmp_dir = Maasha::Biopieces::get_tmpdir();
+
+$options->{ "short_label" } ||= $options->{ 'table' };
+$options->{ "long_label" } ||= $options->{ 'table' };
+$options->{ "color" } ||= join( ",", int( rand( 255 ) ), int( rand( 255 ) ), int( rand( 255 ) ) );
+$options->{ "chunk_size" } ||= 10_000_000_000; # Due to 32-bit UCSC compilation really large tables cannot be loaded in one go.
+
+$file = "$tmp_dir/ucsc_upload.tmp";
+$append = 0;
+$first = 1;
+$i = 0;
+
+$fh_out = Maasha::Filesys::file_write_open( $file );
+
+while ( $record = Maasha::Biopieces::get_record( $in ) )
+{
+ Maasha::Biopieces::put_record( $record, $out ) if not $options->{ "no_stream" };
+
+ if ( $record->{ "REC_TYPE" } eq "fixed_step" )
+ {
+ $format = "WIGGLE";
+
+ if ( $entry = Maasha::UCSC::Wiggle::biopiece2fixedstep( $record ) ) {
+ Maasha::UCSC::Wiggle::fixedstep_entry_put( $entry, $fh_out );
+ }
+ }
+ elsif ( $record->{ "REC_TYPE" } eq "PSL" )
+ {
+ $format = "PSL";
+
+ Maasha::UCSC::PSL::psl_put_header( $fh_out ) if $first;
+ Maasha::UCSC::PSL::psl_put_entry( $record, $fh_out );
+
+ $first = 0;
+ }
+ elsif ( $record->{ "REC_TYPE" } eq "BED" and $record->{ "SEC_STRUCT" } )
+ {
+ # chrom chromStart chromEnd name score strand size secStr conf
+
+ $format = "BED_SS";
+
+ print $fh_out join ( "\t",
+ $record->{ "CHR" },
+ $record->{ "CHR_BEG" },
+ $record->{ "CHR_END" } + 1,
+ $record->{ "Q_ID" },
+ $record->{ "SCORE" },
+ $record->{ "STRAND" },
+ $record->{ "SIZE" },
+ $record->{ "SEC_STRUCT" },
+ $record->{ "CONF" },
+ ), "\n";
+ }
+ elsif ( $record->{ "REC_TYPE" } eq "BED" )
+ {
+ $format = "BED";
+ $columns = $record->{ "BED_COLS" };
+
+ if ( $entry = Maasha::UCSC::BED::biopiece2bed( $record, $columns ) ) {
+ Maasha::UCSC::BED::bed_entry_put( $entry, $fh_out, $columns, $options->{ 'check' } );
+ }
+ }
+ elsif ( $record->{ "REC_TYPE" } eq "PATSCAN" and $record->{ "CHR" } )
+ {
+ $format = "BED";
+ $columns = 6;
+
+ if ( $entry = Maasha::UCSC::BED::biopiece2bed( $record, $columns ) ) {
+ Maasha::UCSC::BED::bed_entry_put( $entry, $fh_out, $columns, $options->{ 'check' } );
+ }
+ }
+ elsif ( $record->{ "REC_TYPE" } eq "BLAST" and $record->{ "S_ID" } =~ /^chr/ )
+ {
+ $format = "BED";
+ $columns = 6;
+
+ $record->{ "SCORE" } = $record->{ "BIT_SCORE" } * 1000;
+
+ if ( $entry = Maasha::UCSC::BED::biopiece2bed( $record, $columns ) ) {
+ Maasha::UCSC::BED::bed_entry_put( $entry, $fh_out, $columns, $options->{ 'check' } );
+ }
+ }
+ elsif ( $record->{ "REC_TYPE" } eq "VMATCH" and $record->{ "S_ID" } =~ /^chr/i )
+ {
+ $format = "BED";
+ $columns = 6;
+
+ if ( $entry = Maasha::UCSC::BED::biopiece2bed( $record, $columns ) ) {
+ Maasha::UCSC::BED::bed_entry_put( $entry, $fh_out, $columns, $options->{ 'check' } );
+ }
+ }
+
+ if ( $i == $options->{ "chunk_size" } )
+ {
+ close $fh_out;
+
+ if ( $format eq "BED" ) {
+ Maasha::UCSC::bed_upload_to_ucsc( $tmp_dir, $file, $options, $append );
+ } elsif ( $format eq "PSL" ) {
+ Maasha::UCSC::psl_upload_to_ucsc( $file, $options, $append );
+ }
+
+ unlink $file;
+
+ $first = 1;
+
+ $append = 1;
+
+ $fh_out = Maasha::Filesys::file_write_open( $file );
+ }
+
+ $i++;
+}
+
+close $fh_out;
+
+if ( $format eq "BED" )
+{
+ $type = "bed $columns";
+
+ Maasha::UCSC::bed_upload_to_ucsc( $tmp_dir, $file, $options, $append );
+}
+elsif ( $format eq "BED_SS" )
+{
+ $type = "type bed 6 +";
+
+ Maasha::UCSC::bed_upload_to_ucsc( $tmp_dir, $file, $options, $append );
+}
+elsif ( $format eq "PSL" )
+{
+ $type = "psl";
+
+ Maasha::UCSC::psl_upload_to_ucsc( $file, $options, $append );
+}
+elsif ( $format eq "WIGGLE" )
+{
+ $options->{ "visibility" } = "full";
+
+ $wig_file = "$options->{ 'table' }.wig";
+ $wib_file = "$options->{ 'table' }.wib";
+
+ $wib_dir = "$ENV{ 'HOME' }/ucsc/wib";
+
+ Maasha::Filesys::dir_create_if_not_exists( $wib_dir );
+
+ if ( $options->{ 'verbose' } ) {
+ `cd $tmp_dir && wigEncode $file $wig_file $wib_file`;
+ } else {
+ `cd $tmp_dir && wigEncode $file $wig_file $wib_file > /dev/null 2>&1`;
+ }
+
+ Maasha::Common::run( "mv", "$tmp_dir/$wib_file $wib_dir" );
+
+ unlink $file;
+
+ $file = $wig_file;
+
+ $type = "wig 0";
+
+ Maasha::UCSC::wiggle_upload_to_ucsc( $tmp_dir, $wib_dir, $file, $options );
+}
+
+unlink $file;
+
+Maasha::UCSC::ucsc_update_config( $options, $type );
+
+Maasha::Biopieces::close_stream( $in );
+Maasha::Biopieces::close_stream( $out );
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+BEGIN
+{
+ Maasha::Biopieces::status_set();
+}
+
+
+END
+{
+ Maasha::Biopieces::status_log();
+}
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+__END__
+++ /dev/null
-#!/usr/bin/env perl
-
-# 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 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-
-# Upload data to local UCSC Genome Browser Database.
-
-# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-
-
-use warnings;
-use strict;
-use Maasha::Common;
-use Maasha::Biopieces;
-use Maasha::Filesys;
-use Maasha::UCSC;
-use Maasha::UCSC::Wiggle;
-use Maasha::UCSC::PSL;
-use Maasha::UCSC::BED;
-
-
-# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-
-
-my ( $options, $in, $out, $record, $tmp_dir, $file, $wib_file, $wig_file, $wib_dir, $fh_out, $i, $first, $format, $type, $columns, $append, $entry );
-
-$options = Maasha::Biopieces::parse_options(
- [
- { long => 'database', short => 'd', type => 'string', mandatory => 'yes', default => undef, allowed => undef, disallowed => undef },
- { long => 'table', short => 't', type => 'string', mandatory => 'yes', default => undef, allowed => undef, disallowed => undef },
- { long => 'no_stream', short => 'x', type => 'flag', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
- { long => 'short_label', short => 's', type => 'string', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
- { long => 'long_label', short => 'l', type => 'string', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
- { long => 'group', short => 'g', type => 'string', mandatory => 'no', default => $ENV{ 'LOGNAME' }, allowed => undef, disallowed => undef },
- { long => 'priority', short => 'p', type => 'float', mandatory => 'no', default => 1, allowed => undef, disallowed => undef },
- { long => 'use_score', short => 'u', type => 'flag', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
- { long => 'visibility', short => 'V', type => 'string', mandatory => 'no', default => 'pack', allowed => 'hide,dense,squish,pack,full', disallowed => undef },
- { long => 'color', short => 'c', type => 'string', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
- { long => 'check', short => 'C', type => 'flag', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
- ]
-);
-
-$in = Maasha::Biopieces::read_stream( $options->{ "stream_in" } );
-$out = Maasha::Biopieces::write_stream( $options->{ "stream_out" } );
-
-$tmp_dir = Maasha::Biopieces::get_tmpdir();
-
-$options->{ "short_label" } ||= $options->{ 'table' };
-$options->{ "long_label" } ||= $options->{ 'table' };
-$options->{ "color" } ||= join( ",", int( rand( 255 ) ), int( rand( 255 ) ), int( rand( 255 ) ) );
-$options->{ "chunk_size" } ||= 10_000_000_000; # Due to 32-bit UCSC compilation really large tables cannot be loaded in one go.
-
-$file = "$tmp_dir/ucsc_upload.tmp";
-$append = 0;
-$first = 1;
-$i = 0;
-
-$fh_out = Maasha::Filesys::file_write_open( $file );
-
-while ( $record = Maasha::Biopieces::get_record( $in ) )
-{
- Maasha::Biopieces::put_record( $record, $out ) if not $options->{ "no_stream" };
-
- if ( $record->{ "REC_TYPE" } eq "fixed_step" )
- {
- $format = "WIGGLE";
-
- if ( $entry = Maasha::UCSC::Wiggle::biopiece2fixedstep( $record ) ) {
- Maasha::UCSC::Wiggle::fixedstep_entry_put( $entry, $fh_out );
- }
- }
- elsif ( $record->{ "REC_TYPE" } eq "PSL" )
- {
- $format = "PSL";
-
- Maasha::UCSC::PSL::psl_put_header( $fh_out ) if $first;
- Maasha::UCSC::PSL::psl_put_entry( $record, $fh_out );
-
- $first = 0;
- }
- elsif ( $record->{ "REC_TYPE" } eq "BED" and $record->{ "SEC_STRUCT" } )
- {
- # chrom chromStart chromEnd name score strand size secStr conf
-
- $format = "BED_SS";
-
- print $fh_out join ( "\t",
- $record->{ "CHR" },
- $record->{ "CHR_BEG" },
- $record->{ "CHR_END" } + 1,
- $record->{ "Q_ID" },
- $record->{ "SCORE" },
- $record->{ "STRAND" },
- $record->{ "SIZE" },
- $record->{ "SEC_STRUCT" },
- $record->{ "CONF" },
- ), "\n";
- }
- elsif ( $record->{ "REC_TYPE" } eq "BED" )
- {
- $format = "BED";
- $columns = $record->{ "BED_COLS" };
-
- if ( $entry = Maasha::UCSC::BED::biopiece2bed( $record, $columns ) ) {
- Maasha::UCSC::BED::bed_entry_put( $entry, $fh_out, $columns, $options->{ 'check' } );
- }
- }
- elsif ( $record->{ "REC_TYPE" } eq "PATSCAN" and $record->{ "CHR" } )
- {
- $format = "BED";
- $columns = 6;
-
- if ( $entry = Maasha::UCSC::BED::biopiece2bed( $record, $columns ) ) {
- Maasha::UCSC::BED::bed_entry_put( $entry, $fh_out, $columns, $options->{ 'check' } );
- }
- }
- elsif ( $record->{ "REC_TYPE" } eq "BLAST" and $record->{ "S_ID" } =~ /^chr/ )
- {
- $format = "BED";
- $columns = 6;
-
- $record->{ "SCORE" } = $record->{ "BIT_SCORE" } * 1000;
-
- if ( $entry = Maasha::UCSC::BED::biopiece2bed( $record, $columns ) ) {
- Maasha::UCSC::BED::bed_entry_put( $entry, $fh_out, $columns, $options->{ 'check' } );
- }
- }
- elsif ( $record->{ "REC_TYPE" } eq "VMATCH" and $record->{ "S_ID" } =~ /^chr/i )
- {
- $format = "BED";
- $columns = 6;
-
- if ( $entry = Maasha::UCSC::BED::biopiece2bed( $record, $columns ) ) {
- Maasha::UCSC::BED::bed_entry_put( $entry, $fh_out, $columns, $options->{ 'check' } );
- }
- }
-
- if ( $i == $options->{ "chunk_size" } )
- {
- close $fh_out;
-
- if ( $format eq "BED" ) {
- Maasha::UCSC::bed_upload_to_ucsc( $tmp_dir, $file, $options, $append );
- } elsif ( $format eq "PSL" ) {
- Maasha::UCSC::psl_upload_to_ucsc( $file, $options, $append );
- }
-
- unlink $file;
-
- $first = 1;
-
- $append = 1;
-
- $fh_out = Maasha::Filesys::file_write_open( $file );
- }
-
- $i++;
-}
-
-close $fh_out;
-
-if ( $format eq "BED" )
-{
- $type = "bed $columns";
-
- Maasha::UCSC::bed_upload_to_ucsc( $tmp_dir, $file, $options, $append );
-}
-elsif ( $format eq "BED_SS" )
-{
- $type = "type bed 6 +";
-
- Maasha::UCSC::bed_upload_to_ucsc( $tmp_dir, $file, $options, $append );
-}
-elsif ( $format eq "PSL" )
-{
- $type = "psl";
-
- Maasha::UCSC::psl_upload_to_ucsc( $file, $options, $append );
-}
-elsif ( $format eq "WIGGLE" )
-{
- $options->{ "visibility" } = "full";
-
- $wig_file = "$options->{ 'table' }.wig";
- $wib_file = "$options->{ 'table' }.wib";
-
- $wib_dir = "$ENV{ 'HOME' }/ucsc/wib";
-
- Maasha::Filesys::dir_create_if_not_exists( $wib_dir );
-
- if ( $options->{ 'verbose' } ) {
- `cd $tmp_dir && wigEncode $file $wig_file $wib_file`;
- } else {
- `cd $tmp_dir && wigEncode $file $wig_file $wib_file > /dev/null 2>&1`;
- }
-
- Maasha::Common::run( "mv", "$tmp_dir/$wib_file $wib_dir" );
-
- unlink $file;
-
- $file = $wig_file;
-
- $type = "wig 0";
-
- Maasha::UCSC::wiggle_upload_to_ucsc( $tmp_dir, $wib_dir, $file, $options );
-}
-
-unlink $file;
-
-Maasha::UCSC::ucsc_update_config( $options, $type );
-
-Maasha::Biopieces::close_stream( $in );
-Maasha::Biopieces::close_stream( $out );
-
-
-# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-
-
-BEGIN
-{
- Maasha::Biopieces::status_set();
-}
-
-
-END
-{
- Maasha::Biopieces::status_log();
-}
-
-
-# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-
-
-__END__
defined $entry->{ 'S_END' }
)
{
+ Maasha::Common::error( qq(Bad S_BEG value: $entry->{ 'S_BEG' } < 0 ) ) if $entry->{ 'S_BEG' } < 0;
+ Maasha::Common::error( qq(Bad S_END value: $entry->{ 'S_END' } < $entry->{ 'S_BEG' }) ) if $entry->{ 'S_END' } < $entry->{ 'S_BEG' };
+
$fh ||= \*STDOUT;
$fields[ S_ID ] = $entry->{ 'S_ID' };
$fields[ S_BEG ] = $entry->{ 'S_BEG' };
$fields[ S_END ] = $entry->{ 'S_END' };
- $fields[ Q_ID ] = $entry->{ 'Q_ID' };
- $fields[ SCORE ] = $entry->{ 'SCORE' };
- $fields[ STRAND ] = $entry->{ 'STRAND' };
- $fields[ HITS ] = $entry->{ 'HITS' };
- $fields[ ALIGN ] = $entry->{ 'ALIGN' };
- $fields[ BLOCK_COUNT ] = $entry->{ 'BLOCK_COUNT' };
- $fields[ BLOCK_BEGS ] = $entry->{ 'BLOCK_BEGS' };
- $fields[ BLOCK_LENS ] = $entry->{ 'BLOCK_LENS' };
- $fields[ BLOCK_TYPE ] = $entry->{ 'BLOCK_TYPE' };
+ $fields[ Q_ID ] = $entry->{ 'Q_ID' } || ".";
+ $fields[ SCORE ] = $entry->{ 'SCORE' } || ".";
+ $fields[ STRAND ] = $entry->{ 'STRAND' } || ".";
+ $fields[ HITS ] = $entry->{ 'HITS' } || ".";
+ $fields[ ALIGN ] = $entry->{ 'ALIGN' } || ".";
+ $fields[ BLOCK_COUNT ] = $entry->{ 'BLOCK_COUNT' } || ".";
+ $fields[ BLOCK_BEGS ] = $entry->{ 'BLOCK_BEGS' } || ".";
+ $fields[ BLOCK_LENS ] = $entry->{ 'BLOCK_LENS' } || ".";
+ $fields[ BLOCK_TYPE ] = $entry->{ 'BLOCK_TYPE' } || ".";
print $fh join( "\t", @fields ), "\n";
}
}
-sub kiss_align
+sub kiss_align_enc
+{
+ # Martin A. Hansen, November 2009.
+
+ # Encodes alignment descriptors for two
+ # aligned sequences.
+
+ my ( $s_seq, # Subject sequence reference
+ $q_seq, # Query sequence reference
+ $offset, # alternate offset - OPTIONAL
+ ) = @_;
+
+ # Returns a list
+
+ my ( $i, $s, $q, @align );
+
+ Maasha::Common::error( "Sequence lengths don't match" ) if length ${ $s_seq } != length ${ $q_seq };
+
+ $offset ||= 0;
+
+ for ( $i = 0; $i < length ${ $s_seq }; $i++ )
+ {
+ $s = uc substr ${ $s_seq }, $i, 1;
+ $q = uc substr ${ $q_seq }, $i, 1;
+
+ if ( $s eq '-' and $q eq '-' )
+ {
+ # do nothing
+ }
+ elsif ( $s eq $q )
+ {
+ $offset++;
+ }
+ else
+ {
+ push @align, "$offset:$s>$q";
+
+ $offset++ if not $s eq '-';
+ }
+ }
+
+ return wantarray ? @align : \@align;
+}
+
+
+sub kiss_align_dec
{
# Martin A. Hansen, November 2009.
projects / biopieces.git / commitdiff