Bio::SeqIO::fastq - fastq sequence input/output stream
Do not use this module directly. Use it via the Bio::SeqIO class.
This object can transform Bio::Seq and Bio::Seq::Quality objects to and from fastq flat file databases.
Fastq is a file format used frequently at the Sanger Centre to bundle a fasta sequence and its quality data. A typical fastaq entry takes the from:
@HCDPQ1D0501 GATTTGGGGTTCAAAGCAGTATCGATCAAATAGTAAATCCATTTGTTCAACTCACAGTTT..... +HCDPQ1D0501 !''*((((***+))%%%++)(%%%%).1***-+*''))**55CCF>>>>>>CCCCCCC65.....
Fastq files have sequence and quality data on a single line and the quality values are single-byte encoded. To retrieve the decimal values for qualities you need to subtract 33 (or Octal 41) from each byte and then convert to a '2 digit + 1 space' integer. You can check if 33 is the right number because the first byte which is always '!' corresponds to a quality value of 0.
User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists
Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web:
http://bugzilla.open-bio.org/
Email: avc@sanger.ac.uk
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
Title : next_seq Usage : $seq = $stream->next_seq() Function: returns the next sequence in the stream Returns : Bio::Seq::Quality object Args : NONE
Title : write_seq Usage : $stream->write_seq(@seq) Function: writes the $seq object into the stream Returns : 1 for success and 0 for error Args : Bio::Seq::Quality or Bio::Seq object
Title : write_qual Usage : $stream->write_qual(@seq) Function: writes the $seq object into the stream Returns : 1 for success and 0 for error Args : Bio::Seq::Quality object
Title : write_fastq Usage : $stream->write_fastq(@seq) Function: writes the $seq object into the stream Returns : 1 for success and 0 for error Args : Bio::Seq::Quality object
To install Bio::Seq, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::Seq
CPAN shell
perl -MCPAN -e shell install Bio::Seq
For more information on module installation, please visit the detailed CPAN module installation guide.