iPE::SequenceReader::Load::FASTA(3)

NAME
iPE::SequenceReader::Load::FASTA - Simple fasta sequence reader.

DESCRIPTION
This is a semi-flexible fasta sequence reader. It allows the option of splitting the sequence into a set of scalars. It only keeps track of the current FASTA entry in the file and discards the old one as the next one is read.

FUNCTIONS

new(memberHash)
    This new function requires a hash reference with the filehandle for the sequence file defined as a typeglob reference. An example of this might be \*STDIN.

    The following keys are required to instantiate iPE::FASTA:

    filename
        The name of the file to parse

    The following are optional keys:

    fh  Filehandle of the file if it is already opened.

    split_string
        If the split_string key is defined, the sequences will be split into arrays which can be accessed via the arr variable.

def (), seqRef (), arrRef ()
    def () returns the definition line of the current sequence. seq () returns a reference to the string of the current sequence. If split_string was supplied in new (), then arr () will return the array of items in the seuquence split on the string that was supplied. All of these are returned as references, since duplicating a large sequence can be costly.

SEE ALSO
iPE::SequenceReader iPE::SequenceReader::Load

AUTHOR
Bob Zimmermann (rpz@cs.wustl.edu).

POD ERRORS
Hey! The above document had some coding errors, which are explained below:

Around line 120:
    You forgot a '=back' before '=head1'