20251125

2025-11-25 00:28:51 +08:00
commit eb3f16c30e
406 changed files with 91653 additions and 0 deletions
@@ -0,0 +1,173 @@
+package Fastq_reader;
+
+use strict;
+use warnings;
+use Carp;
+
+sub new {
+    my ($packagename, $fastqFile) = @_;
+
+	## note: fastqFile can be a filename or an IO::Handle
+	
+
+    my $self = { fastqFile => undef,
+				 fileHandle => undef };
+
+    bless ($self, $packagename);
+    
+    ## create filehandle
+    my $filehandle = undef;
+    
+	if (ref $fastqFile eq 'IO::Handle') {
+		$filehandle = $fastqFile;
+	}
+	else {
+		if ( $fastqFile =~ /\.gz$/ ) {
+		    ## TODO:  need to handle the failure case, since not picked up here as I thought it would!!
+            open ($filehandle, "gunzip -c $fastqFile | ") or die "Error: Couldn't open compressed $fastqFile\n";
+        }
+        elsif ($fastqFile =~ /\.bz2$/) {
+            open ($filehandle, "bunzip2 -c $fastqFile | ") or die "Error, couldn't open compressed $fastqFile $!";
+            
+        } else {
+            open ($filehandle, $fastqFile) or die "Error: Couldn't open $fastqFile\n";
+        }
+        
+		$self->{fastqFile} = $fastqFile;
+	}
+	
+	$self->{fileHandle} = $filehandle;
+
+    return ($self);
+}
+
+
+
+#### next() fetches next Sequence object.
+sub next {
+    my $self = shift;
+    
+    my $filehandle = $self->{fileHandle};
+    my $next_text_input = "";
+    
+    if (! eof($filehandle)) {
+        for (1..4) {
+            $next_text_input .= <$filehandle>;
+        }
+    }
+    
+	my $read_obj = undef;
+    
+	if ($next_text_input) {
+        
+		eval {
+            $read_obj = Fastq_record->new($next_text_input);
+        };
+        if ($@) {
+            confess "Error, $@ :: fastq file: " . $self->{fastqFile};
+        }
+    }
+        
+    return ($read_obj); #returns null if not instantiated.
+
+}
+
+
+#### finish() closes the open filehandle to the query database.
+sub finish {
+    my $self = shift;
+    my $filehandle = $self->{fileHandle};
+    close $filehandle;
+    $self->{fileHandle} = undef;
+}
+
+
+##############################################
+package Fastq_record;
+
+use strict;
+use warnings;
+use Carp;
+
+sub new {
+    my $packagename = shift;
+    my ($text_lines) = @_;
+    
+    my @split_text = split(/\n/, $text_lines);
+    unless (scalar @split_text == 4) {
+        confess "Error, fastQ entry doesn't have 4 lines: " . $text_lines;
+    }
+    
+    my ($name_line, $seq_line, $plus, $qual_line) = @split_text;
+    
+    unless ($name_line =~ /^\@/) { 
+        confess "Error, cannot identify first line as read name line: " . $text_lines;
+    }
+    
+    my ($read_name, $rest) = split(/\s+/, $name_line);
+    $read_name =~ s/^\@//;
+    
+    
+    my $pair_dir = 0; # assume single
+
+    if ($read_name =~ /^(\S+)\/([12])$/) {
+        $read_name = $1;
+        $pair_dir = $2;
+    }
+    elsif (defined($rest) && $rest =~ /^([12]):/) {
+        $pair_dir = $1;
+    }
+    
+    
+    my $self = { core_read_name => $read_name,
+                 pair_dir => $pair_dir, # (0, 1, or 2), with 0 = unpaired.
+                 sequence => $seq_line,
+                 quals => $qual_line,
+                 record => $text_lines,
+             };
+    
+
+    bless ($self, $packagename);
+    return ($self);
+}
+
+####
+sub get_core_read_name {
+    my $self = shift;
+    return ($self->{core_read_name});
+}
+
+####
+sub get_full_read_name {
+    my $self = shift;
+    
+    my $read_name = $self->{core_read_name};
+    if ($self->{pair_dir}) {
+        return(join("/", $read_name, $self->{pair_dir}));
+    }
+}
+
+####
+sub get_sequence {
+    my $self = shift;
+    return($self->{sequence});
+}
+
+####
+sub get_quals {
+    my $self = shift;
+    return($self->{quals});
+}
+
+####
+sub get_fastq_record {
+    my $self = shift;
+    return($self->{record});
+}
+
+
+
+
+1; #EOM
+
+