diff perl/lib/Fastq.pm @ 1:3203097d0a70 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/perl/lib/Fastq.pm	Thu Oct 15 09:53:48 2015 -0400
@@ -0,0 +1,382 @@
+package Tools::Fastq;
+
+use strict;
+use warnings;
+use Logger::Logger;
+use Storable;
+
+
+=head1 INDEXED FASTQ RELATED METHODS
+
+=head2
+
+=head2 new
+
+=head2
+
+=head3 Description
+
+Create a new Tools::Fastq object and index the FASTQ file
+
+=head3 Arguments
+
+=over 4
+
+=item
+
+A hash of parameters.
+
+Currently accepted keys are :
+
+'file' => FASTQ file path
+
+=back
+
+=head3 Returns
+
+=over 4
+
+=item
+
+A Tools::Fastq object
+
+=back
+
+=cut
+
+sub new {
+	my ($class, %attrs) = @_;
+	my $self = {};
+	bless $self;
+	if(defined($attrs{file})){
+		$self->{file} = $attrs{file};
+		open($self->{file_handle},$self->{file}) || $logger->logdie('Error opening file : '. $self->{file}.' : '.$!."\n");
+		$self->indexFastqFile;
+	}
+	return $self;
+}
+
+=head2 indexFastqFile
+
+=head2
+
+=head3 Description
+
+Index a FASTQ file creating a hash reference with the following structure :
+
+$index -> {seq_id} = {'id_begin_position' => integer, 'id_length' => integer}
+
+For each sequence id, the "@" symbol and all the text after space will be removed.
+
+This cleaned id will be used as key for the index.
+
+=head3 Arguments
+
+=over 4
+
+=item
+
+None
+
+=back
+
+=head3 Returns
+
+=over 4
+
+=item
+
+None
+
+=back
+
+=cut
+
+sub indexFastqFile{
+
+	  my ($self) = @_;
+    $logger->info('Indexing file : '.$self->{file}."\n");
+    my $index;
+    my $id;
+    my $id_begin_position = 0;
+		my $fh = $self->{file_handle};
+    while(my $line = <$fh>){
+
+        if($line =~ /^@(\S+)/){
+
+            $id = $1;
+            chomp $id;
+            $index -> {$id} = {'id_begin_position' => $id_begin_position, 'id_length' => length $line};
+            $logger->trace('Indexing sequence' . $id . ' (position_begin_id : '. $index -> {$id}{'id_begin_position'} . ', id_length : '. $index -> {$id}{'id_length'} .') from ' . $self->{file} . "\n");
+            <$fh>; <$fh>; <$fh>;
+        }
+
+        $id_begin_position = tell($fh);
+    }
+
+    $logger->info('File '.$self->{file}.' is now indexed (index contains '.(scalar keys %$index)." sequences)\n");
+    $self->{index} = $index;
+}
+
+=head2 loadFastqIndexFile
+
+=head2
+
+=head3 Description
+
+Retrieve index from file using Storable module
+
+=head3 Arguments
+
+=over 4
+
+An index file
+
+=back
+
+=head3 Returns
+
+=over 4
+
+=item
+
+A hash reference corresponding to the index of the input FASTQ file :
+
+$index -> {seq_id} = {'id_begin_position' => integer, 'id_length' => integer}
+
+=back
+
+=cut
+
+sub loadFastqIndexFile{
+
+	my ($self, $file) = @_;
+  $self->{index} = retrieve($file);
+  $logger->info('File '.$file." is now loaded\n");
+}
+
+=he=head2 writeFastaIndexFile
+
+=head2
+
+=head3 Description
+
+Write index to file using Storable module
+
+=head3 Arguments
+
+=over 4
+
+=item
+
+A hash reference corresponding to FASTQ index.
+
+=item
+
+An output file path where to store the index.
+
+=back
+
+=head3 Returns
+
+=over 4
+
+=item
+
+The output file path containing index
+
+=back
+
+=cut
+
+sub writeFastqIndexFile{
+	my ($self, $file) = @_;
+  $logger->info('Writing index ('.(scalar keys %{$self->{index}}).' sequences) in file : '.$file."\n");
+  store $self->{index}, $file;
+  $logger->info('File '.$file." is now created\n");
+}
+
+=head2 retrieveFastqSequence
+
+=head2
+
+=head3 Description
+
+Retrieve FASTQ sequences using a list of ids
+
+=head3 Arguments
+
+=over 4
+
+=item
+
+A sequence id OR an array reference containing the list of sequences id to retrieve.
+
+=back
+
+=head3 Returns
+
+=over 4
+
+=item
+
+A hash reference containing sequences id as keys and sequences as values
+
+$data -> {seq_id} = sequence_corresponding_to_seq_id
+
+=back
+
+=cut
+
+sub retrieveFastqSequence{
+	my ($self, $ids) = @_;
+	my $data={};
+  my $nbSequences = 0;
+  if(! ref $ids){$ids = [$ids]}
+  $logger->debug('Retrieving sequences of '.scalar(@$ids).' ids from indexed file : '.$self->{file}."\n");
+	my $fh = $self->{file_handle};
+	foreach my $id (@$ids){
+		my $cleanedId = $id;
+      if($id =~ /@(\S+)/){$cleanedId = $1}
+      $logger->trace('Retrieving informations of id ' . $cleanedId. " from index\n");
+      if(exists $self->{index} -> {$cleanedId}){
+        $logger->trace('id ' . $cleanedId . ' is present in index (id_begin_position : '. $self->{index} -> {$cleanedId}{'id_begin_position'}. ', id_length : '. $self->{index} -> {$cleanedId}{'id_length'}.")\n");
+        seek($fh, $self->{index} -> {$cleanedId}{'id_begin_position'}, 0);
+        <$fh>;
+        my $sequence = <$fh>;
+        $data->{$id} = $sequence;
+        $nbSequences ++;
+      	$logger->trace('Sequence of id '.$cleanedId.' is : ' . $sequence . "\n")
+    	}
+    	else{
+				$logger->trace('id ' . $cleanedId. " not found in index\n")
+			}
+	}
+  $logger->debug($nbSequences.'/'.scalar(@$ids).' sequences has been retrieved from indexed file ' . $self->{file} . "\n");
+	return $data;
+}
+
+=head2 retrieveFastqQuality
+
+=head2
+
+=head3 Description
+
+Retrieve FASTQ sequences quality using a list of ids
+
+=head3 Arguments
+
+=over 4
+
+=item
+
+A sequence id OR an array reference containing the list of sequences id to retrieve quality.
+
+=back
+
+=head3 Returns
+
+=over 4
+
+=item
+
+A hash reference containing sequences id as keys and sequences quality as values
+
+$data -> {seq_id} = sequence_quality_corresponding_to_seq_id
+
+=back
+
+=cut
+
+sub retrieveFastqQuality{
+	my ($self, $ids) = @_;
+	my $data;
+  my $nbSequences = 0;
+  if(! ref $ids){$ids = [$ids]}
+  $logger->debug('Retrieving sequence quality of '.scalar(@$ids).' ids from indexed file : '.$self->{file}."\n");
+	my $fh = $self->{file_handle};
+	foreach my $id (@$ids){
+		my $cleanedId = $id;
+		if($id =~ /@(\S+)/){
+			$cleanedId = $1;
+		}
+    $logger->trace('retrieving informations of id ' . $cleanedId. " from index\n");
+    if(exists $self->{index} -> {$cleanedId}){
+      $logger->trace('id ' . $cleanedId . ' is present in index (id_begin_position : '. $self->{index} -> {$cleanedId}{'id_begin_position'}. ', id_length : '. $self->{index} -> {$cleanedId}{'id_length'}.")\n");
+      seek($fh, $self->{index} -> {$cleanedId}{'id_begin_position'}, 0);
+      my $quality .= <$fh>.<$fh>.<$fh>;
+      $quality = <$fh>;
+      $data .= $quality;
+      $nbSequences ++;
+      $logger->trace('Sequence quality of id '.$cleanedId.' is : ' . $quality. "\n")
+    }
+    else{
+			$logger->trace('id ' . $cleanedId. " not found in index\n");
+		}
+	}
+  $logger->debug($nbSequences.'/'.scalar(@$ids).' sequences qualities has been retrieved from indexed file ' . $self->{file} . "\n");
+	return $data;
+}
+
+=head2 retrieveFastqBlock
+
+=head2
+
+=head3 Description
+
+Retrieve FASTQ formatted sequences using a list of ids
+
+=head3 Arguments
+
+=over 4
+
+=item
+
+A sequence id OR an array reference containing the list of sequences id to retrieve.
+
+=back
+
+=head3 Returns
+
+=over 4
+
+=item
+
+A scalar containing the sequences corresponding to ids in FASTQ format
+
+=back
+
+=cut
+
+sub retrieveFastqBlock{
+	my ($self, $ids) = @_;
+	my $data;
+  my $nbSequences = 0;
+
+  if(! ref $ids){$ids = [$ids]}
+
+  $logger->trace('Retrieving fastq block of '.scalar(@$ids).' ids from indexed file : '.$self->{file}."\n");
+	my $fh = $self->{file_handle};
+	foreach my $id (@$ids){
+		my $cleanedId = $id;
+		if($id =~ /@(\S+)/){
+			$cleanedId = $1;
+		}
+    $logger->trace('Retrieving informations of id ' . $cleanedId. " from index\n");
+    if(exists $self->{index} -> {$cleanedId}){
+      $logger->trace('id ' . $cleanedId . ' is present in index (id_begin_position : '. $self->{index} -> {$cleanedId}{'id_begin_position'}. ', id_length : '. $self->{index} -> {$cleanedId}{'id_length'}.")\n");
+      seek($fh, $self->{index} -> {$cleanedId}{'id_begin_position'}, 0);
+    	read($fh, my $block, $self->{index} -> {$cleanedId}{'id_length'});
+      $block .= <$fh>.<$fh>.<$fh>;
+      $data .= $block;
+      $nbSequences++;
+      $logger->trace('fastq block of id '.$cleanedId.' is : ' ."\n". $block. "\n")
+    }
+    else{
+			$logger->trace('id ' . $cleanedId. " not found in index\n");
+		}
+	}
+  $logger->trace($nbSequences.'/'.scalar(@$ids).' fastq block has been retrieved from indexed file ' . $self->{file} . "\n");
+	return $data;
+}
+1;