view release on metacpan or  search on metacpan

lib/Bio/Lite.pm  view on Meta::CPAN

Convert strand from '+/-' standard to '1/-1' standard and the opposite.

Example:

  say "Forward a: ",convertStrand('+');
  say "Forward b: ",convertStrand(1);
  say "Reverse a: ",convertStrand('-');
  say "Reverss b: ",convertStrand(-1);

will print

  Forward a: 1
  Forward b: +
  Reverse a: -1
  Reverse b: -

=head1 PARSING

This are some tools that aim to read (bio) files like

=over

=item Sequence files : FASTA, FASTQ

=item Annotation files : GFF3, GTF2, BED6, BED12, ...

=item Alignement files : SAM, BAM

=back

=head2 seqFileIterator

Open Fasta, or Fastq files (can be gziped).
seqFileIterator has an automatic file extension detection but you can force it
using a second parameter with the format : 'fasta' or 'fastq'.

Example:

  my $it = seqFileIterator('file.fastq','fastq');
  while(my $entry = $it->()) {
    print "Sequence name   : $entry->{name}
           Sequence        : $entry->{seq}
           Sequence quality: $entry->{qual}","\n";
  }

Return: HashRef

  { name => 'sequence_identifier',
    seq  => 'sequence_value',
    qual => 'sequence_quality', # only defined for FASTQ files
  }

seqFileIterator is more than B<50x faster than Bio-Perl> Bio::SeqIO for FASTQ files
seqFileIterator is 4x faster than Bio-Perl Bio::SeqIO for FASTA files

=head2 pairedEndSeqFileIterator

Open Paired-End Sequence files using seqFileIterator()

Paird-End files are generated by Next Generation Sequencing technologies (like Illumina) where two
reads are sequenced from the same DNA fragment and saved in separated files.

Example:

  my $it = pairedEndSeqFileIterator($file);
  while (my $entry = $it->()) {
    print "Read_1 : $entry->{read1}->{seq}
           Read_2 : $entry->{read2}->{seq}";
  }

Return: HashRef

  { read1 => 'see seqFileIterator() return',
    read2 => 'see seqFileIterator() return'
  }

pairedEndSeqFileIterator has no equivalent in Bio-Perl

=head2 gffFileIterator 

manage GFF3 and GTF2 file format

Example:

  my $it = gffFileIterator($file);
  while (my $annot = $it->()) {
    print "chr    : $annot->{chr}
           start  : $annot->{start}
           end    : $annot->{end}";
  }

Return a hashref with the annotation parsed:

  { chr         => 'field_1',
    source      => 'field_2',
    feature     => 'field_3',
    start       => 'field_4',
    end         => 'field_5',
    score       => 'field_6',
    strand      => 'field_7',
    frame       => 'field_8'
    attributes  => { 'attribute_id' => 'attribute_value', ...}
  }

gffFileIterator is B<5x faster than Bio-Perl> Bio::Tools::GFF

=head1 FILES IO

=head2 getReadingFileHandle

Return a file handle for the file in argument.
Display errors if file cannot be oppenned and manage gzipped files (based on .gz file extension)

Example:

  my $fh = getReadingFileHandle('file.txt.gz');
  while(<$fh>) {
    print $_;
  }
  close $fh;