-#!/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 PSL data (BLAT's native output) from one or more files.
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
-use warnings;
use strict;
+use Maasha::Biopieces;
+use Maasha::Filesys;
+use Maasha::UCSC::PSL;
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+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::PSL::psl_get_entry( $data_in ) )
+ {
+ 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__
-#!/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 SOFT entries from one or more files.
+# http://www.ncbi.nlm.nih.gov/geo/info/soft2.html
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
-use warnings;
use strict;
+use Maasha::Biopieces;
+use Maasha::Filesys;
+use Maasha::NCBI;
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+my ( $run_time_beg, $run_time_end, $options, $in, $out, $record, $data_in, $num, $entry, $records, $soft_index,
+ $fh, @platforms, $plat_table, @samples, $sample, $old_end, $skip, $file );
+
+$options = Maasha::Biopieces::parse_options(
+ [
+ { long => 'data_in', short => 'i', type => 'files!', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
+ { long => 'samples', short => 's', type => 'list', 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, $out );
+}
+
+$num = 1;
+
+foreach $file ( @{ $options->{ "data_in" } } )
+{
+ print STDERR "Creating index for file: $file\n" if $options->{ "verbose" };
+
+ $soft_index = Maasha::NCBI::soft_index_file( $file );
+
+ $fh = Maasha::Filesys::file_read_open( $file );
+
+ @platforms = grep { $_->{ "SECTION" } =~ /PLATFORM/ } @{ $soft_index };
+
+ print STDERR "Getting platform tables for file: $file\n" if $options->{ "verbose" };
+
+ $plat_table = Maasha::NCBI::soft_get_platform( $fh, $platforms[ 0 ]->{ "LINE_BEG" }, $platforms[ -1 ]->{ "LINE_END" } );
+
+ @samples = grep { $_->{ "SECTION" } =~ /SAMPLE/ } @{ $soft_index };
+
+ $old_end = $platforms[ -1 ]->{ "LINE_END" };
+
+ foreach $sample ( @samples )
+ {
+ $skip = 0;
+ $skip = 1 if ( $options->{ "samples" } and grep { $sample->{ "SECTION" } !~ /$_/ } @{ $options->{ "samples" } } );
+
+ print STDERR "Getting samples for dataset: $sample->{ 'SECTION' }\n" if $options->{ "verbose" } and not $skip;
+
+ $records = Maasha::NCBI::soft_get_sample( $fh, $plat_table, $sample->{ "LINE_BEG" } - $old_end - 1, $sample->{ "LINE_END" } - $old_end - 1, $skip );
+
+ foreach $record ( @{ $records } )
+ {
+ Maasha::Biopieces::put_record( $record, $out );
+
+ goto NUM if $options->{ "num" } and $num == $options->{ "num" };
+
+ $num++;
+ }
+
+ $old_end = $sample->{ "LINE_END" };
+ }
+
+ close $fh;
+}
+
+NUM:
+
+close $data_in if $data_in;
+close $fh if $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__
-#!/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 Solexa entries from one or more files.
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
-use warnings;
use strict;
+use Maasha::Biopieces;
+use Maasha::Filesys;
+use Maasha::Solexa;
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+my ( $run_time_beg, $run_time_end, $options, $in, $out, $record, $data_in, $num, $entry, @seqs, @scores, $i );
+
+$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 => 'format', short => 'f', type => 'string', mandatory => 'no', default => 'octal', allowed => 'octal,decimal', disallowed => undef },
+ { long => 'quality', short => 'q', type => 'uint', mandatory => 'no', default => 20, allowed => undef, disallowed => undef },
+ ]
+);
+
+$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;
+
+ if ( $options->{ "format" } eq "octal" )
+ {
+ while ( $entry = Maasha::Solexa::solexa_get_entry_octal( $data_in ) )
+ {
+ $record = Maasha::Solexa::solexa2biopiece( $entry, $options->{ "quality" } );
+
+ Maasha::Biopieces::put_record( $record, $out );
+
+ last if $options->{ "num" } and $num == $options->{ "num" };
+
+ $num++;
+ }
+ }
+ else
+ {
+ while ( $entry = Maasha::Solexa::solexa_get_entry_decimal( $data_in ) )
+ {
+ $record = Maasha::Solexa::solexa2biopiece( $entry, $options->{ "quality" } );
+
+ 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__
$out = Maasha::Biopieces::write_stream( $options->{ "stream_out" } );
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_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_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 "uppercase_seq" ) { script_uppercase_seq( $in, $out, $options ) }
data_in|i=s
);
}
- elsif ( $script eq "read_psl" )
- {
- @options = qw(
- data_in|i=s
- num|n=s
- );
- }
elsif ( $script eq "read_stockholm" )
{
@options = qw(
gap|g=s
);
}
- elsif ( $script eq "read_soft" )
- {
- @options = qw(
- data_in|i=s
- samples|s=s
- num|n=s
- );
- }
- elsif ( $script eq "read_solexa" )
- {
- @options = qw(
- data_in|i=s
- num|n=s
- format|f=s
- quality|q=s
- );
- }
elsif ( $script eq "read_solid" )
{
@options = qw(
{
Maasha::Common::error( qq(Argument to --$opt must be AandB, AorB, BorA, AnotB, or BnotA - not "$options{ $opt }") );
}
- elsif ( $opt eq "format" and $script eq "read_solexa" and $options{ $opt } !~ /octal|decimal/ )
- {
- Maasha::Common::error( qq(Argument to --$opt must be octal or decimal - not "$options{ $opt }") );
- }
}
Maasha::Common::error( qq(no --database specified) ) if $script eq "remove_ucsc_tracks" and not $options{ "database" };
}
-sub script_read_psl
-{
- # Martin A. Hansen, August 2007.
-
- # Read psl table from stream or file.
-
- my ( $in, # handle to in stream
- $out, # handle to out stream
- $options, # options hash
- ) = @_;
-
- # Returns nothing.
-
- my ( $record, $file, $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 ( $record = Maasha::UCSC::psl_get_entry( $data_in ) )
- {
- Maasha::Biopieces::put_record( $record, $out );
-
- goto NUM if $options->{ "num" } and $num == $options->{ "num" };
-
- $num++;
- }
- }
-
- NUM:
-}
-
-
sub script_read_stockholm
{
# Martin A. Hansen, August 2007.
}
-sub script_read_soft
-{
- # Martin A. Hansen, December 2007.
-
- # 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, $num, $records, $record, $soft_index, $fh, @platforms, $plat_table, @samples, $sample, $old_end, $skip );
-
- while ( $record = Maasha::Biopieces::get_record( $in ) ) {
- Maasha::Biopieces::put_record( $record, $out );
- }
-
- $num = 1;
-
- foreach $file ( @{ $options->{ "files" } } )
- {
- print STDERR "Creating index for file: $file\n" if $options->{ "verbose" };
-
- $soft_index = Maasha::NCBI::soft_index_file( $file );
-
- $fh = Maasha::Common::read_open( $file );
-
- @platforms = grep { $_->{ "SECTION" } =~ /PLATFORM/ } @{ $soft_index };
-
- print STDERR "Getting platform tables for file: $file\n" if $options->{ "verbose" };
-
- $plat_table = Maasha::NCBI::soft_get_platform( $fh, $platforms[ 0 ]->{ "LINE_BEG" }, $platforms[ -1 ]->{ "LINE_END" } );
-
- @samples = grep { $_->{ "SECTION" } =~ /SAMPLE/ } @{ $soft_index };
-
- $old_end = $platforms[ -1 ]->{ "LINE_END" };
-
- foreach $sample ( @samples )
- {
- $skip = 0;
- $skip = 1 if ( $options->{ "samples" } and grep { $sample->{ "SECTION" } !~ /$_/ } @{ $options->{ "samples" } } );
-
- print STDERR "Getting samples for dataset: $sample->{ 'SECTION' }\n" if $options->{ "verbose" } and not $skip;
-
- $records = Maasha::NCBI::soft_get_sample( $fh, $plat_table, $sample->{ "LINE_BEG" } - $old_end - 1, $sample->{ "LINE_END" } - $old_end - 1, $skip );
-
- foreach $record ( @{ $records } )
- {
- Maasha::Biopieces::put_record( $record, $out );
-
- goto NUM if $options->{ "num" } and $num == $options->{ "num" };
-
- $num++;
- }
-
- $old_end = $sample->{ "LINE_END" };
- }
-
- close $fh;
- }
-
- NUM:
-
- close $data_in if $data_in;
- close $fh if $fh;
-}
-
-
-sub script_read_solexa
-{
- # Martin A. Hansen, March 2008.
-
- # Read Solexa sequence reads from file.
-
- my ( $in, # handle to in stream
- $out, # handle to out stream
- $options, # options hash
- ) = @_;
-
- # Returns nothing.
-
- my ( $record, $file, $data_in, $entry, $num, @seqs, @scores, $i );
-
- $options->{ "format" } ||= "octal";
- $options->{ "quality" } ||= 20;
-
- 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 );
-
- if ( $options->{ "format" } eq "octal" )
- {
- while ( $entry = Maasha::Solexa::solexa_get_entry_octal( $data_in ) )
- {
- $record = Maasha::Solexa::solexa2biopiece( $entry, $options->{ "quality" } );
-
- Maasha::Biopieces::put_record( $record, $out );
-
- goto NUM if $options->{ "num" } and $num == $options->{ "num" };
-
- $num++;
- }
- }
- else
- {
- while ( $entry = Maasha::Solexa::solexa_get_entry_decimal( $data_in ) )
- {
- $record = Maasha::Solexa::solexa2biopiece( $entry, $options->{ "quality" } );
-
- 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_solid
{
# Martin A. Hansen, April 2008.
}
-# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSL format <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-
-
-sub psl_get_entry
-{
- # Martin A. Hansen, August 2008.
-
- # Reads PSL next entry from a PSL file and returns a record.
-
- my ( $fh, # file handle of PSL filefull path to PSL file
- ) = @_;
-
- # Returns hashref.
-
- my ( $line, @fields, %record );
-
- while ( $line = <$fh> )
- {
- chomp $line;
-
- @fields = split "\t", $line;
-
- if ( scalar @fields == 21 )
- {
- %record = (
- REC_TYPE => "PSL",
- MATCHES => $fields[ 0 ],
- MISMATCHES => $fields[ 1 ],
- REPMATCHES => $fields[ 2 ],
- NCOUNT => $fields[ 3 ],
- QNUMINSERT => $fields[ 4 ],
- QBASEINSERT => $fields[ 5 ],
- SNUMINSERT => $fields[ 6 ],
- SBASEINSERT => $fields[ 7 ],
- STRAND => $fields[ 8 ],
- Q_ID => $fields[ 9 ],
- Q_LEN => $fields[ 10 ],
- Q_BEG => $fields[ 11 ],
- Q_END => $fields[ 12 ] - 1,
- S_ID => $fields[ 13 ],
- S_LEN => $fields[ 14 ],
- S_BEG => $fields[ 15 ],
- S_END => $fields[ 16 ] - 1,
- BLOCK_COUNT => $fields[ 17 ],
- BLOCK_LENS => $fields[ 18 ],
- Q_BEGS => $fields[ 19 ],
- S_BEGS => $fields[ 20 ],
- );
-
- $record{ "SCORE" } = $record{ "MATCHES" } + int( $record{ "REPMATCHES" } / 2 ) - $record{ "MISMATCHES" } - $record{ "QNUMINSERT" } - $record{ "SNUMINSERT" };
- $record{ "Q_SPAN" } = $fields[ 12 ] - $fields[ 11 ];
- $record{ "S_SPAN" } = $fields[ 16 ] - $fields[ 15 ];
-
- return wantarray ? %record : \%record;
- }
- }
-
- return undef;
-}
-
-
-sub psl_get_entries
-{
- # Martin A. Hansen, February 2008.
-
- # Reads PSL entries and returns a list of records.
-
- my ( $path, # full path to PSL file
- ) = @_;
-
- # Returns hashref.
-
- my ( $fh, @lines, @fields, $i, %record, @records );
-
- $fh = Maasha::Common::read_open( $path );
-
- @lines = <$fh>;
-
- close $fh;
-
- chomp @lines;
-
- for ( $i = 5; $i < @lines; $i++ )
- {
- @fields = split "\t", $lines[ $i ];
-
- Maasha::Common::error( qq(Bad PSL format in file "$path") ) if not @fields == 21;
-
- undef %record;
-
- %record = (
- REC_TYPE => "PSL",
- MATCHES => $fields[ 0 ],
- MISMATCHES => $fields[ 1 ],
- REPMATCHES => $fields[ 2 ],
- NCOUNT => $fields[ 3 ],
- QNUMINSERT => $fields[ 4 ],
- QBASEINSERT => $fields[ 5 ],
- SNUMINSERT => $fields[ 6 ],
- SBASEINSERT => $fields[ 7 ],
- STRAND => $fields[ 8 ],
- Q_ID => $fields[ 9 ],
- Q_LEN => $fields[ 10 ],
- Q_BEG => $fields[ 11 ],
- Q_END => $fields[ 12 ] - 1,
- S_ID => $fields[ 13 ],
- S_LEN => $fields[ 14 ],
- S_BEG => $fields[ 15 ],
- S_END => $fields[ 16 ] - 1,
- BLOCK_COUNT => $fields[ 17 ],
- BLOCK_LENS => $fields[ 18 ],
- Q_BEGS => $fields[ 19 ],
- S_BEGS => $fields[ 20 ],
- );
-
- $record{ "SCORE" } = $record{ "MATCHES" } + int( $record{ "REPMATCHES" } / 2 ) - $record{ "MISMATCHES" } - $record{ "QNUMINSERT" } - $record{ "SNUMINSERT" };
-
- push @records, { %record };
- }
-
- return wantarray ? @records : \@records;
-}
-
-
sub psl_put_header
{
# Martin A. Hansen, September 2007.
}
-
-
# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
projects / biopieces.git / commitdiff