use strict;
use Maasha::Biopieces;
use Maasha::Common;
+use Maasha::Fastq;
use Maasha::Fasta;
use Maasha::Calc;
# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-my ( $options, $in, $out, $index, $tmp_dir, $tmp_in, $tmp_out, $fh_in, $fh_out, $record, $entry, $line, @fields );
+my ( $options, $in, $out, $index, $tmp_dir, $tmp_in, $tmp_out, $fh_in, $fh_out, $record, $entry, $line, @fields, $type, $args );
$options = Maasha::Biopieces::parse_options(
[
while ( $record = Maasha::Biopieces::get_record( $in ) )
{
- if ( $entry = Maasha::Fasta::biopiece2fasta( $record ) ) {
+ if ( $entry = Maasha::Fastq::biopiece2fastq( $record ) )
+ {
+ Maasha::Common::error( "Mixed FASTA and FASTQ entries in stream" ) if defined $type and $type ne "FASTQ";
+ Maasha::Fastq::put_entry( $entry, $fh_out );
+
+ $type = "FASTQ";
+ }
+ elsif ( $entry = Maasha::Fasta::biopiece2fasta( $record ) )
+ {
+ Maasha::Common::error( "Mixed FASTA and FASTQ entries in stream" ) if defined $type and $type ne "FASTA";
Maasha::Fasta::put_entry( $entry, $fh_out );
+
+ $type = "FASTA";
}
Maasha::Biopieces::put_record( $record, $out );
close $fh_out;
+$args = "";
+$args = "-f" if $type eq "FASTA";
+
if ( $options->{ 'verbose' } ) {
- Maasha::Common::run( "bowtie", "-f $index $tmp_in $tmp_out" );
+ Maasha::Common::run( "bowtie", "$args $index $tmp_in $tmp_out" );
} else {
- Maasha::Common::run( "bowtie", "-f $index $tmp_in $tmp_out > /dev/null 2>&1" );
+ Maasha::Common::run( "bowtie", "$args $index $tmp_in $tmp_out > /dev/null 2>&1" );
}
unlink $tmp_in;
use warnings;
use strict;
+use Data::Dumper;
use Maasha::Biopieces;
use Maasha::Gwiki;
--- /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 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+# Write sequences from stream in FASTQ format.
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+use warnings;
+use strict;
+use Maasha::Fastq;
+use Maasha::Biopieces;
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+my ( $options, $in, $out, $record, $data_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 => '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( $options->{ "stream_out" } );
+
+$data_out = Maasha::Biopieces::write_stream( $options->{ "data_out" }, $options->{ "compress" } );
+
+while ( $record = Maasha::Biopieces::get_record( $in ) )
+{
+ if ( $entry = Maasha::Fastq::biopiece2fastq( $record ) ) {
+ Maasha::Fastq::put_entry( $entry, $data_out, $options->{ "wrap" } );
+ }
+
+ Maasha::Biopieces::put_record( $record, $out ) if not $options->{ "no_stream" };
+}
+
+close $data_out;
+
+Maasha::Biopieces::close_stream( $in );
+Maasha::Biopieces::close_stream( $out );
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+BEGIN
+{
+ Maasha::Biopieces::status_set();
+}
+
+
+END
+{
+ Maasha::Biopieces::status_log();
+}
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+__END__
--- /dev/null
+package Maasha::Fastq;
+
+# Copyright (C) 2006-2009 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 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+# Routines for manipulation of FASTQ files and FASTQ entries.
+
+# http://maq.sourceforge.net/fastq.shtml
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+use warnings;
+use strict;
+use Data::Dumper;
+use Maasha::Calc;
+use vars qw( @ISA @EXPORT );
+
+@ISA = qw( Exporter );
+
+use constant {
+ SEQ_NAME => 0,
+ SEQ => 1,
+ SCORES => 2,
+};
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+sub get_entry
+{
+ # Martin A. Hansen, July 2009.
+
+ # Gets the next FASTQ entry from a given filehandle.
+
+ my ( $fh, # filehandle
+ ) = @_;
+
+ # Returns a list
+
+ my ( $seq, $seq_name, $qual, $qual_name );
+
+ $seq_name = <$fh>;
+ $seq = <$fh>;
+ $qual_name = <$fh>;
+ $qual = <$fh>;
+
+ return unless $seq;
+
+ chomp $seq;
+ chomp $seq_name;
+ chomp $qual;
+ chomp $qual_name;
+
+ $seq_name =~ s/^@//;
+
+ return wantarray ? ( $seq_name, $seq, $qual ) : [ $seq_name, $seq, $qual ];
+}
+
+
+sub put_entry
+{
+ # Martin A. Hansen, July 2009.
+
+ # Output a FASTQ entry to STDOUT or a filehandle.
+
+ my ( $entry, # FASTQ entry
+ $fh, # filehandle - OPTIONAL
+ ) = @_;
+
+ # Returns nothing.
+
+ $fh ||= \*STDOUT;
+
+ print $fh "@" . $entry->[ SEQ_NAME ] . "\n";
+ print $fh $entry->[ SEQ ] . "\n";
+ print $fh "+\n";
+ print $fh $entry->[ SCORES ] . "\n";
+}
+
+
+sub fastq2biopiece
+{
+ # Martin A. Hansen, July 2009.
+
+ # Converts a FASTQ entry to a Biopiece record, where
+ # the FASTQ quality scores are converted to numerics.
+
+ my ( $entry, # FASTQ entry,
+ ) = @_;
+
+ # Returns a hash.
+
+ my ( $record );
+
+ $record->{ 'SEQ' } = $entry->[ SEQ ];
+ $record->{ 'SEQ_NAME' } = $entry->[ SEQ_NAME ];
+ $record->{ 'SCORES' } = $entry->[ SCORES ];
+
+ $record->{ 'SCORES' } =~ s/(.)/ord( $1 ) - 33 . ";"/ge; # http://maq.sourceforge.net/fastq.shtml
+ $record->{ 'SCORE_MEAN' } = sprintf( "%.2f", Maasha::Calc::mean( [ split /;/, $record->{ 'SCORES' } ] ) );
+
+ return wantarray ? %{ $record } : $record;
+}
+
+
+sub biopiece2fastq
+{
+ # Martin A. Hansen, July 2009.
+
+ # Converts a Biopiece record to a FASTQ entry.
+
+ my ( $record, # Biopiece record
+ ) = @_;
+
+ # Returns a list.
+
+ my ( $list );
+
+ if ( exists $record->{ 'SEQ' } and exists $record->{ 'SEQ_NAME' } and exists $record->{ 'SCORES' } )
+ {
+ $list->[ SEQ_NAME ] = $record->{ 'SEQ_NAME' };
+ $list->[ SEQ ] = $record->{ 'SEQ' };
+ $list->[ SCORES ] = $record->{ 'SCORES' };
+
+ $list->[ SCORES ] =~ s/(\d+);/chr( ( $1 <= 93 ? $1 : 93 ) + 33 )/ge;
+
+ return wantarray ? @{ $list } : $list;
+ }
+
+ return;
+}
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
{
undef @block;
- if ( $lines[ $i ] =~ /^(#summary.+)/ )
+ if ( $lines[ $i ] =~ /(#summary.+)/ ) # TODO: unsolved problem with anchor!
{
$section = $1;
if ( exists $bp_record->{ "SCORE" } ) {
$bed_entry[ score ] = $bp_record->{ "SCORE" };
+ } elsif ( exists $bp_record->{ "SCORE_MEAN" } ) {
+ $bed_entry[ score ] = sprintf( "%.0f", $bp_record->{ "SCORE_MEAN" } );
} else {
return wantarray ? @bed_entry : \@bed_entry;
}
projects / biopieces.git / commitdiff