Bio::SeqIO::Raw - Raw sequence input/output stream
It is probably best not to use this object directly, but rather go through the SeqIO handler system. Go:
$stream = Bio::SeqIO->new(-file => $filename, -format => 'Raw'); while $seq ( <$stream> ) { # $seq is a Bio::Seq object }
This object can transform Bio::Seq objects to and from raw textfiles. "Raw" is defined to mean 1 or more sequences separated by a newline. Raw sequences are just lines of data with no formatting or special fields.
The write_seq() method has not been tested yet, should be simple enough.
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Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via email or the web:
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Email birney@sanger.ac.uk
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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 object Args :
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 object
Title : _filehandle Usage : $obj->_filehandle($newval) Function: Example : Returns : value of _filehandle Args : newvalue (optional)
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.